CHANGELOG Copy Section

CHANGELOG

Workspace lab notebook for long-running or resumable research work.

Use this file to track chronology, not release notes. Keep entries short, factual, and operational.

2026-08-15 13:36 EDT — intake-sweep-0.3.23-post-release Copy Section

- Objective: Refresh the complete Feynman AI-researcher intake after the 0.3.23 release and persist the verified state.
- Intake: Open issues and PRs are empty. The recent merged PR #230 is released and verified. All 30 newest forks are behind main except NioZow/feynman, which is 1 commit ahead and 108 behind with only an old Nix packaging commit; no port target exists.
- Upstream: Pi 0.84.2, pi-web-access 0.23.0, pi-docparser 4.0.0, pi-btw 0.4.1, and pi-otel 0.1.0 are current. pi-subagents 0.50.0 is current upstream, but its 391-commit 0.40.0...0.50.0 migration adds missions, schedules, workflows, FleetView, Herdr, worktrees, and administration rather than fixing a Feynman research defect; the bundled 0.40.0 remains the correct scoped choice.
- Security and freshness: Dependabot and repository advisory queues are empty; code scanning has no analysis. Root and website production audits report zero vulnerabilities. npm outdated reports non-security upgrades for general dependencies only; no coordinated research-runtime update is required.
- Verified: 784/784 tests, typecheck, build, architecture check, website lint/typecheck/build (34 pages), root and website audits, diff check, dry and real packs, installed artifact verification, installed RPC/TypeBox/Copilot checks, and document parse/search/screenshot passed. The real pack is 114,755,952 bytes with 29,134 files and SHA-256 95940c60ff9842b568b0c9b7af507081012353d7ad6fe54c53b567de05d0a1dd.
- State: verified and production-live on synchronized main 316e7a6. The nested dirty website checkout and existing ignored research artifacts remain preserved and untouched. Next: refresh the queues on the next scheduled sweep.

2026-08-15 12:30 EDT — pi-copilot-rate-limit-0.3.23-final Copy Section

- Objective: Complete merge, publication, release identity, published-install, intake, and cleanup gates for Feynman 0.3.23.
- Delivery: PR #230 passed run 31889957676 and merged as 413f37e17b3ceeb5037f029f34e86a1ce75741bd. Publish run 31892303159 passed every package, consumer, native, npm, GitHub release, and published-state job.
- Published proof: npm 0.3.23 is latest with integrity sha512-3pk6i0K/c5aPxuRBDwthh+Vg6QQKi2HMVSjgNJB0QojPFyUuK6qcqF+dXxj2JxxemLW03LN8uJ+H/LZp0vFY8Q==. Its verified SLSA provenance resolves to 413f37e; a clean registry install passed audit, package verification, CLI smoke, Pi RPC, TypeBox, Copilot, and document parse/search/screenshot checks.
- Release proof: GitHub v0.3.23 and its tag target 413f37e. All five native assets are valid archives, their downloaded SHA-256 values match SHA256SUMS, and all six downloaded files match GitHub's provider digests.
- Live proof: Post-release run 31895320515 passed published npm installs on Linux, macOS, and Windows across Node 22, 24, and 25; live model and researcher-child runs passed. The live native installers passed on Linux, macOS, and Windows.
- Intake: Open issues and PRs are empty. All 30 recent forks were compared; only NioZow/feynman is ahead, by one old generic Nix packaging commit that remains rejected. Dependabot alerts and repository advisories are empty; code scanning has no analysis. Pi 0.84.2, [email protected], and [email protected] remain current; [email protected] remains rejected for adjacent workflow scope.
- Cleanup: Deleted the release branch, exact owned package, consumer, audit, home, upstream, release-download, and intake temporary paths. Daytona sandbox 0f5c5798-798a-4b71-aea4-b506b10cea9b was deleted and now returns Not Found. Older user-owned sandboxes and the unrelated dirty nested website repository remain untouched.
- State: verified and production-live. Next: start the next intake sweep from synchronized main.

2026-08-15 09:38 EDT — pi-copilot-rate-limit-0.3.23 Copy Section

- Objective: Port Pi's merged GitHub Copilot login fixes into the current 0.84.2 runtime and qualify Feynman 0.3.23.
- Intake: Open Feynman issues and pull requests remain empty. No issue or PR changed after the prior automation cutoff. The 30 newest forks are behind or equal to main except NioZow/feynman, whose old Nix packaging commit remains rejected. Security alert and advisory queues are empty.
- Fixed: Applied upstream Pi commits d5278ea and 086c32e to every root, nested, vendored, and agent-managed Pi AI runtime copy. Copilot policy updates now run sequentially, and model discovery honors Retry-After before one bounded retry.
- Fixed: Consolidated embedded Pi AI target discovery after the first full test found scripts/patch-embedded-pi.mjs above the architecture limit. The script is now 1,170 lines without weakening the guard.
- Verified: Focused patch tests passed (9/9), and the full suite passed (784/784). Typecheck, build, architecture, website lint/typecheck/build (34 pages), root/website/runtime audits, package freshness review, and diff checks passed. The mocked Copilot login proved one active policy request and a successful second model request after 429.
- Package proof: Dry and real packs matched at 114,755,955 bytes and 29,134 files. The tarball SHA-256 is 0c7db229e9cd6d1ae45fd80319f0d82311196c3a77cb65c3d64fdc365ca78728; clean source/runtime/consumer audits and package, stale-upgrade, 15-tool/9-command RPC, TypeBox, Copilot, and document parse/search/screenshot verifiers passed.
- State: unverified for exact-commit Daytona, PR CI, merge, publication, and post-release identity. Next: finish those gates, then publish and verify 0.3.23.

2026-08-15 06:32 EDT — intake-sweep-v0-3-22-daytona-proof Copy Section

- Objective: Complete clean-machine proof for the published Feynman 0.3.22 release and close the intake sweep.
- Clean machine: The first 1 GB Daytona sandbox hit host exit 137 during package build. It was deleted. A replacement 4 GB sandbox checked out exact commit 586b7419d88e0cc95475eccff92e95b6b14f6ed2, passed 783/783 tests, typecheck, build, architecture check, website lint/typecheck/build, root and website production audits, outdated review, and diff check, then remained clean.
- Package proof: Dry and real npm pack passed with 29,134 files and 116,449,033 bytes. The real tarball SHA-256 is f9d65a0b2d202bf6f65a75c1af33eaf06621d3695a7ccda0012086ff821824e7. A clean consumer install passed audit, CLI version/help, package/search status, package-artifact verification, installed 15-tool/9-command RPC and TypeBox checks, and document parse/search/screenshot.
- Intake and delivery: Live GitHub queues remain empty. The release commit remains 586b7419d88e0cc95475eccff92e95b6b14f6ed2; main is now clean and synchronized at docs commit 35cf83c6cc96a7c55d152930b2d2f17ad41201be. GitHub v0.3.22, npm 0.3.22, publish runs 31860841967, 31877648696, 31878044250, and main synchronization run 31879771165 remain successful. The replacement sandbox and prior failed sandbox were deleted; the two older user-owned sandboxes remain untouched.
- State: verified and production-live. No code or dependency changes were made in this run. Next: start the next sweep from synchronized main.

2026-08-15 05:41 EDT — intake-sweep-v0-3-22-completion Copy Section

- Objective: Finish the 0.3.22 release receipts and refresh the full Feynman intake queue.
- Intake: Open issues and pull requests are empty. The 30 newest forks are behind main; NioZow/feynman is 1 commit ahead but 102 behind with only Nix packaging files, so it is rejected. Issue #217 is closed with the semantic-version security-floor fix in v0.3.13. Dependabot alerts and repository advisories are empty. [email protected] is rejected: its upstream v0.49.0...v0.50.0 diff changes 131 files for async missions, schedules, FleetView, Herdr, worktrees, administration, and related control-plane surfaces without fixing a current Feynman research defect.
- Release: PR #229 merged as 586b7419d88e0cc95475eccff92e95b6b14f6ed2. Publish run 31860841967 passed source verification, all six Linux/macOS/Windows package consumers, five native bundles, npm publication, GitHub release creation, provenance, checksums, and published-state verification. GitHub v0.3.22 targets 586b741; npm @companion-ai/[email protected] is latest with integrity sha512-yAJepY8ZGPF7ppNDB4pCEjIBkEbJOqvhwvnn1UDlL0iHC74Gcz/GUdR9AJ0iVAA5tRpLKz4z837HA8xplETgIQ==.
- Verified locally: npm test passed 783/783; typecheck, build, architecture check, production audit, and diff check passed. Dry and real packs both report 114,751,448 bytes, 298,731,472 unpacked bytes, and 29,134 files. A clean installed tarball passed consumer audit, package-artifact verification, 15-tool/9-command RPC and TypeBox checks, and document parse/search/screenshot. A fresh registry install passed the same runtime/document gates and audit; npm provenance resolves to 586b741.
- State: verified and production-live. Post-release workflow 31877648696 passed all six published-package jobs, three native installer jobs, live model smokes, and researcher-child smokes. The nested dirty website repository remains unchanged and preserved. Next: keep main synchronized.

2026-08-14 22:25 EDT — intake-sweep-pi-0.84.2-web-0.23.0 Copy Section

- Objective: Adopt the current Pi and web research runtimes, reconcile the empty intake queues, and qualify Feynman 0.3.22.
- Intake: Open issues and PRs are empty. The 30 newest forks are behind main; NioZow/feynman is 1 commit ahead but 100 behind with only stale Nix packaging work, so it is rejected. Dependabot and published advisory counts are zero. Main workflow runs through 31706066442 are successful. npm and GitHub latest remain 0.3.21.
- Changed: Updated the coordinated Pi package train to 0.84.2, pi-web-access to 0.23.0, exact source fixtures and patch gates, runtime locks and archive, and 0.3.22 release docs. Updated installed TypeBox checks to match Pi 0.84.2: optional non-nullable null values are omitted and malformed non-null values remain rejected. Repaired a stale packaged web verifier marker for the 0.23.0 registration layout.
- Verified locally: Focused checks, full npm test (783/783), typecheck, build, architecture check, website lint/typecheck/build, root/site production audits, outdated review, diff check, package budget, package-artifact verification, clean installed tarball audit, installed 15-tool/9-command RPC and TypeBox checks, installed document parse/search/screenshot, and a live installed openai/gpt-5.5 smoke returning PONG passed. Final pack is 114,751,448 bytes, 29,134 files; runtime SHA-256 is e22e5661f4a8d4a65cb403bbbca20e2d03dbeb2843341232e42249e74944e306.
- State: unverified for the exact commit in Daytona, remote CI, merge, npm/GitHub/native publication, and post-release delivery proof. No GitHub or npm writes occurred. Existing nested dirty website work remains preserved. Next: commit the candidate, run and delete Daytona, then push the exact tested SHA and complete CI and release verification.

2026-08-13 07:21 CDT — liteparse-2.12.0-0.3.21-release Copy Section

- Objective: Complete the LiteParse 2.12.0 research-runtime intake through publication, delivery proof, and cleanup.
- Persistence: PR #228 exact head c0b388c4eee1de9d6fcb84c55d4cabdcb8daaa24 passed run 31690228104 and merged as 186c226ecb4168c7fb5fb4026f99649be1920441.
- Clean-machine proof: Exact head passed the Daytona package, runtime, document, consumer, and release ladder in sandbox 73c70fbf-bc65-4f81-b0eb-7ccb80df5f70; the sandbox was deleted and confirmed absent.
- Delivery: Publish run 31693465638 passed source and package verification, six consumers, five native bundles, npm publication, GitHub release creation, provenance, checksums, and published-state verification. npm @companion-ai/[email protected] is latest with integrity sha512-naoZamvsJRxzcjD0iaUyv3WykWmlSN0lMn7xSUkTJwRkUFad+t5JibP7qbmrOj8hZojI7Kw+FR8eWfilLX4yaQ==, SHA-256 3026f1111823a1406fccf432825758f738382d3c0b27776c004abbf63cbf3e60, and provenance resolving to 186c226.
- Published proof: GitHub v0.3.21 targets 186c226 and contains five native assets plus SHA256SUMS; all asset digests match the manifest. Post-release run 31698860122 passed all six published package installs, all three live native installers, model smokes, and researcher-child smokes on Linux, macOS, and Windows.
- Intake and final state: Open issue and PR queues are empty. Dependabot and repository advisory queues are empty. Main is clean and synchronized. State: verified and production-live. Next: start the next sweep from clean synchronized main.

2026-08-12 08:55 CDT — managed-packages-current-date-0.3.20-release Copy Section

- Objective: Complete the managed-package reconciliation and current-date context intake through merge, publication, delivery proof, and cleanup.
- Persistence: PR #227 exact head ba87fd7dca38717af0260280aa707be08a4c08b6 passed the release candidate, six Linux/macOS/Windows consumers, and Windows native installer checks, then merged as 33685eeea271a28b68f746f7687a31bbe9eb7293.
- Clean-machine proof: Exact head ba87fd7 passed 783/783 tests, typecheck, build, architecture, website, audit, package, runtime, document, model, and researcher-child gates in Daytona. The sandbox was deleted and confirmed absent.
- Delivery: Publish run 31597429220 passed source and package verification, six consumers, five native bundles, npm publication, GitHub release creation, provenance, checksums, and published-state verification. npm @companion-ai/[email protected] is latest with integrity sha512-9atWIA/Jj1K5BRavBTu31mkXIEizU/6SgpWFzfZGXOOHwsQW/HT26GkQ0FTuP+B0wOhyDznNPDSXw/udV+RFfQ==; the 122,787,315-byte registry tarball has SHA-256 6ff5e7ddd673b67a0771162ee5abe536ee27ecc14f34ead6f6952fd1d8fac7ca and provenance resolving to the merge commit.
- Published proof: GitHub v0.3.20 targets 33685ee; all five native asset digests match SHA256SUMS. Post-release run 31603093191 passed all six published package installs, all three live native installers, model smokes, and researcher-child smokes on Linux, macOS, and Windows. A fresh registry consumer passed audit, package, RPC, TypeBox, and document parse/search/screenshot checks.
- Intake and final state: Open issue and PR queues are empty. All 1,019 forks added no current port target. [email protected] remains rejected because its broad workflow, mission, scheduling, worktree, and administration scope replaces Feynman's focused task and chain surface without fixing a current research defect. State: verified and production-live. Next: start the next sweep from clean synchronized main.

2026-08-12 05:18 CDT — intake-sweep-managed-packages-current-date-0.3.20 Copy Section

- Objective: Repair stale Feynman-managed package trees and give current research turns an explicit local date.
- Intake: Open issue and PR queues are empty. Current Pi, pi-web-access, pi-docparser, LiteParse, pi-btw, pi-otel, and alpha-hub releases remain adopted. [email protected] remains rejected because its broad async workflow and administration scope does not fix this intake. Recent TheTechOddBug, nagyist, and dubbypanda forks match main; sk-surya is stale; randomm contributed only the current-date principle.
- Changed: Managed historical package sources now reconcile to exact bundled presets before launch. Feynman removes stale managed shadow installs and seeds bundled packages without replacing custom selectors, filtered package objects, or optional packages. Parent and researcher-child turns receive the local current date through Pi's supported before_agent_start system-prompt result.
- Verified locally: Adversarial review found and repaired degraded-runtime launch failure, stale usable prefix handling, custom-prefix preservation, and omitted historical pins. Focused tests passed 70/70; the full suite passed 782/782; typecheck, build, architecture, website lint/typecheck/build, production audits, and diff checks passed. Dry and real packs matched at 121,045,848 bytes and 40,224 files; local/global consumers, extracted-runtime audit, stale-upgrade, package, RPC, TypeBox, current-date, and docparser checks passed. A live openai/gpt-5.5 probe returned DATE=2026-08-12.
- State: unverified for exact-SHA Daytona, PR CI, merge, and 0.3.20 publication. Next: persist the candidate, pass clean-machine and CI gates, then publish and verify exact release identity.

2026-08-11 23:28 CDT — pi-web-access-0.22.0-and-feynman-0.3.19-release Copy Section

- Objective: Complete the [email protected] research-runtime intake through merge, publication, delivery proof, and cleanup.
- Persistence: PR #226 candidate be39b4859ffa57337c71733435bb607f5344ebbc passed its source, package, six-consumer, and native checks, then merged as fecb7faee6ebebafc71ee2f414573eae3c24a79e. The release branch was removed from origin.
- Clean-machine proof: The exact merged SHA passed the full validation ladder in the larger Daytona sandbox after the initial resource-pressure failure in the smaller sandbox.
- Delivery: Publish run 31559441208 passed source verification, six package consumers, five native bundles, npm publication, GitHub release creation, provenance, checksums, and published-state verification. npm @companion-ai/[email protected] is latest with integrity sha512-rQZgsi4kFewieuBgulJyJI7ECPbPaxBhjmJDjlSkf+aBGFEYkas4SAqWytIkPIfgU5fwwgcJMPpox3IW9BD/wg==. GitHub v0.3.19 targets fecb7fa and contains five native archives plus SHA256SUMS.
- Published proof: Post-release run 31562633273 passed all six published global installs, all three native installers, and the model and researcher-child smokes, including RESULT=PONG. Open issue and PR queues remain empty; Dependabot alerts remain empty.
- Cleanup: Deleted owned Daytona sandboxes 06f1ad9a-388e-4249-92d5-89266cd8a4ef and b18763b2-f19c-4155-b7d5-ca5ec4414dc0, removed the generated runtime archive and 436 owned temporary directories, and confirmed no owned process remains.
- State: verified and production-live. Successor release identity is verified on the completion commit; no fixable residual work remains.

2026-08-11 17:05 CDT — intake-sweep-pi-web-access-0.22.0 Copy Section

- Objective: Adopt the current web-research runtime without reopening adjacent package or control-plane scope.
- Intake: Open issues and pull requests are empty. dubbypanda/feynman is the only fork changed since the prior sweep and matches main. Root and website production audits are clean. [email protected] remains rejected because it replaces Feynman's task and chain contract with broader async workflow and mission surfaces without fixing a current defect.
- Changed: Updated pi-web-access to 0.22.0, adopted upstream fetched-content cache hardening, added Bocha search and configurable 30,000–200,000-character content slices, and preserved Feynman's exact config path, private cache, model scope, browser-cookie opt-in, raw-result default, and 90-second primary-search deadline.
- State: unverified for cumulative tests, clean package consumers, Daytona, CI, merge, and release. Next: pass every source, website, package, runtime, clean-machine, CI, and publication gate for exact 0.3.19.

2026-08-11 11:28 EDT — intake-sweep-windows-consumer-budget-0.3.18 Copy Section

- Objective: Resume the 0.3.18 publication after main run 31499996075 exhausted its Windows Node 25 consumer job budget.
- Evidence: The first clean tarball install passed after 33 minutes. The second clean global install was still running when GitHub cancelled the job at 60 minutes. The same matrix completed in prior runs when both installs finished sooner.
- Changed: Raised the PR and publish package-consumer job budgets from 60 to 90 minutes. All local/global install, audit, package, runtime, RPC, TypeBox, and document gates remain unchanged.
- State: unverified for the successor PR and publish run. Next: pass focused and cumulative checks, merge exact green CI, then finish npm/GitHub/native publication and post-release proof.

2026-08-11 01:35 EDT — intake-sweep-web-cache-hardening-0.3.17 Copy Section

- Objective: Complete the post-0.3.16 fetched-content reliability intake without broadening Feynman beyond the research loop.
- Intake: Feynman has no open issue or PR. The refreshed 1,018-fork snapshot has no push after the 0.3.16 merge. GitHub advisory and Dependabot queues are empty. The nested dirty website repository remains preserved at 67186845.
- Root causes: Short successful fetch_content results kept responseId only in hidden tool details, so a live model guessed fetch_content and get_search_content failed. The new external cache also lacked count and byte limits, stale temporary-file cleanup, permission repair, and symlink checks.
- Changed: Every single-URL fetch now exposes its stored response ID in model-visible text. The exact-gated [email protected] patch ports upstream PR #241 at b3e784f, bounds cache use to 128 entries and 128 MiB, evicts oldest entries, normalizes POSIX permissions, rejects symlinks, writes through exclusive random temporary files, and treats concurrent missing prune targets as success. Exact-source hashes normalize Windows line endings. Cache-specific tests now live in a separate file instead of growing the general web patch suite beyond the architecture threshold.
- Verified locally: Upstream PR #241 passes 13/13 focused tests, 446/446 cumulative tests, typecheck, and runtime audit. Feynman passes 24/24 focused tests, 65/65 affected tests, 767/767 cumulative tests, typecheck, build, architecture, actionlint, website lint/typecheck/build, root/site/runtime/consumer audits, registry signatures, dry and real packs, package budget, local/global installed runtime and document checks, and a four-process cache stress.
- Live proof: Installed openai/gpt-5.5 saw response ID mso97v8wmxdxvf, reused that exact ID with get_search_content, and returned WEB_CACHE_0317_OK mso97v8wmxdxvf. The final cache used 0700 directory and 0600 file modes.
- State: Candidate 0.3.17 is locally verified and uncommitted. Next: commit the exact candidate, prove it in Daytona and CI, then merge and verify npm, GitHub, native, provenance, and live research delivery.

2026-08-10 13:12 EDT — intake-sweep-deepseek-v4-pro-0.3.15-release Copy Section

- Objective: Carry the exact DeepSeek V4 Pro research-model correction through clean-machine proof, merge, publication, delivery checks, and cleanup.
- Persistence: PR #221 exact head 9debe8def114a3443bb6e7624cb35ded5e6596bb passed run 31395933747 and merged as 4fc5a6874d91d1841069d1a4625cac3cb7a9b169. The port keeps Pi's exact DeepSeek IDs and rejects the source fork's broad Pro bypass, provider scripts, duplicate parallel-search bundle, and stale agent changes.
- Clean-machine proof: Exact merge 4fc5a687 passed focused 105/105, cumulative 755/755, typecheck, build, architecture, website lint/typecheck/build, audits, pack, clean consumer, stale-Pi, RPC/TypeBox, and document gates in Daytona sandbox 4c3e449a-f0c1-48de-a59a-7bf2c0419f90 on Node 25.9.0. Its 122,765,124-byte package had SHA-256 cabdcac428a7ba32e11978f084991d3606eb5b018b72ce4b4bf72b603c2fc769; the sandbox was deleted and confirmed absent.
- Delivery: Publish run 31401997236 passed and released npm/GitHub 0.3.15 from the merge commit. The 122,765,082-byte registry tarball has SHA-256 28a5a854f4fcb3c955573c5dc78333e8dc2de8aa91cba766ac082fdd00c715f2, integrity sha512-nIfGSLzFqjimz2WZeLs3y4H2zozxE5XRn81GJuDs4j9Y5P2vnbEvnlWly3s/YQwsiuF1rTfYa/4ls231mztYSQ==, and verified provenance resolving to 4fc5a687. GitHub v0.3.15 targets the same commit; all five native asset digests match SHA256SUMS. Production release docs and both live installers match source.
- Published proof: A fresh registry consumer passed zero-vulnerability package, embedded-runtime, and extracted-runtime audits; 96 signatures with 192 attestations; package/runtime/stale-Pi/RPC/TypeBox/document gates; and exact default persistence. Its model list showed nebius/deepseek-ai/DeepSeek-V4-Pro as current and recommended, the removed environment bypass still rejected Gemini Pro, and a streamed prompt reached /v1/chat/completions with the exact DeepSeek ID and returned DEEPSEEK_V4_PRO_OK.
- Final state: Canonical post-release run 31409934882 passed all six Linux/macOS/Windows Node 22/24/25 consumers and all three live native installers. Issue and PR queues are empty, security advisory queues are empty, and the unrelated nested website repository remains preserved. State: verified and production-live. Next: start the next sweep from clean synchronized main.

2026-08-10 09:35 EDT — intake-sweep-deepseek-v4-pro-0.3.15 Copy Section

- Objective: Port the valid research-model correction from randomm/feynman without importing its fork-only provider scripts, broad Pro bypass, or duplicate parallel-search surface.
- Intake: Open issues and PRs are empty. All 1,017 forks were refreshed; only nagyist/feynman and randomm/feynman changed after the cutoff. nagyist/main has no commit ahead of upstream. randomm/main contributes the DeepSeek correction in 2fa0437; its parallel-search and agent-discovery commits remain rejected because current [email protected] already batches web queries, and removing bundled [email protected] would remove Feynman's verified subagent runtime.
- Changed: Exact DeepSeek V4 Pro IDs from Pi's direct, DeepSeek, Nebius, and Fireworks catalogs now pass the Pro-class cost guard. Premium service models such as Gemini Pro and o1-pro remain blocked. No FEYNMAN_ALLOW_PRO_MODELS or other broad bypass exists. Updated model listing, recommendation, explicit selection, default persistence and repair, CLI copy, command metadata, setup guidance, website documentation, release notes, and candidate version 0.3.15.
- Verified locally: Focused model and content coverage passed 105/105; the cumulative suite passed 755/755. Typecheck, build, architecture check, website lint/typecheck/build (34 pages), root/site/runtime/consumer/extracted-runtime production audits, package freshness review, and git diff --check passed. Only existing dependency build warnings and recorded architecture debt remain.
- Package proof: The rebuilt candidate contains 40,223 files, is 121,026,469 bytes compressed and 342,291,561 bytes unpacked, and has SHA-256 91f55cfd83deb14cc917bed444750cdb5ff439e375be06cb93a2195ab7c66811. A clean installed consumer passed package, stale-Pi, 9 RPC command, 15 tool/TypeBox schema, document parse/search/screenshot, and all runtime audits.
- User path: An installed-package model list exposed nebius/deepseek-ai/DeepSeek-V4-Pro as current and recommended, model set persisted it, FEYNMAN_ALLOW_PRO_MODELS=1 did not expose a premium Gemini model, and a mocked OpenAI-compatible prompt reached /v1/chat/completions with the exact DeepSeek model ID and returned DEEPSEEK_V4_PRO_OK.
- State: verified locally and unverified for the exact commit in Daytona, PR CI, merge, and npm/GitHub/native publication. Next: commit with contributor attribution, prove the exact pushed SHA in Daytona and CI, then merge and verify every 0.3.15 delivery surface.

2026-08-10 09:13 EDT — intake-sweep-pi-web-access-0.20.0-release Copy Section

- Objective: Carry the verified [email protected] research-runtime candidate through merge, publication, independent delivery proof, and cleanup.
- Persistence: PR #220 exact head 22fa33604307ec82dbd6ad41f563964c5ec1a4f0 passed run 31380143935, including the release candidate, six Linux/macOS/Windows Node 22/24/25 consumers, and Windows PowerShell 5.1/Core native installation. It merged as 3d59c3d7130d0e7ae87c09e61c3669977c8d1575; origin now exposes only main.
- Clean-machine proof: Exact head 22fa336 passed the complete source, website, package, runtime, document, model, DuckDuckGo, Datalab, and AlphaXiv ladder in Daytona sandbox 155e1fa0-5b19-4690-a7a0-81c101d8eedb. The successful sandbox and low-memory diagnostic sandbox f522149f-00dc-47d3-9765-e2b869c80b51 were deleted and confirmed absent.
- Delivery: Main run 31383652197 passed source/package verification, all six package consumers, five native builds, npm publication, GitHub release creation, provenance, checksums, and published-state verification. npm @companion-ai/[email protected] is latest; its 122,764,823-byte registry tarball is byte-identical to the CI artifact at SHA-256 d3d7bee2579be5220f8ab0386710a033e2e1d608c61d05c575d4a97449bddc3c, and its attestation resolves to the merge commit. GitHub v0.3.14 targets the same commit with five nonempty native archives plus SHA256SUMS; every provider digest matches the manifest.
- Published proof: A clean registry consumer passed zero-vulnerability audit, 96 package signatures with 192 attestations, package/runtime/RPC/TypeBox/document gates, two live domain-filtered arXiv results through DuckDuckGo, Datalab missing-key handling, openai/gpt-5.5, and the authenticated 36,090-byte AlphaXiv paper question. Canonical post-release run 31390092634 passed all six published consumers and all three live native installers for exact version 0.3.14.
- Intake and preservation: The issue and PR queues are empty, all 1,017 forks added no port target, the release branch is deleted, and deployed release docs plus both live installers match source. Concurrent unrelated work on local branch codex/non-premium-pro-models remains untouched with its 12 dirty model/release paths. State: verified and production-live. Next: start the next sweep from synchronized main while preserving that separate work.

2026-08-10 05:21 EDT — intake-sweep-pi-web-access-0.20.0 Copy Section

- Objective: Refresh the complete maintainer intake and adopt only current package changes that improve Feynman's research retrieval, document extraction, or runtime reliability.
- Intake: Open issues and PRs are empty. Origin exposes only main; all 1,017 forks were inspected, and none changed after the prior cutoff. No active workflow, Dependabot alert, or repository advisory exists. The unrelated nested dirty website repository remains preserved.
- Changed: Updated bundled pi-web-access from 0.19.0 to 0.20.0, retained Feynman's exact config path, project-local fetch cache, session model scope, browser-cookie opt-in, and search deadline patches, and added migration from the 0.3.13 package set. Added package gates for keyless DuckDuckGo search and optional Datalab PDF-to-Markdown extraction. Updated root and packaged runtime ip-address to 10.5.0 for graceful non-IPv6 parsing. Bumped the candidate and public release notes to 0.3.14.
- Source proof: Registry [email protected] resolves to upstream commit 00b2271d0f1603ac780df3f324aed0fc92f3e849, whose exact source passed 425/425 tests, typecheck, production audit, and package inspection. Registry [email protected] resolves to ef98e0a0e77fbef1fdf8bc3bd33288b00b3103c9; upstream CI run 31359175734 passed. Kept [email protected] because the current 1.3.11 changes schema-engine semantics without a current defect, and kept [email protected] because 0.45.2 still replaces Feynman's task/chain contract with broad async mission, schedule, Herdr, worktree, and administration surfaces.
- Verified locally: Focused affected coverage passed 102/102; all tests passed 751/751. Typecheck, build, architecture check, website lint/typecheck/build (34 pages), actionlint, root/site/runtime/consumer audits, registry signatures (760 packages and 188 attestations), package freshness review, and git diff --check passed. The rebuilt runtime carries [email protected] and [email protected] with archive SHA-256 f6b27fbdf1cf976fc7ec9c2970407e36dacb0e63f8d4cc2e7df2a825985ecc65.
- Package proof: Dry and real packs matched at 121,025,688 bytes, 342,289,989 unpacked bytes, and 40,223 files; the tarball SHA-256 is 6bfd9ef05ae1317a3e9158b526a22c873f0a87f810e5fe981371fc4e0f017a96. Clean local and global installs passed package, stale-Pi, 9 RPC command, 15 tool/TypeBox schema, and document parse/search/screenshot gates. The installed runtime returned two live domain-filtered arXiv results through DuckDuckGo, rejected Datalab without a key, returned INTAKE_0314_OK from openai/gpt-5.5, and returned 36,090 bytes from the exact authenticated AlphaXiv paper question with empty stderr.
- State: verified for source, local cumulative checks, packaging, installed runtime, and live research paths. Exact-commit Daytona, PR CI, merge, and npm/GitHub/native publication remain unverified. Next: commit the exact candidate, validate it in Daytona and CI, then merge and verify every 0.3.14 delivery surface.

2026-08-09 18:19 EDT — intake-sweep-nanoid-3.3.18-audit-repair Copy Section

- Objective: Refresh the complete maintainer intake and clear every current production audit finding without broadening Feynman's research scope.
- Intake: Open issues and PRs were empty. All 1,016 forks were refreshed; nagyist, pseudoctor, and TheTechOddBug matched upstream, while sk-surya exposed only stale Dependabot branches 196 commits behind. Dependabot and repository-advisory queues were empty. Code scanning has no analysis, and secret scanning is disabled.
- Root cause: Root and website locks still selected [email protected], affected by GHSA-2v37-7h3g-55p8. Upstream 3.3.17 repaired most zero-size loops, while 3.3.18 also repaired the omitted React Native async path.
- Changed: Root and website overrides now require exact [email protected]; both locks were refreshed, and the package security regression enforces the patched resolution. Kept [email protected]; current 0.45.1 removes Feynman's task/chain contract and adds async missions, schedules, Herdr, worktrees, and administration without fixing a current defect.
- Local and clean-machine proof: Focused regressions passed 15/15; the cumulative suite passed 750/750. Typecheck, build, architecture, website lint/typecheck/build, actionlint, root/site/runtime audits, registry signatures, dry and real pack, clean consumer/global installs, package/runtime/RPC/TypeBox checks, and document parse/search/screenshot passed. Exact head ed067e14bb29e1aad88b81b59d563fa04f883e9c passed the same ladder in Daytona on Node 25.9.0; its 122,763,413-byte tarball had SHA-256 31dcd53fcb6147f0ab87b675531a6679287300f6291366b714448d76f331e683.
- Persistence: PR #219 passed run 31336147879, including all Linux/macOS/Windows Node 22/24/25 consumers and Windows PowerShell 5.1/Core native installation. It merged as c0231bf8edfda15d72e9cdd63c63ba9812a23c45; the local and remote repair branches were deleted.
- Release state: Main run 31338927707 passed version identity and correctly skipped republication because version 0.3.13 already exists. npm 0.3.13 and GitHub v0.3.13 remain unchanged, and a fresh published consumer audit found zero vulnerabilities. Vercel reported a successful exact-main deployment.
- Cleanup: The exact-head Daytona sandbox and current-run consumer were deleted. The unrelated nested dirty website repository remains unchanged at 67186845 with 51 paths. State: verified on main with empty intake queues and no fixable residual item. Next: start the next sweep from clean synchronized main.

2026-08-09 07:50 EDT — intake-sweep-brace-forward-compat-0.3.13-release Copy Section

- Objective: Carry issue #217 through exact-candidate verification, merge, publication, delivery proof, and cleanup.
- Persistence: PR #218 exact head 5177a12785972d09a023b35c418b8e57ea2390b9 passed the complete install matrix and merged as f7ead4144746ff34cd8f6dc18c1cb2e2a9f6c891. The source and remote release branches were deleted.
- Clean-machine proof: Daytona sandbox 99ff14c2-8913-405a-a45b-11f27518bd76 checked out exact head 5177a12 on Node 25.9.0 and passed 750/750 tests, typecheck, build, architecture, website checks, all production audits, pack and consumer/global installation, package/runtime/RPC/document verification, stale-Pi repair, and a fabricated [email protected] launch. Its sandbox and the earlier undersized exit-137 sandbox were deleted.
- CI and delivery: PR run 31306432848 passed the release candidate, six Node 22/24/25 Linux/macOS/Windows consumers, and Windows PowerShell 5.1/Core native installation. Main run 31308625569 passed source/package verification, the same consumer matrix, five native builds, npm publication, GitHub release creation, provenance, checksums, and published-state verification.
- Release identity: npm @companion-ai/[email protected] has integrity sha512-UkXPQz+jv1OTI42pIwNW5jr0IwUc1RErwsFulaj50Xfml2KQ3jmEPRNw47oc9wq+4kKmAzduDTnb/dhObcsK7Q==; its attestation resolves to f7ead414. GitHub v0.3.13 targets the same commit and exposes exactly five nonempty native archives plus SHA256SUMS; each provider digest matches the checksum manifest.
- Published smoke: Fresh local and global npm installs passed zero-vulnerability consumer audit, version/help/package/search commands, package-artifact verification, installed runtime verification, and document parse/search/screenshot. Issue #217 was commented with these receipts and closed.
- Intake and cleanup: The issue and PR queues are empty. No duplicate PR, temporary tarball, consumer, process, release branch, or Daytona sandbox remains. The unrelated dirty nested website repository and prunable Lima worktree record remain preserved.
- State: verified and production-live. [email protected] remains intentionally unadopted because its broad task/chain, async, schedules, missions, Herdr, worktree, and administration migration does not serve this issue-specific research-runtime fix.

2026-08-09 05:15 EDT — intake-sweep-brace-forward-compat-0.3.13 Copy Section

- Objective: Resolve issue #217 without weakening Pi's launch-time dependency repair, then release the exact verified candidate.
- Intake: Issue #217 is the only open issue and no PR is open. Two forks changed after the automation cutoff; both still match upstream main. The other 1,014 inspected forks add no current port target. The preserved Lima worktree is 92 commits behind main with no unique commit. The unrelated nested website repository remains dirty and unchanged outside the tracked release page.
- Root cause: The security patch accepted only exact reviewed brace-expansion versions. Pi's agent-managed <agentDir>/npm tree can resolve a later secure release, so the next registry update would stop Feynman before CLI startup. Advisory GHSA-rgw5-rvv9-x895 confirms 5.0.9 as the patched 5.x floor.
- Changed: Valid semantic versions at or above 5.0.9 now remain intact in Pi shrinkwraps, owning locks, and installed trees. Reviewed vulnerable 5.0.6 through 5.0.8 trees still upgrade to exact 5.0.9; malformed and older unsupported versions still fail closed. Added source, package-lock, installed-tree, and exact agent-managed runtime regressions. Bumped the candidate and public release notes to 0.3.13.
- Verified locally: Focused regressions passed 70/70; all tests passed 750/750; typecheck, build, architecture check, website lint/typecheck/build (34 pages), root/site/runtime/consumer audits, npm registry signatures, and git diff --check passed. Clean local and global tarball installs passed version/help/package/search, stale-Pi upgrade, source and installed artifact verification, installed RPC/TypeBox tools, document parse/search/screenshot, and a fabricated agent-managed [email protected] launch.
- Package proof: Dry and real packs matched at 121,011,306 bytes, 342,270,111 unpacked bytes, and 40,223 entries. The tarball SHA-256 is c7d1a439af9a9d70e3f90375efd03ba776f4af85e1d8346192861b3d4987c7e0; the embedded runtime SHA-256 is d803f701a3e32ff90a38d175891b413d83ca4f722ecf20f89f6b0ae2715f058d.
- Freshness: [email protected] was reviewed but not adopted. Versions after bundled 0.40.0 remove public task/chain surfaces, make launches asynchronous by default, and add schedules, missions, Herdr, and administration paths. That broad contract migration has no issue-specific security or research-loop requirement. Other root and website drift has no current advisory or proven defect.
- State: verified locally and unverified for the exact commit in Daytona, PR CI, merge, and npm/GitHub/native publication. Next: commit the candidate, prove that exact SHA in Daytona and CI, then merge, publish, verify delivery, and close #217.

2026-08-08 21:44 EDT — intake-sweep-0.3.12-release-completion Copy Section

- Objective: Complete issue #214 through merge, publication, live delivery proof, and queue cleanup.
- Persistence: PR #216 exact head 3922342c4e9f8576627a661eadc953b5ee0e514e merged as bf6e415c83d702c6b3c280b463ed7a7e998861d3. PR #215 closed as superseded because it retained the obsolete alphaXiv fallback and added no unique repair. Origin now exposes only main.
- Delivery: Publish run 31285624271 passed every source, package, Linux, macOS, Windows, native-bundle, provenance, release, and published-state job. npm 0.3.12 is latest; its attestation resolves to the merge commit. GitHub v0.3.12 targets that commit with five nonempty native archives and matching SHA256SUMS.
- User path: A clean global install of the published package authenticated with alphaXiv. The exact reported feynman alpha ask 2401.12345 "What optimizer did they use?" command returned paper content without MCP error -32602.
- Live verification: Post-release run 31288182374 passed six npm consumers on Linux, macOS, and Windows across Node 22, 24, and 25. It also passed all three live native installers plus every enabled one-shot model, text-model, and subagent call.
- Intake: Issue #214 closed with delivery receipts and no issue or PR remains open. The sweep checked all 1,015 forks and every branch in the 20 forks active since August 1. The duplicate alphaXiv branch was superseded; stale security branches were already covered; the fork-only parallel-search prompt bundle remained outside the focused research-runtime fix.
- Freshness: Pi 0.84.1, [email protected], [email protected], and LiteParse 2.11.1 remain current. [email protected] was reviewed but not adopted: its post-0.40.0 line makes direct launches asynchronous and adds default schedules, missions, Herdr, worktree, and administration surfaces that cross Feynman's research-only boundary. Other root and website drift has no current advisory or proven research-loop defect.
- State: verified and production-live. Root, website, runtime, and installed-consumer audits found zero vulnerabilities. The next daily sweep should start from npm/GitHub 0.3.12, clean main, and an empty issue/PR queue.

2026-08-08 05:10 EDT — intake-sweep-alpha-ask-0.3.12 Copy Section

- Objective: Fix issue #214, reconcile the preserved 0.3.12 candidate, and complete its unpublished release without adding a new product surface.
- Intake: Issue #214 is the only open issue and no PR is open. Live main remains daa7f47; GitHub and npm still serve 0.3.11. Recent active forks either match or trail main; fuzzywigg security commits are superseded, and randomm documents its provider-specific parallel-cli bundle as fork-only, so neither earns a port.
- Root cause: @companion-ai/[email protected] sends answer_pdf_queries first as { urls, queries }, then retries as { url, query }. The current alphaXiv contract requires { paper, queries }, matching the provider's reported validation schema.
- Changed: The removable alpha-hub package patch now sends { paper: url, queries: [query] }, repairs an already search-patched runtime, fails closed on unknown Q&A layouts, and is enforced in source and archived package verification. Public 0.3.12 release notes now describe the user-visible repair.
- Reconciled: The preserved candidate now includes Pi 0.84.1, [email protected], LiteParse 2.11.1, PDF.js 6.2.108, current root and website security resolutions, and Pi delta-only Workbench RPC text updates. The open contributor PR duplicates the alphaXiv repair but retains the obsolete fallback, so it adds no change to port.
- Adversarial repair: The first package-artifact run found the verifier checking nested Pi's obsolete dist/tui.js after Pi moved rendering to dist/tui-main-screen.js; the verifier and its regression now target the actual patched module. Review also corrected both public release surfaces from LiteParse 2.11.0 to the exact runtime 2.11.1.
- Verified locally: The exact source tree passed focused patch and release regressions, all 748/748 tests, typecheck, production build, architecture check, website lint/typecheck/build (34 pages), root and website production audits (0 vulnerabilities), actionlint, and git diff --check. Live feynman alpha ask 2401.12345 "What optimizer did they use?" returned paper content without an MCP schema error.
- CI repair: PR #216 proved the Linux-built npm tarball on Linux, but its macOS and Windows consumers could not load LiteParse's matching native module because the archived runtime only carries its build host's optional package. The published package now requests every supported LiteParse native package as an optional dependency, allowing npm to install the consumer's matching binary outside the portable runtime archive.
- Verified CI repair locally: Focused regressions and all 748/748 tests passed. The source, website, audit, build, architecture, and diff ladders stayed green. A 121,011,394-byte tarball passed budget, runtime audit, clean macOS consumer and global installs, artifact/runtime verification, and document parse/search/screenshot with the installed darwin-arm64 package.
- State: verified for the successor local source and macOS package paths, plus exact-SHA Daytona for predecessor fb3cc6f. PR CI must prove the successor across Linux, macOS, Windows, and native installers. Next: push the focused native-package repair, merge only green CI, then verify every 0.3.12 delivery surface.

2026-08-05 01:00 EDT — intake-sweep-0.3.12-release-hardening Copy Section

- Objective: Repair the remaining packaged web-config and document-tool verification gaps, adopt current research-runtime dependencies, and complete the unpublished 0.3.12 release.
- Intake: Open issues and PRs are empty. main and origin/main match merge daa7f47; npm and GitHub still serve 0.3.11. Recent forks are behind main except NioZow's stale one-commit Nix packaging branch, which is broad platform work with no current research defect or current-release validation and is not ported. The Lima worktree is clean and has no unique commit.
- Changed: Web configuration now reads and writes through getWebSearchConfigPath() and creates that exact file's parent. Added an installed verifier that loads pi-docparser through Pi's bundled Jiti and executes parse, search, and screenshot tools in package, consumer, native, publish, and live-delivery gates. Updated direct, nested Pi, and runtime Undici to 8.10.0; overrode pi-docparser's LiteParse 2.10.1 pin with removable runtime version 2.11.0.
- Source proof: Undici 8.10.0 is official release commit c8d80e6 with idle-loop, readable-body, retry, HTTP/2, proxy IPv6, and DNS-origin fixes. LiteParse 2.11.0 is official package commit 0f579ee; its reviewed range adds document provenance, RTL/LTR ordering, table extraction improvements, and PDFium 1.5.0. [email protected] and its current upstream main still pin LiteParse 2.10.1, which defines the override removal condition.
- Verified so far: Dependency, runtime, package-seeding, exact web-fixture, release-workflow, and runtime-lock regressions passed 59/59. The installed document verifier parsed one page, found one exact phrase hit, and wrote a nonempty 22,539-byte PNG. Package-artifact verification passed with runtime SHA-256 a7211debc8cc2cd254bf4e4b7cfb613d5e7332f6f3917fd159ae1e8995fbb093.
- State: verified for focused local paths and unverified for the cumulative local ladder, exact-commit Daytona, PR CI, merge, and published delivery. Next: complete every local gate, commit the exact candidate, prove it in Daytona and CI, then merge and verify npm, GitHub, native assets, and live installers.

2026-08-04 21:21 EDT — intake-sweep-0.3.12-final-candidate Copy Section

- Objective: Finish the open 0.3.12 web-runtime follow-up after its Windows installer verifier failed, refresh the complete maintainer intake, and add the smallest current document-research and security repairs before publication.
- Changed: Made the [email protected] patch validate every target before any write, reject unsupported versions and layouts, and verify all live session-scope paths in the packaged runtime. Updated pi-docparser to 4.0.0 for isolated cancellable native workers, atomic bounded outputs, stable JSON, and LiteParse 2.10.1. Updated the audited Hono, fast-uri, ip-address, express-rate-limit, and website brace-expansion overrides. The Windows verifier now buffers the mutable checksum file while continuing to stream the large archive, which removes the retained checksum handle that failed the previous Windows job.
- Intake: No open issues exist. PR #213 is the only open PR and remains the owning merge path. PR #212 already owns the 0.3.12 version. The newest kunalkcube, gs034, and Interested-Deving-1896 forks match main; the other sampled recent forks are behind with no ahead commits. Dependabot and repository security-advisory queues are empty. Code scanning and secret scanning are not enabled, so those two empty-state claims remain unavailable rather than inferred.
- Source proof: npm [email protected] resolves to upstream commit 931a0995067062c91bd81798ef226d120c31bd84, whose workflow 30816481652 and local upstream 57/57 check passed. npm latest remains Pi 0.83.0, [email protected], [email protected], and [email protected].
- Verified locally: Final focused runtime, package, release, and Windows coverage passed 97/97; the exact upstream web fixture and fail-closed artifact coverage passed 25/25; the full suite passed 737/737. Root typecheck, build, architecture check, website lint/typecheck/build (34 pages), root/site/runtime/extracted-runtime/consumer audits, actionlint, registry signature verification (754 packages and 182 attestations, zero missing or invalid), package freshness review, and git diff --check passed. The exact bundled runtime SHA-256 is 62a11862fc7cec8235c7d17111b5520dbd52371a1177ccdab158c9d0b02f40ef.
- Runtime proof: Clean local and global tarball consumers, package-artifact verification, stale-Pi migration, RPC extension loading, and TypeBox validation passed. The final installed tarball retained a textual HTTP 418, found a stored teapot passage case-insensitively, and registered all three web tools. A generated two-page PDF passed document_parse, document_search, and document_screenshot; the final screenshot was a nonempty 47,023-byte PNG. A final installed openai/gpt-5.5 request returned exact PONG.
- Package proof: Final dry and real packs match at 119,891,973 bytes, 336,971,093 unpacked bytes, and 39,702 files. The tarball SHA-1 is 168932760db4c3733961b1807219c0e0dc57c427, its SHA-256 is 26137da41f64b7cab7ba75c1041d5177a30fc1ded735632b837330aac5d7623e, and its embedded runtime SHA-256 is 62a11862fc7cec8235c7d17111b5520dbd52371a1177ccdab158c9d0b02f40ef.
- State: verified locally and unverified for the successor exact commit in Daytona, successor PR CI, merge, and npm/GitHub/native/live-installer publication. Next: commit and push the exact candidate, prove it in a disposable Daytona sandbox and required CI, merge only that head, then verify every 0.3.12 delivery surface.

2026-08-02 23:53 PDT — intake-sweep-pi-web-access-0.18 Copy Section

- Objective: Refresh the empty issue/PR queue and recent contributor/fork state, then qualify [email protected] as the smallest current research-retrieval upgrade from the clean 0.3.11 release baseline.
- Changed: Updated Feynman's bundled/default/runtime-locked web package to 0.18.0, retained migration for the 0.3.11, 0.3.10, and older bundled defaults, and bumped the release candidate to 0.3.12. Adopted upstream raw and page-grounded fetches, direct images, stored-content passage lookup, provider additions, curator isolation, and Git cancellation while preserving project-local PDF scratch files, opt-in browser cookies, no-curator defaults, and the bounded primary-search deadline. Nested page-answer and summary model calls now follow Pi's live resolved session scope instead of rereading .pi settings; exact-version and artifact gates fail closed around the local patch. BSD runtime archives omit host ACL, flags, macOS metadata, and xattrs so those host records no longer change package bytes.
- Intake: GitHub has no open issues or PRs, origin exposes only main, and the preserved Lima worktree at 6a81316 has no unique commits. Recently pushed forks are identical to or behind main; fuzzywigg/feynman is 128 commits behind and its security changes are superseded by current safe versions. No contributor change earned a port.
- Source proof: npm [email protected] resolves to upstream git head d2aab00dcf0547572276d9de4bc4a2a49d640e13. Its exact source passed 363/363 tests, typecheck, production audit, and a 58-file dry pack before integration.
- Verified locally: Focused final model-scope/runtime/package coverage passed 47/47, and the full suite passed 734/734; root typecheck, build, architecture check, root/site/runtime/consumer audits, website lint/typecheck/build (34 pages), registry signatures (754 packages and 181 attestations), actionlint, package freshness review, and git diff --check passed. The exact installed web extension retained a textual HTTP 418 response, found a stored TEAPOT passage case-insensitively, registered fetch_content, get_search_content, and web_search, rejected an out-of-scope answer override, and enforced a scope narrowed after context creation.
- Package proof: Dry and real packs were byte-identical at 111,490,673 bytes, 328,503,777 unpacked bytes, and 39,705 files. The tarball SHA-1 is 66b878d0d5ca64617c56e4c45db72617fed99e05, its SHA-256 is 33f183d6d31658083ce2e2d71fbe2d586a15b99509f664c06b1ae9415dec8fc4, and the embedded runtime SHA-256 is 7784202e9e3019bc86d01de9292936add9698b653f5c01ec3d5c6db01e25e8d3; the runtime archive contains no host PAX/xattr metadata. Clean local/global installs, stale-Pi upgrade, CLI/package/search flows, package-artifact verification, extracted-runtime/consumer audits, installed RPC, extension loading, TypeBox checks, and a real installed openai/gpt-5.5 prompt returning PONG passed.
- State: verified locally and unverified for committed exact-SHA Daytona, PR CI, merge, and npm/GitHub/native/live-installer publication. Next: commit the exact candidate, prove it in a disposable Daytona sandbox and required CI, merge only the green head, then verify every 0.3.12 delivery surface.

2026-08-02 00:45 PDT — intake-sweep-0.3.11-release-completion Copy Section

- Objective: Finish the [email protected] intake through exact-commit proof, publication, live installer verification, successor CI, and queue/worktree reconciliation.
- Exact-head proof: Candidate 03fdb2a4c816e2de5c128821c0e48bf0011b2f73 passed the full local 728/728 ladder, authenticated parent/subagent smokes, exact-commit Daytona sandbox 7e3db21f-b329-4331-b4e2-4ce07e156dc4, and PR run 30733954782; PR #210 merged as 26a55bd0cf9acf539413c3177da9ddb27029a5ce.
- Released: Main run 30735432891 passed source/package verification, all six Linux/macOS/Windows Node consumers, all five native builds, npm publication, GitHub release creation, and published-state verification. npm latest is @companion-ai/[email protected] with integrity sha512-L/cWUqE1MitHhTntq57wcZdZEjQT2x2NZytMjXFn+JxeeVE5wmnearF5+/kMKiHq/tSArrqpBTMaFM/mUJ62bA==; the 113,095,746-byte registry tarball has SHA-256 12d36457caa982e8d4cdde292c4aef70a935a7d06aeabad52a1108c51859fada, exactly matches the main workflow artifact, and verified provenance resolves to 26a55bd.
- Release identity: GitHub v0.3.11 targets 26a55bd and contains five nonempty native archives plus SHA256SUMS; every GitHub asset digest matches the manifest. Clean registry local/global consumers, source/runtime audits, package-artifact verification, installed RPC/TypeBox checks, the direct macOS one-line installer, and deployed feynman.is release docs all passed.
- Installer gate: PR #211 added durable post-release checks for the public Unix and Windows one-line installers and merged as b67abf280d19eecc6c978fcfddeb2201b6178e1c after local 729/729 validation and PR run 30736017829. Dispatch 30737679781 passed all six published-package jobs plus live native installation on Ubuntu, macOS, and Windows; successor main run 30738324530 verified the existing release identity and skipped rebuild/publication.
- Reconciled: Open issue and PR queues are empty; recent fork heads are behind main; root, website, and bundled runtime audits are clean; the unrelated Lima worktree remains preserved at 6a81316. State: completed. Next: start future intake from the clean 0.3.11 release baseline.

2026-08-01 22:00 PDT — intake-sweep-pi-subagents-0.40 Copy Section

- Objective: Process the only post-0.3.10 in-scope intake change, preserve the clean unrelated Lima worktree, and carry [email protected] through a 0.3.11 release.
- Changed: Updated the bundled/default/runtime-locked subagent package to 0.40.0; retained automatic migration for both the 0.3.10 ([email protected]) and 0.3.6 (0.37.2) default package sets; bumped Feynman to 0.3.11; and added matching repository/website release notes. TypeBox remains at Pi 0.83.0's exact 1.3.7 contract.
- Source proof: npm [email protected] resolves to upstream tag commit d4d2ab706b612ccd173caad2bc202eef07e7eda3; upstream CI 30721272104 passed Ubuntu and Windows. The installed package exposes the reviewed capability ceilings, usage budgets, approval checkpoints, runtime-extension acknowledgement, signal status, process/output separation, and model/thinking visibility paths.
- Verified locally: Focused package/settings/runtime/release coverage passed 92/92; full tests passed 728/728; typecheck, build, architecture check, website lint/typecheck/build (34 pages), root/site/runtime/consumer audits, package freshness review, git diff --check, package-artifact verification, stale-Pi upgrade, and clean local/global installed-runtime RPC/TypeBox checks passed. Registry signature audit reported zero invalid or missing packages, and real authenticated openai/gpt-5.5 parent plus researcher subagent smokes returned PARENT_OK and RESULT=PONG.
- Package proof: Dry and real packs matched at 112,546,426 bytes, 329,608,636 unpacked bytes, and 39,705 files. The tarball SHA-256 is 79f8a976fc9dc4a4e2d4ffd1616b42798a6fd18ad0716241e35ab6933a108612; the embedded runtime SHA-256 is cad4ab09354c89cc5026ecbf78573ff6e0a4b08ae95b72a5205a6b3be7471ab3.
- State: verified locally and unverified for exact-commit Daytona, PR CI, merge, and npm/GitHub/native publication. Next: commit and push the candidate, prove that exact commit in a disposable Daytona sandbox and required CI, then merge and verify every 0.3.11 release surface.

2026-08-01 10:00 PDT — intake-sweep-0.3.10-release-completion Copy Section

- Objective: Finish the Pi 0.83.0 migration, Windows installer, package-update, and blocked-telemetry queue through exact-head proof, merge, publication, issue reconciliation, and cleanup.
- Exact-head proof: Commit b5c43a1508b26e7be12f0f54a09b3089c181bd40 passed the complete 727/727 suite, typecheck, build, architecture check, website lint/typecheck/build, all production audits, dry and real packs, package budget, clean local/global installs, stale-Pi and package-artifact verification, and installed RPC/TypeBox checks in Daytona sandbox 8423796e-c70c-4c61-bab4-d43ab8aa188f. Its 113,079,330-byte, 39,702-file tarball had SHA-256 e68cdab8074ec84d6833d4c296aeddf68fe5e6a5e8f3365c88eec1002559d365; the sandbox was deleted and confirmed absent.
- CI and merge: PR run 30704056177 passed the release candidate, both Windows PowerShell installer paths, and all six Linux/macOS/Windows Node 22.22.0/24.18.0/25 consumers. PR #206 merged as 162a26a14c07576e44f2e579bc97a56de81a169e; the release branch was deleted and local main fast-forwarded.
- Released: Main run 30705796129 passed source/package verification, all six package consumers, all five native bundles, npm publication, GitHub release creation, and published-state verification. npm @companion-ai/[email protected] has integrity sha512-yZQSjB6GmTo/m41lra8WaavQ3jFFxbWQkNvcmw1EV7zZAO8xSSdZ/G81Pd1UKBKJS/wJ5uR32PLtyiQvjTGhvQ==; its verified SLSA/Fulcio provenance resolves to 162a26a, and the registry tarball exactly matches the Daytona SHA-256.
- Release identity: GitHub v0.3.10 targets 162a26a and contains five native archives plus SHA256SUMS; every provider asset digest matches the manifest. GitHub latest resolves to v0.3.10, the live Unix and Windows installer bytes match main, and the deployed release page names v0.3.10.
- Reconciled: Issues #207, #208, and #209 are closed with release receipts; the open issue and PR queues are empty. State: completed. Next: start future intake from the clean 0.3.10 release baseline and remove the remaining temporary fork-inspection refs.

2026-08-01 07:30 PDT — intake-sweep-native-nested-pi-repair Copy Section

- Failed: Exact-SHA PR run 30703039353 reached the Windows native bundle and rejected the freshly installed nested @earendil-works/pi-agent-core because patch-embedded-pi.mjs patched only hoisted and runtime-workspace copies before artifact verification.
- Fixed: The embedded patch now applies the reviewed AgentCore, TUI, editor, and package-update-notice repairs to hoisted and nested Pi copies in both the application dependency tree and vendored runtime workspace, with exact Pi-version guards.
- Verified: A clean production-only dependency install began with all four affected files unpatched, then the embedded patch added every required marker; focused embedded/runtime regressions passed 8/8; full tests passed 727/727; typecheck, build, architecture check, and git diff --check passed.
- State: verified locally and unverified for successor-SHA Daytona, Windows native CI, merge, and publication. Next: push the repair, prove the exact successor commit in Daytona and CI, then merge and reconcile the release.

2026-08-01 06:12 PDT — intake-sweep-0.3.10-current-queue Copy Section

- Objective: Finish PR #206 and issues #207/#208/#209 as one 0.3.10 reliability release without losing the coordinated Pi 0.83.0 candidate.
- Fixed: The Windows installer now extracts through a unique short same-volume drive and cleans up transactionally; package updates target the effective managed/project root and verify the update actually landed; PostHog transport failures open a silent per-process circuit breaker; TypeBox schemas reject null arrays; installed RPC verification reaps complete process trees; Pi package notices use the supported feynman update command; and the bundled [email protected] / [email protected] defaults now migrate consistently across settings, runtime, package-list, and release surfaces.
- Hardened: Adversarial review replaced version-dependent Windows path lengths with a calculated boundary fixture, requires successful taskkill, corrects patch removal conditions, resolves hoisted direct dependencies during artifact verification, prevents tests from mutating the vendored Pi tree through legacy symlinks, and follows symlinked temp paths when deciding whether the installed verifier should execute. A final review also restricted exact-pin reconciliation to valid semantic versions while preserving range/tag selectors, and changed the bundled tracer preflight to an authenticated, status-checked OPTIONS request so retriable HTTP failures never enable the exporter.
- Verified locally: focused review regressions passed 54/54; full tests passed 726/726; typecheck, build, architecture check, actionlint, website lint/typecheck/build (34 pages), source/runtime/site/consumer audits, source and installed artifact checks, runtime tree reconciliation, stale-Pi upgrade, local/global installed RPC checks, healthy PostHog/OTLP log/trace delivery, blocked-collector silence, and git diff --check passed.
- Package proof: dry and real packs matched at 112,524,540 bytes, 329,580,850 unpacked bytes, 39,705 files, SHA-1 bfecb172351c30fddfe3a5b2aedfe8dea708e4d6, and integrity sha512-bZMJhGiA0F5YzasK6ehOLciAWfkv5WQMCKrmsdk2ja7Utn7aTSM4qmcukVE2fZTmERKiyuas2nzB3NUBeClo1w==. Tarball SHA-256 is 1c459ea70d98f1f09e66057d1192bd23bf592e7674c0fd464bcfbe18411f1617; runtime SHA-256 is fa4828de88c37d559de58eef449be255f5b97d2de0f9a6a6eb8a66f2a2c1d069.
- State: verified locally and unverified for committed exact-SHA Daytona, PR CI, merge, published 0.3.10, and terminal issue reconciliation. Next: commit/push the exact candidate, run and delete Daytona, require green Windows/consumer CI, merge, verify npm/GitHub/native release identity, then close #207/#208/#209.

2026-07-30 02:02 PDT — intake-sweep-0.3.10-release-candidate Copy Section

- Fixed: PaperRank now reads only Pi's finalized assistant message and rejects provider errors, aborts, output-limit truncation, and other non-completion stop reasons before generated synthesis is written. Pi's top-level cli extension source classification no longer hides Feynman's 15 built-in research tools.
- Hardened: Installed-package verification now inventories 9 Feynman commands and 15 tools over RPC, compiles all 15 installed schemas, exercises a genuinely nullable array through Pi's TypeBox tool path, and proves malformed arguments fail before tool execution.
- Verified locally: focused release gates passed 10/10; full tests passed 688/688; typecheck, build, architecture check, website lint/typecheck/build, git diff --check, root/site/runtime/consumer audits, mixed-Pi rejection, stale-Pi upgrade, package-artifact verification, dry/real pack, package budget, clean consumer install, and global install all passed. The real tarball is 112,476,954 bytes with 39,700 files; runtime archive SHA-256 is ec22f6bae0eadbe56012818ebc4fa9c42345159adbd8a2c540efd436f3a26bb7.
- Verified user paths: the installed runtime exposed all 9 commands and 15 tools, rejected malformed TypeBox input, completed a real authenticated openai/gpt-5.5 prompt, and generated a real PaperRank synthesis artifact from the fixture source.
- State: verified locally and unverified for exact-SHA Daytona, PR CI, merge, and published 0.3.10 reconciliation. Next: commit and push the exact candidate, run Daytona, merge only green CI, then verify npm provenance and GitHub/native assets.

2026-07-29 16:07 PDT — intake-sweep-0.3.10-pi-0.83 Copy Section

- Objective: Continue the terminal intake from released 0.3.9 and adopt the new coordinated Pi runtime rather than leave a fixable dependency migration deferred.
- Found: Pi 0.83.0 was published from upstream commit 845d6ff1 during this sweep. Its TypeBox 1.3.7 change requires an explicit compatibility pass; its llama.cpp source now requests streaming usage, but old models-store.json entries still preserve the false capability. Upstream issues #7150 and #7053 remain open, and Pi's shrinkwrap still carries vulnerable [email protected] plus proxy-broken Undici 8.5.0.
- Fixed: Moved all four Pi packages, root/runtime locks, fallback pins, correctness gates, declarations, artifact checks, and fixtures to exact 0.83.0. Retained the compaction-loss and eager parallel-result repairs, rebased llama.cpp handling to keep only the serialized cached-metadata migration on top of Pi's upstream usage fix, and reapplied the exact [email protected] and Undici 8.9.0 repairs. Mixed Pi trains and unreviewed older/newer versions now fail closed.
- Verified so far: Focused runtime, llama.cpp, TypeBox-compatible extension/model, package, audit, integrity, and release-workflow tests passed 92/92; root and generated-runtime production audits, typecheck, architecture check, and git diff --check passed. npm metadata and the official v0.83.0 tag/release all resolve the four-package train to 845d6ff1.
- State: verified for the focused migration and unverified for the full source/site/package/native/clean-machine/CI/release ladder. Next: complete cumulative validation, exact-SHA Daytona proof, PR CI, merge, and 0.3.10 npm/GitHub/native release reconciliation.

2026-07-29 05:18 PDT — intake-sweep-0.3.9-runtime-correctness Copy Section

- Objective: Close the post-0.3.8 release-gate findings and current Pi 0.82.1 runtime correctness gaps instead of leaving them as upstream or dependency deferrals.
- Found: The stale-Pi gate omitted the shrinkwrap-owned security subtree, allowed Windows .cmd launches through Node's deprecated shell-with-arguments path, and recorded the prior release date incorrectly. Current Pi also acknowledges then drops a default RPC prompt during manual compaction, delays every parallel tool result behind the slowest sibling before persistence, pins Undici 8.5.0, whose EnvHttpProxyAgent tunnels plain HTTP proxy traffic, and disables llama.cpp streaming usage so session token totals remain zero. The first correctness candidate persisted completed results only after extension dispatch, accepted extension-rewritten tool-call identities that could duplicate accounting, and verified broad artifact markers without Pi's own shrinkwrap metadata.
- Fixed: Bound stale verification to the exact source/npm/native candidate and pre-launch runtime baselines; require complete core-fixture mutation accounting, exact trusted brace/pi-otel trees, dereferenced second-pass identity, and explicitly escaped ComSpec launches. Added removable, exact-version-gated Pi 0.82.1 patches that reject manual-compaction prompts before a success acknowledgment and eagerly persist completed parallel tool results before extension dispatch while restoring source order. Extension-modified results now replace that eager entry under the original protocol identity instead of duplicating session usage. Updated Feynman's direct, nested Pi, committed runtime, and current user/global Pi Undici resolution to 8.9.0 while leaving stale Pi versions untouched. Ported upstream Pi PR #7258, repaired stale llama.cpp models-store.json capability metadata in place, and serialized that migration against concurrent network catalog refreshes. Artifact verification now checks every load-bearing correctness fragment and exact Pi shrinkwrap Undici version, resolved URL, and integrity.
- Verified so far: Adversarial review findings were closed with exact migration, real file-store, concurrent-refresh, mock SSE usage, and semantic artifact-mutation regressions. Full tests passed 681/681; typecheck, build, architecture check, actionlint, website lint/typecheck/build (34 pages), root/site/runtime/consumer production audits, freshness review, source artifact verification, and git diff --check passed. Dry and real packs matched at 112,154,998 bytes / 39,706 entries with tarball SHA-256 c0e0e1947d1de0882ca7ed1bd01cd10554a180ac2278f7a0b29f11d2deb04571 and runtime SHA-256 8224927047fadd5cf77fb012cc70574ec660980ee77e0aeb1fd6d5689b3940eb. A clean local/global install passed version/help/package/search, two-launch stale-Pi, real RPC (112 commands), runtime and consumer audits, artifact verification, and persisted llama.cpp cache repair. The macOS arm64 native bundle passed version/help and the same stale-Pi gate at SHA-256 535ab3f514fb79b5f7c67d0f6c73ad8f8ea6fb24dcd4d73fef60eeec4cf28af9.
- Release gate: PR run 30464663836 passed the complete source/site/package matrix, every Linux/macOS/Windows Node consumer, and the Windows installer at exact head e6ecd34; PR #204 merged as d062cd3. Main run 30468941628 then exposed a Windows-native-only verifier defect after every source, package-consumer, and other native job passed: fixture snapshots combined a slash-bearing scoped package label with Windows path separators, so the valid nested brace-expansion repair missed its allowlist. Snapshot and allowlist keys now use one canonical separator. The focused path/workflow suite passed 9/9, typecheck and git diff --check passed, and the local two-launch stale-Pi verifier passed.
- Final exact-head proof: Commit 8fc4ed9 passed the focused path/workflow suite (12/12), full tests (683/683), typecheck, build, architecture check, website lint/typecheck/build, source/runtime/consumer audits, dry/real pack, installed package and Linux native smokes, artifact verification, and the stale-Pi gate. Disposable Daytona sandbox feynman-039-path-20260729204251 repeated the complete ladder on Node 25.9.0 / npm 11.12.1; its 112,753,043-byte tarball had SHA-256 4eb46f2ca02ca18b0a53195813475dd99a614f90c8bd7f2edc857198b4af4028. The sandbox was deleted and confirmed absent. PR run 30489379792 then passed the release candidate, all six Linux/macOS/Windows Node consumers, and both Windows PowerShell installer paths.
- Released: PR #205 merged as 8dac290. Main run 30491968966 passed source verification, all six package consumers, all five native bundles, npm publication, GitHub release creation, and published-state verification. npm @companion-ai/[email protected] integrity is sha512-dX6A9lghZazeT83tKUv8KVoIL77xsm6RPMonzqDF50J8+xmKcXXBQGxPPIEA/oL1wWm+yyvm/JWOxDfFrDYxVA==; independently verified SLSA/Fulcio provenance resolves to 8dac290. GitHub v0.3.9 targets the same commit and contains five nonempty native assets plus SHA256SUMS, with every provider digest matching the manifest. A clean registry consumer and global install passed version/help/package/search, runtime and consumer audits, artifact verification, and the two-launch stale-Pi smoke.
- State: completed. The existing v0.3.8 GitHub release body was reconciled to the corrected July 29 source notes. Next: continue future intake from the clean 0.3.9 release baseline.

2026-07-29 01:45 PDT — intake-sweep-0.3.8-windows-native-cleanup Copy Section

- Objective: Finish the 0.3.8 release after all source and package-consumer gates passed but the Windows native stale-Pi smoke failed.
- Found: Main run 30432364527 passed source verification, all six Linux/macOS/Windows package consumers, and four native bundles. The Windows native smoke then ran exactly to the verifier's 120-second launch limit; its primary timeout was hidden when immediate temp-tree removal hit a live Windows handle and threw EPERM.
- Fixed: Give Windows native runtime extraction and launch a bounded five-minute pass budget, retry only transient filesystem cleanup errors with capped backoff, preserve a verification error when cleanup also fails, and keep a successful verification red when cleanup cannot complete.
- Verified locally: Focused cleanup/workflow tests passed 12/12; full tests passed 659/659; typecheck, build, architecture check, actionlint, website lint/typecheck/build (34 pages), full and production audits, package freshness review, and git diff --check passed. A clean installed tarball passed budget, artifact, consumer/runtime audit, version/help/package/search, and two-launch stale-Pi gates. A separate exact Pi 0.82.0 user-root reproduction launched twice with all four stale Pi versions and affected core-file hashes unchanged.
- Clean machine: Disposable Daytona sandbox ab03dc5c-7228-485b-b1cc-88eaf4d2f131 verified exact 544832028368fc28bb408b3054a77782356b7736 on Node 24.18.0 and npm 11.16.0 through the same 659 tests, source/site/package/runtime/consumer ladder, and stale-upgrade smoke. Its tarball SHA-256 was b3f5ddb109a4a724d746229cb829bf19ec4ea86128068ba98b3dec3b495578d8; runtime SHA-256 was 05da056664d0009df87795a834e480998546db9393cf3752a9912e1b9aa8893c. The sandbox was deleted and confirmed absent.
- Released: Main run 30437805935 passed all source gates, six package consumers, five native bundles, npm publish, GitHub release, and published-state verification. The repaired Windows native stale-Pi smoke passed twice in 2m52s. npm 0.3.8 integrity is sha512-6y6Yf7NgOFsht/HxpdncV+8AfjxYo+C3F04ymSqEDF8Iq6B5qVBGwcwoI/ZGk/9iAlAZLBGf3uwaFgCwosy4Ag==; verified SLSA provenance, GitHub tag, and release all resolve to 5448320. All five nonempty native asset digests match SHA256SUMS.
- State: completed. Issue #202 received the release and exact Pi 0.82.0 receipts. Next: keep the stale-user-package gates in future releases and re-run the intake from this terminal baseline.

2026-07-28 21:20 PDT — intake-sweep-stale-pi-editor-upgrade Copy Section

- Objective: Reproduce and fix issue #202, where a standalone 0.3.7 install failed at launch with Unsupported Pi editor layout: required import patch anchor was not found.
- Found: Pi stores user packages under <agentDir>/npm. An upgrade can retain Pi 0.80.6 core dependencies there. The exact published 0.3.7 RPC launch failed against the official stale editor, and a one-anchor editor compatibility patch then failed against the same release's ModelRegistry. Pi 0.82.1 already aliases extension peer imports to the current bundled core, so patching each historical core layout is unnecessary and brittle.
- Fixed: Resolve Feynman's bundled Pi version from package metadata and skip core patchers only for Pi packages with a different explicit version. Security, MCP, and extension patching still covers user roots. Package and native release gates now launch twice with staged stale editor and ModelRegistry files, prove those core files remain byte-identical, and prove extension patching remains idempotent.
- Verified locally: Fresh official Pi 0.80.6 packages passed two idempotent patch passes (true, then false) with editor and ModelRegistry hashes unchanged, followed by two clean RPC launches. Focused tests passed 22/22; full tests passed 655/655; typecheck, build, architecture check, actionlint, website lint/typecheck/build (34 pages), root/website/runtime/clean-consumer audits, and git diff --check passed. Dry and real packs matched at 111,634,612 bytes / 39,692 entries with SHA-256 daaf0e114b4e708269629edc99b166f782990f0940105265f6efa2dade0c1376. The clean installed tarball passed artifact verification and the two-pass stale upgrade smoke with runtime archive SHA-256 5dee5447b585bab835bcb3dd74b5a832a69b4e7cbea57aa4ca3d75794242d788; the native macOS arm64 bundle passed the same smoke at SHA-256 6db6e81d58b91a0b78d043e9532b078341aaae0bf965dfa8c65d158690c1660f.
- State: verified locally. Next: prove the exact commit in Daytona and required GitHub CI, then merge and verify the 0.3.8 npm/GitHub/native release before closing #202.

2026-07-29 00:35 PDT — intake-sweep-0.3.8-windows-release-budget Copy Section

- Objective: Finish the merged 0.3.8 release without dropping the supported Windows Node 24.18.0 local/global installation gate.
- Failed: Main run 30428654129 passed source/package verification and the Linux, macOS, and Windows Node 25 consumers. The Windows Node 24.18.0 consumer spent 26m on the first exact-tarball install, then the former 45-minute job budget cancelled the second required global install before runtime audit and artifact verification; npm/GitHub remained at 0.3.7.
- Fixed: Keep every package, audit, local/global launch, runtime extraction, and artifact check intact while raising only the PR and release package-consumer job budget to a bounded 60 minutes. Next: validate, push, and require the successor main release run to publish and verify 0.3.8.

2026-07-28 14:30 PDT — intake-sweep-global-npm-install Copy Section

- Objective: Re-run the terminal intake after 0.3.6, including the documented global npm install path rather than treating a clean project-prefix consumer as equivalent.
- Found: Both an upgrade under ~/.npm-global and a fresh disposable npm install --prefix ... @companion-ai/[email protected] produced an empty node_modules/@opentelemetry/api directory. feynman --version then failed before command dispatch from the direct telemetry import, while the existing non-global consumer gate passed because npm could hoist @opentelemetry/[email protected] above the package root.
- Fixed: Bundle the exact direct OpenTelemetry API with the five existing runtime packages, and exercise the exact global install/version/help path across every supported package-consumer matrix plus post-publication registry verification.
- Exact-head CI: Run 30402843325 passed the release candidate, all Linux/macOS consumers, Windows Node 25, and the native installer. Windows Node 24.18.0 completed both local and global version/help checks but hit the former 30-minute job limit six seconds into runtime extraction; the identical Node 25 path completed in 29m38s. Both PR and release consumer matrices now use a bounded 45-minute timeout.
- Verified locally: Scoped workflow tests passed (7/7); the complete suite passed (654/654); typecheck, build, architecture check, actionlint, website lint/typecheck/build (34 pages), root and website full/production audits, package freshness review, and git diff --check passed. Dry and real packs matched at 111,637,876 bytes / 328,227,251 unpacked / 39,692 files with npm integrity sha512-PFChM+N8VQsNZQ64uFLb9EDytP96vKFvThpooai5P0KnmYfyspXyFrleW5gHeQipEH5zuIxTZnbJZ2Fv/jC/SQ== and tarball SHA-256 941389ca83a06b49105a4c07515fad1e250617ced593192ad2a90c4b851b61a0.
- Installed proof: A clean consumer and extracted runtime each audited at zero, artifact verification passed with runtime SHA-256 c31b7db649f47997abfc6a3622c5af1758af71789a5eae9c96c98932c3d96ac1, and clean global installs under npm 11.16.0 and 11.18.0 each contained nonempty bundled OpenTelemetry API 1.9.1 trees and passed version/help. Installed RPC loaded 112 commands including thinking and web-results.
- Released: PR #201 merged as 6248ac3; push run 30408266001 passed source verification, all six package consumers, all five native bundles, npm publication, GitHub release creation, and published-state verification. Windows Node 24.18.0 completed the release consumer path in 39m.
- Registry proof: npm latest is 0.3.7 with integrity sha512-zl9Jov8XYoJHE+pbfAeO9iwvciyyWerYq68ryEg+TpH3ehijMwOlTa7YIeDhgDoTd23GqIBZ0se/rVMGsTvdxQ==; its verified SLSA provenance resolves to 6248ac3. GitHub v0.3.7 targets the same commit and has five nonempty native archives plus a SHA256SUMS file that matches every GitHub asset digest.
- User install: The broken ~/.npm-global 0.3.6 install reproduced the missing OpenTelemetry entry point, then an in-place registry upgrade passed version/help and installed @opentelemetry/[email protected] with 588 files. The package artifact verifier passed with runtime archive SHA-256 5599cb62bfa015479cc942b5051c8335b637999dc276deeb853ea5b6cdf86e88.
- State: completed. Next: keep the global-install and bounded Windows consumer gates in every future release.

2026-07-28 08:30 PDT — intake-sweep-manual-release-provenance-gate Copy Section

- Objective: Keep manual release recovery from creating an immutable npm package whose provenance the push-only identity policy would reject.
- Found: workflow_dispatch could publish a previously absent version, but npm would correctly attest the certificate trigger as workflow_dispatch; post-publish and every later reconciliation would then fail the required push identity check.
- Fixed: Manual runs may reconcile an already-published npm version and complete its GitHub release, but they fail before authorizing npm publication for a new version. The publish-npm job independently requires a push event.
- Verified: The gate is scoped to version-check, executes before should_publish_npm=true, and the publication job has a second event guard. Adversarial review confirmed manual reconciliation remains fail-closed and found one test-only hardening gap, now fixed by scoping downstream skip-condition assertions to their owning jobs. Focused provenance/workflow tests (7/7), full tests (652/652), actionlint, and git diff --check pass.
- Completed: Commit a3aebe4 is on main; run 30375131813 verified the complete 0.3.6 identity without republishing. A disposable Daytona daytona-large sandbox re-ran the exact commit's focused suite (7/7), full suite (652/652), full/production audits, and clean-tree check on Node 24.18.0, then was deleted.

2026-07-28 08:16 PDT — intake-sweep-0.3.6-release-completion Copy Section

- Objective: Complete the 0.3.6 npm/GitHub release, reconcile every tracked user issue, and preserve the final development-audit refresh.
- Published: Main run 30367434326 published the exact verified 39,102-file npm tarball and six-asset GitHub release from ccc8030c1090efb6afab8c4f907115309d1eb788. The package integrity is sha512-DKIzet0eGtJt8lAN307j6pfGrpT+Vu+Lmrju/YbW+DDHJ+/hO/jmxavu494EwqPk2Sied3kvmtGQzhqb6Eqo0g==; GitHub targets the same commit and publishes five nonempty native archives plus SHA256SUMS.
- Failed: npm 11.18.0 does not add gitHead when publishing a prebuilt tarball, so the original final verification stopped before testing the installed package and release assets even though npm's signed SLSA provenance binds the package digest to ccc8030.
- Fixed: Release reconciliation now uses npm audit signatures --include-attestations, validates the verified SLSA subject digest and source claims, and binds them to the Fulcio certificate's GitHub workflow SAN plus OIDC issuer, workflow/ref, source SHA, push trigger, invocation, public visibility, and repository-subject extensions instead of relying on optional registry gitHead metadata.
- Verified: The live npm attestation resolves only to ccc8030; adversarial certificate/source/commit/invocation mismatches fail closed. Focused provenance/workflow tests pass (7/7), full tests pass (652/652), typecheck, build, architecture check, actionlint, root and website full/production audits, website lint/typecheck/build (34 pages), and git diff --check pass. The post-release dry/real package remains within its release budgets; source, clean installed-consumer, and extracted-runtime verification/audits pass.
- Completed: Commit d2cce1f persisted the provenance verifier and dev-lock refresh. Successor run 30373237537 verified the published npm/GitHub identity without republishing; issues #182/#185/#186/#187/#188/#190/#193/#196 were closed with release receipts, and the two superseded remote branches were deleted.

2026-07-28 07:30 PDT — intake-sweep-root-dev-audit-refresh Copy Section

- Objective: Clear the one remaining root development-only advisory without changing the validated 0.3.6 production graph.
- Fixed: Refreshed Vite's transitive postcss from 8.5.16 to patched 8.5.24 and its nanoid dependency from 3.3.15 to 3.3.16 in the root lockfile. package.json, the runtime lock, website dependencies, and published package inputs remain unchanged.
- Verified: Root full and production audits, website full and production audits, focused release tests (5/5), full tests (650/650), typecheck, build, architecture check, website lint/typecheck/build (34 pages), and git diff --check pass. Non-security package drift remains intentionally deferred.
- Next: Persist the lock refresh after the in-flight 0.3.6 release reaches terminal identity, then require the successor main workflow to skip release work cleanly at the already-published version.

2026-07-28 07:12 PDT — intake-sweep-release-tarball-publish-path Copy Section

- Objective: Repair npm publication after all successor package consumers and native bundles passed.
- Found: Run 30364141613 passed source verification, all six Linux/macOS/Windows consumer jobs, and all five native bundles. publish-npm job 90300538798 then passed the downloaded artifact as bare relative path npm-package/companion-ai-feynman-0.3.6.tgz; npm 11.18.0 interpreted that as a Git dependency and attempted ssh://[email protected]/npm-package/...tgz.git. npm 0.3.6 and GitHub v0.3.6 remain absent, so no partial release occurred.
- Fixed: Resolve the single downloaded tarball to an absolute filesystem path before inspecting and publishing it, and scope the regression to the publish-npm job.
- Verified: Full tests (650/650), the focused workflow suite (5/5), actionlint, and git diff --check pass.
- Next: Push the exact successor, then require npm provenance publication, six GitHub assets, checksums, installability, and final release identity before issue closure.

2026-07-28 06:32 PDT — intake-sweep-release-consumer-job-path Copy Section

- Objective: Correct the first release-workflow repair after successor run 30361556647 repeated the Windows runtime-audit failure.
- Found: Commit c67c99c normalized the source-verification consumer block, but the failing cross-platform verify-package-consumers matrix was a separate duplicated block and remained unchanged. The regression asserted against the whole workflow, so the unrelated first block satisfied it. Both Windows Node 24.18.0 and 25 receipts show the old native D:\... archive argument at the failure.
- Fixed: Normalize the runtime archive and extraction paths inside the matrix job itself, and scope the regression to the verify-package-consumers job so another block cannot false-green it.
- Verified: Full tests (650/650), the focused workflow suite (5/5), actionlint, and git diff --check pass.
- Next: Push the exact successor and require both Windows consumers plus native/publish/release identity to pass before issue closure.

2026-07-28 06:00 PDT — intake-sweep-release-windows-runtime-path Copy Section

- Objective: Repair the first post-merge 0.3.6 release run without allowing a partially published release.
- Fixed: Main run 30359204278 passed source/package verification and Linux/macOS consumers, then Windows Node 25 job 90277101520 proved that the publish workflow handed GNU tar the native D:\... path of the installed runtime archive. Git Bash interpreted the drive colon as a remote host separator. The release consumer now converts the runtime archive and extraction destination through cygpath, matching the already-green PR consumer path.
- Verified: npm publication and GitHub release jobs remained gated and never started; the failed run was cancelled after the discriminator receipt was retained. Full tests (650/650), typecheck, focused workflow tests (5/5), actionlint, and git diff --check pass. Exact successor Windows consumers and terminal release identity remain pending.
- Next: Validate and push the workflow-only repair to main, require the successor release run to pass every consumer/native/publish job, then verify npm/GitHub assets and close the eight released issues.

2026-07-28 01:49 PDT — intake-sweep-pi-web-access-0-15 Copy Section

- Objective: Resolve the post-cutoff [email protected] research-search release before publishing Feynman 0.3.6.
- Changed: Pinned the bundled and seeded web-access package to 0.15.0, refreshed the committed runtime lock/archive, documented simultaneous all-provider search, TinyFish search/extraction, and configurable OpenAI Responses-compatible gateways, and extended Feynman's package patch so current upstream utils.ts continues to honor the exact FEYNMAN_WEB_SEARCH_CONFIG file instead of falling back to Pi's agent directory.
- Verified: The exact upstream tag/commit passed its patched test suite (215/215), typecheck, runtime production audit, idempotency, and diff check. Focused Feynman package/runtime/settings/integrity regressions passed (50/50); full tests passed (649/649); typecheck, build, architecture, actionlint, website lint/typecheck/build, root/site/runtime/consumer audits, and diff check passed. Dry and real packs matched at SHA-1 ae23ce2976abe5a3d5920435ad4f4f9a68a8a395; the real tarball SHA-256 is b6d10e01f6bea37984016b7b4a294a8a038ac5e295ccc38c826040583cfa025d. Clean installed-artifact verification reports Pi 0.82.1, [email protected], and runtime SHA-256 2ec33eae33d1d994b73a6826703200daf0883295b2e52a786ea268f5b94375ef; isolated RPC loaded web-results while ignoring an intentionally invalid agent-directory web config in favor of Feynman's exact config path.
- Next: Commit and push the exact candidate, run the clean Daytona ladder at that SHA, require the final GitHub Windows/Node matrix to pass, then merge and verify npm/GitHub release identity.

2026-07-28 01:24 PDT — intake-sweep-windows-consumer-path Copy Section

- Objective: Repair the final exact-head PR #192 platform failure without weakening the shared candidate-tarball gate.
- Fixed: Run 30341296771 proved that both Windows Node 24.18.0 and Node 25 consumers converted the downloaded tarball to a native D:\... path, which GNU tar interpreted as a remote host. The PR consumer gate now retains a native absolute tarball for npm, derives an MSYS path for GNU tar, and normalizes shell-owned consumer and runtime extraction paths under Git Bash.
- Verified: The exact parent candidate passed the GitHub release-candidate source/package job and entered both Windows installer hosts; actionlint, the focused release-workflow suite (5/5), and git diff --check pass with the path repair. Exact successor CI, final clean Daytona verification, merge, and publication remain pending.
- Next: Commit and push the repair, require every Windows/Node/native job to pass, rerun clean-machine proof at the successor SHA, then merge and verify the 0.3.6 release.

2026-07-28 01:07 PDT — intake-sweep-0-3-6-final-candidate Copy Section

- Objective: Finish PR #192 as the single release path for issues #182/#185/#186/#187/#188/#190/#193/#196, including the remaining Windows, supported-Node, packaged-runtime, and live-auth gates.
- Fixed: Raised the Node 22 floor to 22.22.0; made candidate-tarball paths absolute; kept the PowerShell launcher while validating it under execution-policy bypass; normalized Windows runtime hardlinks; updated MCP to 1.30.0, Hono to 2.0.12, and pi-subagents to 0.37.2; made installed-consumer CI audit the extracted runtime archive; made runtime recovery verify every manifest package; and made both alphaXiv status paths refresh and verify credentials against live user-info.
- Verified: Full tests passed (648/648); typecheck, build, architecture, actionlint, website lint/typecheck/build (34 pages), root/site/runtime/consumer audits, and git diff --check passed. Final tarball SHA-256 is 06cdfd606a52e5a59d15d7276c68a9e542f3b40dfa120a4fda5a970e2676fa2b (111572902 bytes, 327212330 unpacked, 39105 files); source and installed artifact verification passed with Pi 0.82.1 and runtime SHA-256 7a858a29c51dcf977be07ba6be1c64ba023b4eaad3aacf0f7ed03414c9679056. Exact-package RPC proved extension/prompt loading, direct bash, and /thinking clamping; live OpenAI model, researcher subagent, and refreshed alphaXiv user-info smokes passed.
- Next: Commit and push the exact candidate, run and delete a disposable Daytona sandbox at that SHA, require the full GitHub Windows and Node 22/24/25 matrix to pass, merge, then verify npm/GitHub/native release identity and issue closure.

2026-07-26 17:48 PDT — intake-sweep-windows-runtime-hardlinks Copy Section

- Objective: Repair PR #192 Windows native job 89859997454 at exact head 8bf9f1a2e5af48787c2eb47eae3726b86cacb9c1 without weakening runtime archive integrity.
- Fixed: Windows tar preserved npm-created NTFS hardlinks, while the live workspace hash treated each hardlink as its regular-file contents and the archive hash treated it as a distinct entry type. Runtime archive verification now resolves in-archive hardlinks to their target file or symlink content, rejects targets outside npm/, duplicate entries, missing targets, and cycles, and compares the same logical tree on every platform.
- Further fixed: All public Windows PowerShell downloads now use -UseBasicParsing, which Microsoft requires after the CVE-2025-54100 PowerShell 5.1 update to avoid an interactive script-execution prompt. PR and publish gates now reuse the exact packed candidate across Node 22.19.0, 24.18.0, and 25, including Windows Node 25 plus macOS and Windows Node 24 consumers, instead of leaving the supported-major matrix manual and post-publication.
- Verified: A minimal hardlink repro failed against the prior archive parser; the focused archive/runtime regression suite passes (8/8), the installer/workflow suite passes (8/8), actionlint passes, both public Windows installers are byte-identical, and root typecheck/full tests/build/architecture plus git diff --check passed at the hardlink commit (642/642). Exact Windows native/install and supported-major consumer proof remain pending the next pushed-head CI run.
- Next: Push the remaining gate repairs, require the complete PR matrix to pass, then finish clean-machine, merge, and release verification.

2026-07-26 17:16 PDT — intake-sweep-0-3-6-windows-ci-repair Copy Section

- Objective: Repair the first exact-head PR CI failure at f5974f96ae9b1950ced68093c6ee1abdb9acc5d9 without weakening the release verifier.
- Fixed: Windows native build run 30226243548, job 89856784343, proved that the production dependency install replaced the patched MCP manifest before artifact verification. The embedded runtime patch now repairs MCP manifests in the installed package and vendored workspace graphs. The Windows installer also validates downloaded PowerShell launchers through the current host with a process-scoped execution-policy bypass, preserving the public in-memory installer under Windows PowerShell's default Restricted policy. A follow-up adversarial check found that the StrictMode verifier used $installBinDir without defining it; the verifier now derives that path explicitly and tests the assignment.
- Verified: Focused archive, installer, MCP, runtime-patch, and release-workflow tests passed (18/18) before the StrictMode follow-up; both public Windows installer copies are byte-identical; actionlint and git diff --check passed. Exact Windows native/install proof remains pending the next pushed-head CI run.
- Next: Commit and push the repair, require both Windows PowerShell 5.1 and PowerShell Core jobs to pass, then continue clean-machine and release verification.

2026-07-26 16:48 PDT — intake-sweep-0-3-6-release-candidate Copy Section

- Objective: Reconcile the inherited 0.3.6 work into PR #192, finish the Pi 0.82.1/security/package/installer release blockers, and prove the exact candidate before merge and publication.
- Changes: Migrated Feynman's model/auth/session paths to Pi 0.82.1 ModelRuntime; added model-aware /thinking; preserved Pi follow-up while adding Option+Enter newline input; pinned and integrity-bound the packaged runtime graph; repaired Pi brace-expansion and MCP/Hono consumer advisories; made runtime/native archives deterministic; made Windows replacement transactional and checksum-ambiguous inputs fail closed; added Windows Desktop/Core, clean-consumer, package-budget, native matrix, exact-tarball publication, and release-reconciliation gates. The publish gate now accepts a complete npm/GitHub release at an ancestor commit while still requiring exact commit identity for incomplete-release recovery, so ordinary later main commits do not false-fail the prior release.
- Intake: PR #192 is the owning merge path. PR #200 is superseded by the independently prepared model-aware implementation and should close after the replacement commit is pushed. Issues #182/#185/#186/#187/#188/#190/#193/#196 are implemented and remain open only until exact-head CI, merge, and release verification.
- Verified locally: Focused regressions passed (64/64); full npm test passed (639/639); typecheck, build, architecture check, website lint/typecheck/build (34 pages), actionlint, root/site/runtime/consumer production audits, and git diff --check passed. Exact tarball companion-ai-feynman-0.3.6.tgz is 111547961 bytes with 39088 files, SHA-256 d95cd2bdce96069653707b85f06a6d1e453113893a354d46a02f676d25503e26; source and installed artifact verification passed with Pi 0.82.1 and runtime archive SHA-256 0bb4e8c6049a1a9d3742f36350cd978c46d249d22c4cbf6942fac8ff6d4dd8ae. An installed Pi session reached the expected missing OpenAI credential only after runtime load and workspace scaffolding.
- Next: Commit and push the exact candidate, run and delete a disposable Daytona proof, repair PR CI to green, merge, then verify npm/GitHub/native release identity and terminally reconcile the eight issues plus PR #200.

2026-07-22 20:10 EDT — intake-sweep-package-floor Copy Section

- Objective: Finish the check-new-issues release-candidate proof after the queue audit, preserve the existing PR branch, and correct package metadata that made supported Node 22 installs noisy or inconsistent.
- Changes: Raised the website engine contract from Node >=20.19.0 <25 to >=22.19.0 <26, matching Astro 7 and the root Feynman runtime. Moved ketcher-core, ketcher-react, and ketcher-standalone from production dependencies to exact 3.15.0 development dependencies because they are build-only inputs already bundled into dist.
- Verified: Clean root and website installs passed; the complete suite passed (595/595); focused runtime/MCP tests passed (24/24); root typecheck/build and architecture checks passed with existing warnings; website lint/typecheck/build passed (34 pages); website audit found 0 vulnerabilities; root audit still reports only Pi-shrinkwrapped [email protected] and [email protected]; npm pack --dry-run --json passed with 402 entries. The exact tarball /tmp/feynman-pack-release-20260722-2010/companion-ai-feynman-0.3.6.tgz is 71043279 bytes with SHA-256 6b9e4150f6b28233345bd99b4f3222371fe3d0e354ec7665740dac6a03cc9732.
- Installed smoke: A fresh Node 22.22.3 install emitted no Ketcher engine warnings and passed version/help, alpha help, package listing, unknown --extensions guidance, alt+enter, packaged workspace scaffold creation, launch-before-spawn wiring, alphaXiv OAuth markers, project-local fetch-cache markers, and runtime archive entries for Pi 0.80.6, pi-btw 0.4.1, and pi-web-access 0.13.0.
- Blocked: A consumer-side tarball audit additionally resolves @modelcontextprotocol/[email protected] to vulnerable @hono/[email protected]. The repository is clean because its root override selects 2.0.11, but npm package overrides do not propagate to consumers and the latest MCP SDK still declares @hono/node-server@^1.19.9; no safe package-local version bump is currently available.
- Next: Keep PR #192 unmerged and unpublished without explicit authorization; verify issue #199 on a tool-capable Ubuntu/Ollama model before calling it fully fixed; resolve or explicitly accept the consumer-install MCP/Hono audit blocker before publishing 0.3.6.

2026-07-22 15:36 EDT — intake-sweep-workspace-scaffold Copy Section

- Objective: Re-run check-new-issues, preserve existing dirty release-candidate work, refresh live GitHub/release/package/workflow state, classify open issues/PRs/contributor refs, and fix safe repo-local validation or artifact failures without GitHub writes.
- Checked: New issue #199 reports fresh Ubuntu/Ollama runs printing planned outputs/.plans writes without actually creating files because the workspace lacks outputs/.plans. Open issues are now #199, #198, #196, #193, #190, #188, #187, #186, #185, #184, and #182; open PRs remain #197, #192, #191, and #189. Latest main Publish and Release run remains green at 54d08a3; GitHub release and npm latest remain v0.3.5 / 0.3.5; local package remains 0.3.6; bundled Pi remains 0.80.6; npm Pi latest remains 0.81.1.
- Decisions: Ported a smallest root-cause local fix for #199: Pi launch now scaffolds outputs/.plans, outputs/.drafts, papers, and notes under the selected --cwd before the child runtime starts. PR #192 remains merge/defer pending explicit authorization; PR #189 remains already ported into #192; PR #191 remains reject/defer as broader extension inventory surface; PR #197 remains reject/defer as generic provider catalog expansion. Issue #198 remains outside the AI-researcher product bar; #196 remains upstream Pi TUI slash-command scope; #193/#182/#190/#188/#187/#186/#185 remain covered by #192; #184 remains support/content scope.
- Contributor refs: Remote refs were refreshed. origin/fix/deepresearch-local-model-warning remains 74 behind / 1 ahead; pr4fork/main remains 73 behind / 0 ahead; visible fork refs did not introduce a fresh safe research-loop port target.
- Freshness: Root and website npm outdated --json show non-security drift. No dependency edit was made because the actionable defect was workspace artifact scaffolding, not dependency freshness.
- Verified: npm test passed (595/595); root npm run typecheck; root npm run build with existing RDKit/3Dmol/direct-eval/chunk warnings; npm run architecture:check with existing split-debt warnings; website lint/typecheck/build passed (34 pages); website audit found 0 vulnerabilities; root audit remains blocked by Pi-shrinkwrapped [email protected] and [email protected]; git diff --check passed; npm pack --dry-run --json passed with entryCount: 402, shasum ff8c9b527f00bee5588e7fbb43bc3660d97d044b, size 71041173; installed-tarball smoke passed for package 0.3.6, help, and fresh-workspace scaffold creation.
- Next: Review/commit the scaffold fix with the existing 0.3.6 release-candidate work; merge/publish PR #192 only when authorized; keep dependency freshness drift separate from #199.

2026-07-22 07:32 EDT — intake-sweep-copilot-review-rejected Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve the existing dirty release-candidate worktree, refresh live GitHub/release/package/workflow state, classify open issues/PRs/contributor refs, and validate the local 0.3.6 package without GitHub writes.
- Checked: Open issues are #198, #196, #193, #190, #188, #187, #186, #185, #184, and #182; open PRs are #197, #192, #191, and #189. Latest main Publish and Release run remains green at 54d08a3; GitHub release and npm latest remain v0.3.5 / 0.3.5; local package remains 0.3.6; bundled Pi remains 0.80.6; npm Pi latest remains 0.81.1; alpha-hub remains 0.1.3; pi-btw remains 0.4.1.
- Decisions: Issue #198 is reject/defer because Microsoft Copilot reviewer/checklist automation is external review/admin workflow rather than a concrete Feynman-owned research-loop defect or smallest research artifact verification improvement. PR #192 remains merge/defer pending explicit authorization; PR #189 remains already ported into #192; PR #191 remains reject/defer as broader extension inventory surface; PR #197 remains reject/defer as generic curated provider expansion. Issue #196 remains upstream Pi TUI slash-command scope; #193/#182/#190/#188/#187/#186/#185 remain covered by #192; #184 remains support/content scope.
- Contributor refs: Remote refs were refreshed. origin/fix/deepresearch-local-model-warning, pr4fork/main, and visible fork refs did not introduce a fresh safe research-loop port target.
- Freshness: Root and website npm outdated --json show non-security drift. No dependency edit was made because no queue-specific root-cause failure requires dependency churn and the remaining root audit blocker is still Pi-owned nested shrinkwrap state.
- Verified: Focused runtime test passed (15/15); npm run typecheck; npm run build with existing RDKit/3Dmol/direct-eval/chunk warnings; npm run architecture:check with existing split-debt warnings; npm test passed (594/594); website lint/typecheck/build passed (34 pages); website audit found 0 vulnerabilities; root audit remains blocked only by Pi-shrinkwrapped [email protected] and [email protected]; git diff --check passed; npm pack --dry-run --json passed with entryCount: 402, shasum c698bb6c66c37756ba677c0a45af49c532f6a6d9, size 71041144; installed-tarball smoke passed for 0.3.6, help, alpha help, packages list including pi-btw and pi-web-access, update --extensions help hint, alt+enter, runtime archive markers, alpha auth patch, and project-local fetch cache patch.
- Next: Merge/publish PR #192 only when authorized; keep #198, #197, and #191 out unless product scope explicitly changes.

2026-07-13 23:35 PDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve existing dirty local work, refresh GitHub issue/PR/workflow/release/package/branch state, classify the queue against the AI-researcher product bar, and validate the local package without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues; open issues remain #193, #190, #188, #187, #186, #185, #184, and #182; open PRs remain #192, #191, and #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local package remains 0.3.6; Pi remains 0.80.6; @companion-ai/alpha-hub remains ^0.1.3.
- Decisions: No new code changes. Keep draft PR #192 as the merge path for #182, #185, #186, #187, #188, #190, and #193; it already includes PR #189 as cherry-pick 79aa7b2. Reject/defer PR #191 because feynman extensions is still a broader extension-inventory surface than the reported update/help failure requires and its Vercel status remains failing. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: Remote refs were refreshed. origin/fix/deepresearch-local-model-warning remains stale local-model warning work; visible fork refs were prompt/Overleaf/admin surfaces, provider/platform changes, fork docs, broad Windows rewrites, or already-covered installer/runtime/auth work. No new safe port target was found.
- Freshness: Root and website npm outdated --json show dependency drift only; root and website npm audit --omit=dev found 0 vulnerabilities. No dependency change was made.
- Verified: Focused runtime test passed (15/15); npm test passed (594/594); root npm run typecheck; root npm run build with existing Vite/RDKit/3Dmol/chunk warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev; git diff --check; npm pack --dry-run --json (entryCount: 402, shasum f0b50e989c04095e9a4b3b65628bcf6def9921aa); installed-tarball smoke proved package 0.3.6, CLI help, feynman alpha --help, feynman packages list including npm:pi-btw and npm:pi-web-access, runtime archive presence, and the hoisted alpha CLI resolver.
- Note: The installed tarball emitted dependency deprecation warnings during npm install, but completed successfully. No GitHub write was made.
- Next: Commit the hoisted alpha CLI resolver and merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-13 11:34 PDT — intake-sweep-alpha-193-covered Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve existing dirty local work, refresh GitHub issue/PR/workflow/release/package state, classify the queue against the AI-researcher product bar, and validate the local package without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; origin/main remains 54d08a3. Open issues are now #193, #190, #188, #187, #186, #185, #184, and #182; open PRs remain #192, #191, and #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local package remains 0.3.6; Pi latest/current remains 0.80.6; @companion-ai/alpha-hub latest/current remains 0.1.3.
- Decisions: No GitHub writes. Treat new issue #193 as covered by the #192 alphaXiv auth patch plus the current local hoisted-alpha CLI resolver in src/cli.ts; clerk.alphaxiv.org still fails with ENOTFOUND, while local patched alpha-hub uses https://api.alphaxiv.org/auth. Keep draft PR #192 as the merge path for #182, #185, #186, #187, #188, #190, and #193; it already includes contributor PR #189 as cherry-pick 79aa7b2. Reject/defer PR #191 because feynman extensions remains broader than the update/help failure requires and its Vercel status remains failing. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: Remote refs were refreshed. No new safe port target was found beyond #189, already included in #192; visible fork refs remain stale, broader provider/platform/admin work, docs/export material, or already-covered installer/runtime/auth work.
- Freshness: Root and website npm outdated --json show non-security drift only. No dependency change was made.
- Verified: Focused alpha/runtime tests passed (20/20); npm test passed (594/594); root npm run typecheck; root npm run build with existing Vite/RDKit/3Dmol/chunk warnings; npm run architecture:check with existing split-debt warnings; root and website npm audit --omit=dev (0 vulnerabilities); website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum f0b50e989c04095e9a4b3b65628bcf6def9921aa); installed-tarball smoke proved package 0.3.6, CLI help, feynman alpha --help, hoisted alpha resolver presence, and installed alpha-hub auth issuer https://api.alphaxiv.org/auth.
- Note: Early focused and pack probes failed only from invocation/parser assumptions: raw node --test on TS files without tsx, then mixed npm pack --json output containing prepack [feynman] logs. Corrected commands passed.
- Next: Commit the hoisted alpha CLI resolver and merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-13 03:37 PDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve existing dirty local work, refresh GitHub/package/release/branch state, classify open issues/PRs/contributor refs, and run repo-local validation without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; origin/main remains 54d08a3. Open issues remain #190, #188, #187, #186, #185, #184, and #182; open PRs remain #192, #191, and #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local package remains 0.3.6; Pi latest/current remains 0.80.6; @companion-ai/alpha-hub latest/current remains 0.1.3.
- Decisions: No new code changes. Keep draft PR #192 as the merge path for #182, #185, #186, #187, #188, and #190; it includes contributor PR #189 as cherry-pick 79aa7b2, has green Vercel status, and the latest PR comment still reports the alpha auth patch worked for another user. Reject/defer PR #191 because feynman extensions is broader than the update/help failure requires and its Vercel status is still failing. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: Remote refs and recent public forks were refreshed/spot-checked. No new safe port target was found beyond #189, already included in #192; recent visible forks were either at 54d08a3, behind, broader provider/platform work, docs/export material, or already-covered Windows/install/auth work.
- Freshness: npm outdated --json shows non-security drift only in root and website packages. No dependency change was made.
- Verified: Focused runtime/auth/web/install regressions passed (51/51); npm test passed (594/594); root npm run typecheck; root npm run build with existing Vite/RDKit/3Dmol/chunk warnings; npm run architecture:check with existing split-debt warnings; root and website npm audit --omit=dev (0 vulnerabilities); website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum f0b50e989c04095e9a4b3b65628bcf6def9921aa); corrected installed-tarball smoke proved package/CLI 0.3.6, CLI help, package listing, alpha status, bundled alt+enter, runtime archive, alphaXiv OAuth2 patch, project-local fetch cache patch, and archive entries for pi-btw, pi-web-access, and @earendil-works/pi-coding-agent.
- Note: Early smoke wrappers failed only from probe assumptions: mixed npm pack --json parsing, stale alpha-hub archive path, and stale pi-web-access source path. The corrected smoke used actual archive paths and passed; temp artifacts were cleaned.
- Next: Review/merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-12 06:15 EDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve unrelated local work, refresh GitHub/package/release/branch state, classify open issues/PRs/contributor refs, and run repo-local validation without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; origin/main remains 54d08a3. Open issues remain #190, #188, #187, #186, #185, #184, and #182; open PRs remain #192, #191, and #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local package remains 0.3.6; Pi latest/current remains 0.80.6; @companion-ai/alpha-hub latest/current remains 0.1.3.
- Decisions: No new code changes. Keep draft PR #192 as the merge path for #182, #185, #186, #187, #188, and #190; it includes contributor PR #189 as cherry-pick 79aa7b2, has green Vercel status, and the latest PR comment still reports the alpha auth patch worked for another user. Reject/defer PR #191 because feynman extensions is broader than the update/help failure requires and its Vercel status is still failing. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: Remote refs were refreshed. No new safe port target was found beyond #189, already included in #192; older visible refs remain stale, broader provider/platform work, docs/export material, or already-covered Windows/install/auth work.
- Freshness: npm outdated --json shows non-security drift only in root and website packages. No dependency change was made.
- Verified: npm run architecture:check with existing split-debt warnings; npm test passed (593/593); root npm run typecheck; root npm run build with existing Vite/RDKit/3Dmol/chunk warnings; root and website npm audit --omit=dev (0 vulnerabilities); website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum 167a902ecc8b2ea71e6b3402052f3a45c7ab2b11); corrected installed-tarball smoke proved package 0.3.6, CLI --version, CLI --help exit, packages list, alpha status, runtime archive entries for pi-btw and pi-web-access, and the alphaXiv OAuth2 patch in the runtime archive.
- Note: One early smoke wrapper failed only from a mixed npm pack --json parser grabbing an inner files array. The corrected parser and smoke passed; temp installs and tarballs were cleaned.
- Next: Review/merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-12 02:15 EDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve unrelated local work, refresh GitHub/package/release/branch state, classify open issues/PRs/contributor refs, and run repo-local validation without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; origin/main remains 54d08a3. Open issues remain #190, #188, #187, #186, #185, #184, and #182; open PRs remain #192, #191, and #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local package remains 0.3.6; Pi latest/current remains 0.80.6; @companion-ai/alpha-hub latest/current remains 0.1.3.
- Decisions: No new code changes. Keep draft PR #192 as the merge path for #182, #185, #186, #187, #188, and #190; it includes contributor PR #189 as cherry-pick 79aa7b2, has green Vercel status, and the latest PR comment still reports the alpha auth patch worked for another user. Reject/defer PR #191 because feynman extensions is broader than the update/help failure requires and its Vercel status is still failing. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: Remote refs were refreshed. No new safe port target was found beyond #189, already included in #192; older visible refs remain stale, broader provider/platform work, docs/export material, or already-covered Windows/install/auth work.
- Freshness: npm outdated --json shows non-security drift only in root and website packages. No dependency change was made.
- Verified: npm test passed (593/593); root npm run typecheck; root npm run build with existing Vite/RDKit/3Dmol/chunk warnings; root and website npm audit --omit=dev (0 vulnerabilities); npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum 167a902ecc8b2ea71e6b3402052f3a45c7ab2b11); corrected installed-tarball smoke proved package 0.3.6, CLI --version, packages list, alpha status, bundled alt+enter, runtime archive entries for pi-btw and pi-web-access, and the alphaXiv OAuth2 patch in the runtime archive.
- Note: Two early smoke wrappers failed only from probe assumptions: first parsing the [feynman] prepack log prefix as JSON, then sampling archive paths under pipefail/a stale alpha-hub path. The corrected checks passed and temp artifacts were cleaned.
- Next: Review/merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-11 22:11 EDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve unrelated local work, refresh GitHub/package/release/branch state, classify open issues/PRs/contributor refs, and run repo-local validation without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; origin/main remains 54d08a3. Open issues remain #190, #188, #187, #186, #185, #184, and #182; open PRs remain #192, #191, and #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local package remains 0.3.6; Pi latest/current remains 0.80.6; @companion-ai/alpha-hub latest/current remains 0.1.3.
- Decisions: No new code changes. Keep draft PR #192 as the merge path for #182, #185, #186, #187, #188, and #190; it includes contributor PR #189 as cherry-pick 79aa7b2, and the latest PR comment still reports the alpha auth patch worked for another user. Reject/defer PR #191 because feynman extensions is broader than the update/help failure requires and its Vercel status is still failing. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: Remote refs were refreshed. No new safe port target was found beyond #189, already included in #192; older visible refs remain stale, broader provider/platform work, docs/export material, or already-covered Windows/install/auth work.
- Freshness: npm outdated --json shows non-security drift only in root and website packages. No dependency change was made.
- Verified: npm test passed (593/593); root npm run typecheck; root and website npm audit --omit=dev (0 vulnerabilities); root npm run build with existing Vite/RDKit/3Dmol/chunk warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); npm run architecture:check with existing split-debt warnings; git diff --check; npm pack --dry-run --json (entryCount: 402, shasum 167a902ecc8b2ea71e6b3402052f3a45c7ab2b11); corrected installed-tarball smoke proved package 0.3.6, CLI --version, --help, packages list, alpha status, bundled alt+enter, runtime archive, and archive entries for pi-btw, pi-web-access, and @earendil-works/pi-coding-agent.
- Note: One installed-smoke wrapper failed from a bad mixed-log JSON parser; the corrected strict smoke passed and temp artifacts were cleaned.
- Next: Review/merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-11 18:09 EDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve unrelated local work, refresh GitHub/package/release/branch state, classify open issues/PRs/contributor refs, and run repo-local validation without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; origin/main remains 54d08a3. Open issues remain #190, #188, #187, #186, #185, #184, and #182; open PRs remain #192, #191, and #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local package remains 0.3.6; Pi latest/current remains 0.80.6; alpha-hub latest/current remains 0.1.3.
- Decisions: No new code changes. Keep draft PR #192 as the merge path for #182, #185, #186, #187, #188, and #190; it includes contributor PR #189 as cherry-pick 79aa7b2, and the latest PR comment reports the alpha auth patch worked for another user. Reject/defer PR #191 because feynman extensions is broader than the update/help failure requires and its Vercel status is still failing. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: Remote refs were refreshed. No new safe port target was found beyond #189, already included in #192; older visible refs remain stale, broader provider/platform work, docs/export material, or already-covered Windows/install/auth work.
- Freshness: npm outdated --json shows non-security drift only in root and website packages. No dependency change was made.
- Verified: npm test passed (593/593); root npm run typecheck; website npm run lint and npm run typecheck (0 errors, 0 warnings, 0 hints); root and website npm audit --omit=dev (0 vulnerabilities); npm run architecture:check with existing split-debt warnings; root npm run build with existing Vite/RDKit/3Dmol/chunk warnings; website npm run build (34 pages); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum 167a902ecc8b2ea71e6b3402052f3a45c7ab2b11); strict installed-tarball smoke proved package 0.3.6, CLI --version, --help, packages list, alpha status, bundled alt+enter, runtime archive, and archive entries for pi-btw, pi-web-access, and @earendil-works/pi-coding-agent.
- Note: One installed-smoke wrapper failed from a bad mixed-log JSON parser and missing set -e; the corrected strict smoke passed and temp artifacts were cleaned.
- Next: Review/merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-11 09:16 EDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve the existing dirty CHANGELOG.md, refresh GitHub/package/release/branch state, classify open issues/PRs/contributor refs, and run repo-local validation without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; origin/main remains 54d08a3. Open issues remain #190, #188, #187, #186, #185, #184, and #182; open PRs remain #192, #191, and #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local package remains 0.3.6; Pi latest/current remains 0.80.6; alpha-hub latest/current remains 0.1.3.
- Decisions: No new code changes. Keep draft PR #192 as the merge path for #182, #185, #186, #187, #188, and #190; it includes contributor PR #189 as cherry-pick 79aa7b2. Reject/defer PR #191 because feynman extensions is broader than the update/help failure requires and its Vercel status is failing. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: origin/fix/deepresearch-local-model-warning, pr4fork/main, and fork refs were checked. No new safe port target was found: visible refs were either already represented in #192, broader platform/provider/admin work, docs-only walkthrough/export material, fork-specific changes, or stale Windows/install work already covered by the current branch.
- Freshness: npm outdated --long shows non-security drift only (@clack/prompts, OpenTelemetry packages, TypeBox, Node types, fast-xml-parser, lucide-react, patristic, posthog-node, radix-ui, tsx, TypeScript, undici, vite). No dependency change was made.
- Verified: npm test passed (593/593); npm run typecheck; npm run architecture:check with existing split-debt warnings; root npm run build with existing Vite/RDKit/3Dmol warnings; root and website npm audit --omit=dev (0 vulnerabilities); website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum 167a902ecc8b2ea71e6b3402052f3a45c7ab2b11); installed-tarball smoke proved package 0.3.6, CLI --version, --help, packages list, alpha status, bundled alt+enter, and runtime archive entries for pi-btw, pi-web-access, and @earendil-works/pi-coding-agent.
- Note: Two initial smoke wrappers failed only from probe assumptions: first reading hoisted dependencies under the package-local node_modules, then resolving non-exported dependency package.json files. The final smoke used CLI/archive checks and passed; generated temp installs and tarballs were removed.
- Next: Review/merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-11 05:15 EDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve the existing dirty CHANGELOG.md, refresh live GitHub/package/release/branch state, classify open issues/PRs, and run repo-local validation without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; origin/main remains 54d08a3. Live queue remains issues #190, #188, #187, #186, #185, #184, #182 and PRs #192, #191, #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local candidate remains 0.3.6; Pi remains latest/current at 0.80.6; alpha-hub remains latest/current at 0.1.3.
- Decisions: No new code changes. Keep draft PR #192 as the merge path for #182, #185, #186, #187, #188, and #190; it already includes contributor PR #189 as cherry-pick 79aa7b2 with original authorship. Reject/defer PR #191 because a new feynman extensions inventory command is broader than the update --extensions help/update failure requires and its Vercel check is failing. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: origin/fix/deepresearch-local-model-warning, pr4fork/main, and older fork refs were checked as remote branch state; none introduced a current safe port target beyond #189, already included in #192.
- Freshness: npm outdated --long shows non-security drift only (@clack/prompts, OpenTelemetry packages, TypeBox, Node types, fast-xml-parser, lucide-react, patristic, posthog-node, radix-ui, tsx, TypeScript, undici, vite). No dependency change was made.
- Verified: npm test passed (593/593); npm run typecheck; npm run architecture:check with existing split-debt warnings; root npm run build with existing Vite/RDKit/3Dmol warnings; root and website npm audit --omit=dev (0 vulnerabilities); website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum 167a902ecc8b2ea71e6b3402052f3a45c7ab2b11); corrected installed-tarball smoke proved feynman --version, feynman --help, feynman packages list, feynman alpha status, package 0.3.6, Pi 0.80.6, alpha-hub ^0.1.3, bundled alt+enter, and runtime archive entries for pi-btw, pi-web-access, and @earendil-works/pi-coding-agent.
- Note: An initial installed-smoke wrapper hit the known mixed npm pack --json log parser issue; it was rerun with a stricter extractor and passed. Generated temp installs and tarballs were removed.
- Next: Review/merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-11 01:29 EDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve existing local work, refresh live GitHub/package/release/branch state, classify every open issue/PR, and run repo-local validation without GitHub writes.
- Checked: Current branch remains codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; pre-existing dirty state was CHANGELOG.md only. Live queue remains issues #190, #188, #187, #186, #185, #184, #182 and PRs #192, #191, #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local candidate remains 0.3.6; Pi remains latest/current at 0.80.6; alpha-hub remains latest/current at 0.1.3.
- Decisions: No new code changes. Keep PR #192 as the merge path for #182, #185, #186, #187, #188, and #190; it already includes contributor PR #189 as cherry-pick 79aa7b2. Reject/defer PR #191 because feynman extensions is broader extension-inventory surface than the reported update/help failure needs and has a failing Vercel status. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: origin/fix/deepresearch-local-model-warning, pr4fork/main, and older fork refs were observed; none introduced a current safe port target beyond #189, already included in #192.
- Verified: npm test passed (593/593); npm run typecheck; npm run architecture:check with existing split-debt warnings; root npm run build with existing Vite/RDKit/3Dmol warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum 167a902ecc8b2ea71e6b3402052f3a45c7ab2b11); installed tarball smoke proved feynman --version, feynman --help, feynman packages list, feynman alpha status, package 0.3.6, Pi 0.80.6, alpha-hub 0.1.3, bundled alt+enter, staged Windows installer extraction, fetch cache patch, and alphaXiv OAuth2 patch. Direct archive listing proved bundled pi-btw and pi-web-access.
- Note: Earlier smoke wrappers failed only from parser/probe mistakes: mixed npm pack --json logs, package export restrictions on direct package.json requires, and a stale runtime archive prefix. Corrected checks passed and temp artifacts were removed.
- Next: Review/merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-10 21:13 EDT — intake-sweep-pr-192-still-clean Copy Section

- Objective: Re-run check-new-issues from /Users/advaitpaliwal/Companion/Code/feynman, preserve existing local work, refresh live GitHub/package/release state, classify every open issue/PR, and run repo-local validation without GitHub writes.
- Checked: Current branch is codex/fix-feynman-user-issues at 8ad8d55 tracking origin/codex/fix-feynman-user-issues; pre-existing dirty state was CHANGELOG.md only. Live queue remains issues #190, #188, #187, #186, #185, #184, #182 and PRs #192, #191, #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman remains 0.3.5; local candidate remains 0.3.6; Pi remains latest/current at 0.80.6; alpha-hub remains latest/current at 0.1.3.
- Decisions: No new code changes. Keep PR #192 as the merge path for #182, #185, #186, #187, #188, and #190; it already includes contributor PR #189 as cherry-pick 79aa7b2. Reject/defer PR #191 because feynman extensions is broader extension-inventory surface than the reported update/help failure needs. Issue #184 remains outside Feynman's AI-researcher product bar.
- Contributor refs: origin/fix/deepresearch-local-model-warning and pr4fork/main were the only non-main refs observed; neither introduced a current safe port target for this queue.
- Verified: npm test passed (593/593); npm run typecheck; npm run architecture:check with existing split-debt warnings; root npm run build with existing Vite/RDKit/3Dmol warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum 167a902ecc8b2ea71e6b3402052f3a45c7ab2b11); installed tarball smoke proved feynman --version, feynman --help, feynman packages list, package 0.3.6, Pi 0.80.6, bundled alt+enter, staged Windows installer extraction, fetch cache patch, alphaXiv OAuth2 patch, runtime archive, and bundled pi-btw/pi-web-access archive entries.
- Note: The smoke command exited 141 only after successful checks because tar | grep | head hit SIGPIPE under pipefail; temp install and tarball artifacts were removed.
- Next: Review/merge/publish PR #192 when authorized; keep PR #191 out unless product scope explicitly expands to extension inventory.

2026-07-10 17:12 EDT — intake-sweep-pr-192-validated Copy Section

- Objective: Re-run check-new-issues from the current codex/fix-feynman-user-issues checkout, preserve local branch state, and classify the now-open issues/PRs without GitHub writes.
- Checked: Current branch tracks origin/codex/fix-feynman-user-issues at 8ad8d55 with no dirty files. Open issues are #190, #188, #187, #186, #185, #184, and #182. Open PRs are #192, #191, and #189. Latest main Publish and Release run remains 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest remains 0.3.5; local candidate is 0.3.6; Pi latest/current is 0.80.6; alpha-hub latest/current is 0.1.3.
- Decisions: PR #192 is the preferred merge path after review because it bundles the smallest research-loop reliability fixes for #182, #185, #186, #187, #188, and #190, includes contributor PR #189 as a cherry-pick, and leaves #191 out. PR #189 should be ported via #192 rather than merged separately. PR #191 should be rejected/deferred because a new feynman extensions management/discovery surface is broader than the issue requires; update guidance is enough for #187. Issue #184 remains outside the AI-researcher product bar as support/advice.
- Contributor refs: Existing fork refs remain stale or broad provider/admin/platform churn. No additional contributor branch was ported beyond #189, which is already included in local PR #192 as commit 79aa7b2.
- Freshness: npm outdated --long shows non-security dependency drift only (@clack/prompts, OpenTelemetry packages, TypeBox, Node types, fast-xml-parser, lucide-react, patristic, posthog-node, radix-ui, tsx, TypeScript, undici, vite). No queue-specific freshness patch was needed.
- Verified: Focused regressions passed (88/88); full npm test passed (593/593), including the two workbench tests that failed in the prior run; npm run typecheck; npm run build with existing RDKit/3Dmol/chunk warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 402, shasum 167a902ecc8b2ea71e6b3402052f3a45c7ab2b11); installed tarball smoke passed for feynman --version, feynman --help, feynman packages list, package 0.3.6, Pi 0.80.6, bundled alt+enter keybinding, staged Windows installer extraction, runtime archive presence, fetch cache patch, and alphaXiv OAuth2 patch.
- Note: A first installed-smoke helper failed only because it parsed mixed npm pack --json logs and then used overly literal probe strings. The corrected smoke passed and temp tarball artifacts were removed.
- Next: Review and merge/publish PR #192 when authorized; leave #191 out unless the product scope explicitly expands to extension inventory.

2026-07-10 13:14 EDT — intake-sweep-current-queue-flaky-workbench Copy Section

- Objective: Re-run check-new-issues against the current dirty checkout, preserve pending Pi 0.80.6, alpha OAuth, and Windows installer work, and verify whether the live queue or local validation requires another local fix.
- Checked: Local main remains aligned with origin/main at 54d08a3. Live GitHub queue still has open issues #186, #185, #184, and #182, with zero open PRs. Latest main Publish and Release run 28835967900 is green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest/current remains 0.3.5; @earendil-works/pi-coding-agent latest/current is 0.80.6; @companion-ai/alpha-hub latest/current is 0.1.3.
- Decisions: No new code changes were needed. Issue #186 remains covered by the pending staged Windows installer extraction fix; issue #185 remains covered by bundled pi-btw; issue #184 remains outside the AI-researcher product bar as support/advice; issue #182 remains covered by the pending alphaXiv OAuth2 endpoint patch. No PRs were available to merge, port, reject, or defer.
- Contributor refs: origin/fix/deepresearch-local-model-warning is behind current main with one already-covered ahead commit. Sampled fork refs were behind by 91-142 commits with Bedrock/provider setup, Overleaf/export/admin prompts, Claude CLI bypass, architecture notes, fork-specific search tooling, or broad Windows/platform churn; no clean core-research patch was ported.
- Freshness: Root npm outdated --json shows non-security dependency drift only, with Pi already current at 0.80.6. Root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: Root npm run typecheck; npm run build with existing RDKit/3Dmol/chunk/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 401, shasum 78cbe7bc2a43ce7aec95c42c10077b4754a9afe1); installed tarball smoke reached feynman --version, feynman --help, feynman packages list, feynman alpha status, packaged scripts/install/install.ps1 staged-extraction checks, and runtime archive inspection showing api.alphaxiv.org/auth, oauth2/authorize, and openid profile email offline_access.
- Validation note: The full npm test run failed 2/589 in tests/workbench.test.ts (notebook Python session kernel persists variables across cells saw one execution record instead of two; workbench server streams chat messages through the authenticated API saw missing final message status). The same two tests passed when rerun in isolation with node --import tsx --test --test-concurrency=1 --test-name-pattern='notebook Python session kernel persists variables across cells|workbench server streams chat messages through the authenticated API' tests/workbench.test.ts, so this remains a repo-local full-suite flake/failure to investigate.
- Note: The first real-pack smoke parser failed on mixed npm pack --json logs, and the corrected smoke later failed only because it expected website/public/install.ps1 inside the npm package. The shipped package includes scripts/install/install.ps1, which was verified; temp smoke artifacts and the root tarball were removed.
- Next: Investigate the two full-suite workbench flakes before claiming a fully green local validation ladder; commit or push only when explicitly authorized.

2026-07-10 09:09 EDT — intake-sweep-windows-installer-staging Copy Section

- Objective: Re-run check-new-issues against the current dirty checkout, preserve the pending Pi 0.80.6 and alpha OAuth work, and evaluate the new Windows installer issue.
- Checked: Local main remains aligned with origin/main at 54d08a3. Live GitHub queue has open issues #186, #185, #184, and #182, with zero open PRs. Latest main Publish and Release run 28835967900 is green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest/current remains 0.3.5; @companion-ai/alpha-hub latest/current remains 0.1.3; @earendil-works/pi-* remains 0.80.6; root and website have non-security dependency drift only.
- Decisions: Ported the smallest safe fix for issue #186 because install reliability supports Feynman's research-loop reliability. The Windows installer now extracts the release zip into temp staging, validates the expected bundle directory, then swaps that bundle into %LOCALAPPDATA%\Programs\feynman, avoiding Expand-Archive -Force cleanup against the live install root. Issue #185 remains covered by bundled pi-btw; issue #184 remains outside the AI-researcher product bar; issue #182 remains covered by the pending alphaXiv OAuth2 endpoint patch. No PRs to merge, port, reject, or defer.
- Contributor refs: Configured refs remain stale or non-actionable. origin/fix/deepresearch-local-model-warning is behind current main with one already-covered ahead commit; pr4fork/main is behind with zero ahead. Sampled fork refs remain older provider/setup/platform/admin or broad fork work rather than a fresh core research-loop fix.
- Changed: Updated scripts/install/install.ps1, synced website/public/install.ps1, and added tests/install-windows.test.ts. Existing dirty changes in package.json, package-lock.json, scripts/lib/alpha-hub-auth-patch.mjs, scripts/prepare-runtime-workspace.mjs, src/pi/package-ops.ts, and tests/alpha-hub-auth-patch.test.ts were preserved.
- Verified: Focused installer tests passed (6/6); full npm test passed (588/588); npm run typecheck; npm run build with existing RDKit/3Dmol/chunk/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 401, shasum 53c8090ca3fb238122d5f0942b0fee5c99b692b0); real installed tarball smoke passed for feynman --version, feynman --help, feynman packages list, feynman alpha status, and packaged install.ps1 staged-extraction checks. No local PowerShell runtime was available for a live Windows script execution.
- Next: Commit or push only when explicitly authorized; otherwise keep the Windows installer staging fix, Pi 0.80.6 refresh, and alpha OAuth patch local-only.

2026-07-09 21:15 EDT — intake-sweep-pi-0806-refresh Copy Section

- Objective: Re-run the check-new-issues intake sweep against the current dirty checkout, preserve unrelated local work, and port only safe core-research/runtime fixes.
- Checked: Local main remains aligned with origin/main at 54d08a3. Live GitHub queue still has open issues #185, #184, and #182, with zero open PRs. Latest main Publish and Release run 28835967900 is green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest/current remains 0.3.5; @companion-ai/alpha-hub latest/current remains 0.1.3; pi-btw latest/current remains 0.4.1; @earendil-works/pi-* latest is now 0.80.6.
- Decisions: Ported the smallest safe runtime freshness fix by bumping Feynman's pinned Pi runtime packages from the pending 0.80.5 refresh to 0.80.6. The upstream package diff directly affects the research loop: post-compaction output-token budgeting, GPT-5.6/GPT-5.5 long-context cost accounting, OpenAI cache-write usage accounting, GPT-5.6 Codex metadata, max thinking-level support, Claude thinking-block preservation, and shellPath home expansion. Issue #182 remains locally covered by the pending alphaXiv OAuth2 endpoint patch; issue #185 remains covered by bundled pi-btw; issue #184 remains outside Feynman's AI-researcher product bar as support/advice. No PRs to merge, port, reject, or defer.
- Contributor refs: Configured refs remain stale or non-actionable. origin/fix/deepresearch-local-model-warning is behind current main with one already-covered ahead commit; pr4fork/main is behind with zero ahead. Sampled fork refs are still behind current main with small ahead diffs in old provider/setup/platform/fork-specific lanes rather than fresh core research-loop fixes.
- Changed: Updated package.json and package-lock.json to @earendil-works/pi-agent-core, pi-ai, pi-coding-agent, and pi-tui 0.80.6; updated Pi runtime fallback constants in src/pi/package-ops.ts and scripts/prepare-runtime-workspace.mjs.
- Freshness: Root npm outdated --long --json now shows non-Pi dependency drift only; website drift remains non-security dependency drift. Root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: Focused package/runtime/alpha tests passed (27/27); full npm test passed (586/586); npm run typecheck; npm run build with existing RDKit/3Dmol/chunk/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 401, shasum 35c88e81b93f395c695cab93e46bbde1f6f27bd6); real tarball smoke passed for feynman --version, current help, feynman packages list showing npm:pi-btw, feynman alpha status, installed Pi 0.80.6, runtime archive Pi 0.80.6, runtime pi-btw 0.4.1, and alpha OAuth2 runtime archive inspection.
- Note: The real-pack metadata parser again hit mixed prepack logs/JSON after the tarball was created; the produced tarball was used directly. A first installed-smoke assertion looked for Pi under a nested dependency path and failed after npm hoisted Pi to top-level; the corrected direct package metadata check passed. Temp smoke artifacts and the root tarball were removed.
- Next: Commit or push only when explicitly authorized; otherwise keep the local Pi 0.80.6 refresh plus existing alpha OAuth patch local-only.

2026-07-08 21:03 EDT — intake-sweep-no-new-action Copy Section

- Objective: Re-run the check-new-issues intake sweep against the current Feynman checkout, preserving the pending alpha-auth patch while checking live GitHub issues/PRs, contributor refs, main workflows, release/package state, freshness, and local validation.
- Checked: Local main and origin/main both resolve to 54d08a3 after fetch. Open issues remain #185, #184, and #182; open PR list is empty. Latest main Publish and Release run remains 28835967900, succeeded at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest remains 0.3.5; Pi latest/current remains 0.80.3; alpha-hub latest/current remains 0.1.3; pi-btw latest/current remains 0.4.1.
- Decisions: No new queue-driven code changes were needed. #182 remains locally actionable but already covered by the pending local alpha-hub auth compatibility patch that rewrites bundled auth to https://api.alphaxiv.org/auth/oauth2/* with openid profile email offline_access. #185 remains covered by bundled pi-btw, which directly improves long-running research-loop steering. #184 remains outside Feynman's AI-researcher product bar as support/advice rather than a repo feature. There were no PRs to merge, port, reject, or defer.
- Contributor state: Configured contributor refs are stale, behind, or non-actionable. origin/fix/deepresearch-local-model-warning is behind by 74 commits with one ahead local-model-warning commit; pr4fork/main is behind by 73 with zero ahead. Sampled fork refs were behind by 91-142 commits with small ahead diffs focused on provider setup, Overleaf/export/admin prompts, Claude CLI bypass, architecture notes, fork-specific search tooling, broad platform churn, or runtime/setup churn; none was a clean core-research patch to port in this run.
- Freshness: Root and website have dependency drift only. Root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: Focused alpha/runtime tests passed (16/16); full npm test passed (586/586); npm run typecheck; npm run build with existing RDKit/3Dmol/chunk/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 401, shasum 01d621ba42cd8d159489a18aef58778887ade7e9); real installed tarball smoke passed for feynman --version, feynman --help, feynman packages list, feynman alpha status, alpha OAuth2 runtime archive inspection, and bundled pi-btw archive files. The first installed-smoke wrapper failed before install because it parsed [feynman] prepack logs as JSON; the corrected parser succeeded, and temp smoke artifacts were removed.
- Next: Commit or push only if explicitly authorized; otherwise keep the local alpha auth compatibility patch pending review.

2026-07-08 16:58 EDT — intake-sweep-no-new-action Copy Section

- Objective: Re-run the check-new-issues intake sweep against the current Feynman checkout, preserving existing local alpha-auth patch work while checking live GitHub issues/PRs, contributor branches, main workflows, release/package state, freshness, and validation.
- Checked: Local main and origin/main both resolve to 54d08a3. Open issues are #185, #184, and #182; open PR list is empty. Latest main Publish and Release run remains 28835967900, succeeded at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest remains 0.3.5; Pi latest/current remains 0.80.3; alpha-hub latest/current remains 0.1.3; pi-btw latest/current remains 0.4.1.
- Decisions: No new queue-driven code changes were needed. #182 remains locally actionable but already covered by the pending local alpha-hub auth compatibility patch. #185 remains covered by bundled pi-btw, which directly improves long-running research-loop steering. #184 remains outside Feynman's AI-researcher product bar as support/advice rather than a repo feature. There were no PRs to merge, port, reject, or defer.
- Contributor state: Configured contributor refs are stale, behind, or non-actionable. origin/fix/deepresearch-local-model-warning is behind by 74 commits with one local-model-warning commit ahead; pr4fork/main is behind by 73 with zero ahead. Sampled fork refs were behind by 91-142 commits with small ahead diffs focused on Overleaf/export/admin prompts, broad platform churn, provider setup, Claude CLI bypass, architecture notes, or fork-specific search tooling; none was a clean core-research patch to port in this run.
- Freshness: Root and website have dependency drift only. Root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: Focused alpha/runtime tests passed (16/16); full npm test passed (586/586); npm run typecheck; npm run build with existing RDKit/3Dmol/chunk/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 401, shasum 01d621ba42cd8d159489a18aef58778887ade7e9); real installed tarball smoke from /tmp/feynman-pack-smoke-lcIijJ/ passed for feynman --version, feynman --help, feynman packages list, feynman alpha status, alpha OAuth2 runtime archive inspection, and bundled pi-btw archive files. The temp smoke directory and root tarball were removed.
- Next: Commit or push only if explicitly authorized; otherwise keep the local alpha auth compatibility patch pending review.

2026-07-08 12:56 EDT — intake-sweep-no-new-action Copy Section

- Objective: Re-run the check-new-issues intake sweep against the current Feynman checkout, preserving existing local work while checking live GitHub issues/PRs, contributor branches/forks, main workflows, release/package state, freshness, and local validation.
- Checked: Local main is aligned with origin/main at 54d08a3 after fetch. Open issues remain #185, #184, and #182; open PR list is empty. Issue #182's newest comment still matches the already-pending alphaXiv OAuth2 endpoint/scope patch. Latest main Publish and Release run is 28835967900, succeeded at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest/current remains 0.3.5; Pi latest/current remains 0.80.3; alpha-hub latest/current remains 0.1.3; pi-btw latest/current remains 0.4.1.
- Decisions: No new queue-driven code changes were needed. #182 remains the only locally actionable issue and is already covered by the pending local alpha-hub auth compatibility patch that rewrites bundled auth to https://api.alphaxiv.org/auth/oauth2/* with openid profile email offline_access. #185 remains covered by bundled pi-btw, which directly improves long-running research-loop steering. #184 remains outside Feynman's AI-researcher product bar as support/advice rather than a repo feature. There were no PRs to merge, port, reject, or defer.
- Contributor/fork state: Configured contributor refs are behind, stale, or old already-reviewed changes. origin/fix/deepresearch-local-model-warning is behind by 74 commits with one ahead local-model warning commit; pr4fork/main is behind by 73 commits with zero ahead commits. Recent public fork heads checked: QuantumKuba/feynman, ivnvalex/feynman, and colindomoney/feynman match 54d08a3; ussdeveloper/feynman is behind at fa26693; advaitpaliwal/feynman is behind at cb5fa56.
- Freshness: Root and website have dependency drift only. Root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: Focused alpha/runtime tests passed (16/16); full npm test passed (586/586); npm run typecheck; npm run build with existing RDKit/3Dmol/chunk/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 401, shasum 01d621ba42cd8d159489a18aef58778887ade7e9); real installed tarball smoke from /tmp/feynman-pack-smoke-OqsQM0/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list, feynman alpha status, and runtime archive inspection for api.alphaxiv.org/auth, oauth2/authorize, oauth2/token, oauth2/register, oauth2/userinfo, openid profile email offline_access, and bundled pi-btw.
- Next: Commit or push only if explicitly authorized; otherwise keep the local alpha auth compatibility patch pending review.

2026-07-08 08:54 EDT — intake-sweep-no-new-action Copy Section

- Objective: Re-run the check-new-issues intake sweep against the current Feynman checkout, preserving existing local work while checking live GitHub issues/PRs, contributor refs/forks, workflows, release/package state, freshness, and local validation.
- Checked: Local main is aligned with origin/main at 54d08a3 after fetch. Open issues remain #185, #184, and #182; open PR list is empty. Issue #182 has a new comment suggesting the same alphaXiv OAuth2 endpoint/scope rewrite already present in the pending local patch. Latest main Publish and Release run is 28835967900, succeeded at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest/current remains 0.3.5; Pi latest/current remains 0.80.3; alpha-hub latest/current remains 0.1.3; pi-btw latest/current remains 0.4.1.
- Decisions: No new queue-driven code changes were needed. #182 remains the only locally actionable issue and is already covered by the pending local alpha-hub auth compatibility patch that rewrites bundled auth to https://api.alphaxiv.org/auth/oauth2/* with openid profile email offline_access. #185 remains covered by bundled pi-btw, which directly improves long-running research-loop steering. #184 remains outside Feynman's AI-researcher product bar as support/advice rather than a repo feature. There were no PRs to merge, port, reject, or defer.
- Contributor/fork state: Configured contributor refs are behind, stale, or old already-reviewed changes. origin/fix/deepresearch-local-model-warning is behind by 74 commits with one ahead local-model warning commit; pr4fork/main is behind by 73 commits with zero ahead commits. Recent public fork discovery showed colindomoney/feynman identical to main; ussdeveloper/feynman and advaitpaliwal/feynman are behind with zero ahead commits.
- Freshness: Root and website have dependency drift only. Root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: Focused alpha/runtime tests passed (16/16); full npm test passed (586/586); npm run typecheck; npm run build with existing RDKit/3Dmol/chunk/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 401, shasum 01d621ba42cd8d159489a18aef58778887ade7e9); real installed tarball smoke from /tmp/feynman-pack-smoke-x31nAy/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list, feynman alpha status, and runtime archive inspection for api.alphaxiv.org/auth, oauth2/authorize, oauth2/token, oauth2/register, oauth2/userinfo, openid profile email offline_access, and bundled pi-btw.
- Note: The first installed-smoke wrapper exited nonzero after successful CLI checks because it looked for package/npm/... inside the nested runtime archive; the correct nested path is npm/node_modules/..., and the follow-up archive inspection passed. The temp smoke directory was removed.
- Next: Commit or push only if explicitly authorized; otherwise keep the local alpha auth compatibility patch pending review.

2026-07-08 04:53 EDT — intake-sweep-no-new-action Copy Section

- Objective: Re-run the check-new-issues intake sweep against the current Feynman checkout, preserving existing local work while checking live GitHub issues/PRs, contributor refs/forks, workflows, release/package state, freshness, and local validation.
- Checked: Local main is aligned with origin/main at 54d08a3 after fetch. Open issues remain #185, #184, and #182; open PR list is empty. Latest main Publish and Release run is 28835967900, succeeded at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest/current remains 0.3.5; Pi latest/current remains 0.80.3; alpha-hub latest/current remains 0.1.3; pi-btw latest/current remains 0.4.1 with Pi peer range >=0.74.0 <1.
- Decisions: No new queue-driven code changes were needed. #182 remains the only locally actionable issue and is already covered by the pending local alpha-hub auth compatibility patch that rewrites bundled auth to https://api.alphaxiv.org/auth/oauth2/* with openid profile email offline_access. #185 remains covered by bundled pi-btw, which directly improves long-running research-loop steering. #184 remains outside Feynman's AI-researcher product bar as support/advice rather than a repo feature. There were no PRs to merge, port, reject, or defer.
- Contributor/fork state: Configured contributor refs are behind, stale, or broad fork-specific churn. pr4fork/main is behind by 73 commits with zero ahead commits; origin/fix/deepresearch-local-model-warning is behind by 74 commits with one already-considered ahead commit. Public fork discovery showed only advaitpaliwal/feynman as recently pushed, still behind current origin/main at cb5fa56.
- Freshness: Root and website have dependency drift only. Root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: Focused alpha/runtime tests passed (16/16); full npm test passed (586/586); npm run typecheck; npm run build with existing RDKit/3Dmol/chunk/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 401, shasum 01d621ba42cd8d159489a18aef58778887ade7e9); real installed tarball smoke from /tmp/feynman-pack-smoke-nGtsGm/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list, feynman alpha status, and runtime archive inspection for api.alphaxiv.org/auth, oauth2/authorize, openid profile email offline_access, and bundled pi-btw.
- Next: Commit or push only if explicitly authorized; otherwise keep the local alpha auth compatibility patch pending review.

2026-07-08 00:52 EDT — intake-sweep-alpha-auth-patch-validated Copy Section

- Objective: Re-run the check-new-issues intake sweep against the current Feynman checkout, preserve existing local work, and verify whether fresh GitHub, release, package, contributor, or validation state requires another change.
- Checked: Live GitHub queue still has open issues #185, #184, and #182, with zero open PRs. Latest main publish run is Publish and Release 28835967900, green at 54d08a3; GitHub release remains v0.3.5; npm @companion-ai/feynman latest/current remains 0.3.5; Pi latest/current is 0.80.3; alpha-hub latest/current is 0.1.3; pi-btw latest/current is 0.4.1 with Pi peer range >=0.74.0 <1. The newest public forks checked, founderqiang/feynman and colindomoney/feynman, are identical to main; ussdeveloper/feynman, Sourabhsubhasish/feynman, and advaitpaliwal/feynman are behind with zero ahead commits. Configured contributor remotes remain stale or behind.
- Decisions: No new code changes were needed beyond the existing local #182 alpha auth compatibility patch. Issue #182 remains the only locally actionable queue item because its newest comment points at alphaXiv's migrated OAuth endpoints and the local package patch already rewrites bundled alpha-hub auth to https://api.alphaxiv.org/auth/oauth2/* with openid profile email offline_access. Issue #185 remains covered by bundled pi-btw, which directly improves long-running research-loop steering. Issue #184 remains outside Feynman's AI-researcher product bar as support/advice, not a repo feature. No PRs to merge, port, reject, or defer.
- Freshness: Root and website have dependency drift only. Root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: Full npm test passed (586/586); npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json (entryCount: 401, shasum 01d621ba42cd8d159489a18aef58778887ade7e9); real tarball smoke from /tmp/feynman-pack-smoke-8S4oAQ/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list, feynman alpha status, and runtime archive inspection for api.alphaxiv.org/auth, oauth2/authorize, openid profile email offline_access, and bundled pi-btw.
- Next: Commit or push only when explicitly authorized; otherwise keep the local alpha auth compatibility patch pending review.

2026-07-07 21:07 EDT — check-new-issues-alpha-auth-endpoint Copy Section

- Objective: Run the recurring Feynman intake sweep against live GitHub issues, PRs, contributor branches/forks, recent main workflows, release/npm state, package freshness, and local validation while preserving unrelated worktree changes.
- Checked: Live open issues stayed #185, #184, and #182; open PR list was empty; local main is aligned with origin/main at 54d08a3; latest main Publish and Release run 28835967900 succeeded at 54d08a3; latest GitHub release and npm package remain v0.3.5 / @companion-ai/[email protected]; runtime/package versions remain @earendil-works/[email protected], @companion-ai/[email protected], and [email protected]. New public fork colindomoney/feynman is identical to main; recent forks ussdeveloper, advaitpaliwal, skandanyal, and gaurav-g-alva are behind with zero ahead commits; configured contributor refs are old/behind or non-actionable.
- Decisions: Ported the safe core of the new #182 evidence by updating Feynman's alpha-hub runtime patch to use alphaXiv's current https://api.alphaxiv.org/auth/oauth2/* endpoints and openid profile email offline_access scope. This directly restores a research-source login path without taking the fork's broader search-mode collapse or manual-token workflow. #185 remains covered on main by bundled pi-btw; #184 remains outside the AI-researcher product bar as support/advice. No open PRs needed merge/port/reject/defer action.
- Changed: scripts/lib/alpha-hub-auth-patch.mjs rewrites legacy Clerk endpoint constants to the current alphaXiv OAuth2 host; scripts/prepare-runtime-workspace.mjs now hashes/imports/applies the auth patch when building .feynman/runtime-workspace.tgz; tests/alpha-hub-auth-patch.test.ts covers the endpoint rewrite.
- Verified: node --import tsx --test --test-concurrency=1 tests/alpha-hub-auth-patch.test.ts tests/package-seeding.test.ts (16/16); full npm test twice after the endpoint patch (586/586, final run 586/586 after the runtime-archive fix); npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json with entryCount: 401, shasum 01d621ba42cd8d159489a18aef58778887ade7e9; actual temp tarball smoke from /tmp/feynman-pack-smoke-e3qffD/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list showing npm:@companion-ai/alpha-hub and npm:pi-btw, feynman alpha status, and nested runtime archive inspection showing api.alphaxiv.org/auth, oauth2/authorize, and openid profile email offline_access.
- Next: Keep the patch local until explicitly authorized to commit/push; issue #182 can be rechecked with a fresh logged-out login flow when an affected user or release test environment is available.

2026-07-07 12:50 EDT — check-new-issues-clean-main Copy Section

- Objective: Run the recurring Feynman intake sweep against live GitHub issues, PRs, contributor branches/forks, recent main workflows, release/npm state, package freshness, and local validation while preserving unrelated worktree changes.
- Checked: Live open issues stayed #185, #184, and #182; open PR list was empty; local main is aligned with origin/main at 54d08a3; latest main Publish and Release run 28835967900 succeeded at 54d08a3; latest GitHub release and npm package remain v0.3.5 / @companion-ai/[email protected]; runtime/package versions remain @earendil-works/[email protected], @companion-ai/[email protected], and [email protected]; recent public forks checked (nagyist/feynman, TheTechOddBug/feynman, and dubbypanda/feynman) are identical to main, while founderqiang/feynman, gaadha1985/feynman, and ussdeveloper/feynman are behind by three commits with zero ahead commits. Configured contributor refs are old/behind or non-actionable.
- Decisions: No queue-driven code changes were needed. #185 remains covered on main by bundling existing pi-btw in the core Pi package stack because it improves long-running research-loop steering without inventing a Feynman-owned interrupt protocol. #184 remains outside the AI-researcher product bar because it is a thesis-planning/support request, not a repo feature or defect. #182 has one new affected-user comment but no new Feynman-owned repro or diagnostic; it remains deferred/external because Feynman delegates alpha auth to @companion-ai/alpha-hub, the installed alpha-hub source owns Clerk registration, localhost callback, token exchange, and auth storage, issue diagnostics still point at alphaXiv/Clerk redirect/token handoff outside Feynman, and the current installed-tarball alpha status succeeds. No open PRs needed merge/port/reject/defer action.
- Freshness: Root and website have dependency drift only; root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: npm test (585/585); npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json with entryCount: 401, shasum dff26e588536c8184e30f2e39e208a47bea011c3; actual temp tarball smoke from /tmp/feynman-pack-smoke-I0Ypru/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list showing npm:pi-btw in Core, feynman alpha status, and runtime archive inspection for npm/node_modules/pi-btw/package.json plus npm/node_modules/pi-btw/extensions/btw.ts.
- Next: Keep sweeps read-only unless a fresh Feynman-owned repro or core-research PR appears; current main contains unreleased workbench commits after v0.3.5.

2026-07-07 08:49 EDT — check-new-issues-clean-main Copy Section

- Objective: Run the recurring Feynman intake sweep against live GitHub issues, PRs, contributor branches/forks, recent main workflows, release/npm state, package freshness, and local validation while preserving unrelated worktree changes.
- Checked: Live open issues stayed #185, #184, and #182; open PR list was empty; local main is aligned with origin/main at 54d08a3; latest main Publish and Release run 28835967900 succeeded at 54d08a3; latest GitHub release and npm package remain v0.3.5 / @companion-ai/[email protected]; runtime/package versions remain @earendil-works/[email protected], @companion-ai/[email protected], and [email protected]; the newest public forks checked (nagyist/feynman, TheTechOddBug/feynman, and dubbypanda/feynman) are identical to main, while founderqiang/feynman, gaadha1985/feynman, and ussdeveloper/feynman are behind by three commits with zero ahead commits. Configured contributor refs are old/behind or non-actionable.
- Decisions: No queue-driven code changes were needed. #185 remains covered on main by bundling existing pi-btw in the core Pi package stack because it improves long-running research-loop steering without inventing a Feynman-owned interrupt protocol. #184 remains outside the AI-researcher product bar because it is a thesis-planning/support request, not a repo feature or defect. #182 remains deferred/external because Feynman delegates alpha auth to @companion-ai/alpha-hub, issue diagnostics point at alphaXiv/Clerk redirect/token handoff outside Feynman, and the current installed-tarball alpha status succeeds. No open PRs needed merge/port/reject/defer action.
- Freshness: Root and website have dependency drift only; root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: npm test (585/585); npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json with entryCount: 401, shasum dff26e588536c8184e30f2e39e208a47bea011c3; actual temp tarball smoke from /tmp/feynman-pack-smoke-C38rex/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list showing npm:pi-btw in Core, feynman alpha status, and runtime archive inspection for npm/node_modules/pi-btw/package.json plus npm/node_modules/pi-btw/extensions/btw.ts.
- Note: one real-pack metadata parser attempt failed after successful tarball creation because mixed prepack logs preceded/embedded JSON; the produced tarball was used directly for archive inspection and installed smoke.
- Next: Keep sweeps read-only unless a fresh Feynman-owned repro or core-research PR appears; current main contains unreleased workbench commits after v0.3.5.

2026-07-07 04:48 EDT — check-new-issues-clean-main Copy Section

- Objective: Run the recurring Feynman intake sweep against live GitHub issues, PRs, contributor branches/forks, recent main workflows, release/npm state, package freshness, and local validation while preserving unrelated worktree changes.
- Checked: Live open issues stayed #185, #184, and #182; open PR list was empty; local main is aligned with origin/main at 54d08a3; latest main Publish and Release run 28835967900 succeeded at 54d08a3; latest GitHub release and npm package remain v0.3.5 / @companion-ai/[email protected]; runtime/package versions remain @earendil-works/[email protected], @companion-ai/[email protected], and [email protected]; the newest public fork checked (ussdeveloper/feynman) is behind main by three commits with zero ahead commits, and configured contributor refs are old/behind or non-actionable.
- Decisions: No queue-driven code changes were needed. #185 remains covered on main by bundling existing pi-btw in the core Pi package stack because it improves long-running research-loop steering without inventing a Feynman-owned interrupt protocol. #184 remains outside the AI-researcher product bar because it is a thesis-planning/support request, not a repo feature or defect. #182 remains deferred/external because Feynman delegates alpha auth to @companion-ai/alpha-hub, issue diagnostics point at alphaXiv/Clerk redirect/token handoff outside Feynman, and the current installed-tarball alpha status succeeds. No open PRs needed merge/port/reject/defer action.
- Freshness: Root and website have dependency drift only; root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: npm test (585/585); npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json with entryCount: 401, shasum dff26e588536c8184e30f2e39e208a47bea011c3; actual temp tarball smoke from /tmp/feynman-pack-smoke-T0C0Hw/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list showing npm:pi-btw in Core, feynman alpha status, and runtime archive inspection for npm/node_modules/pi-btw/package.json plus npm/node_modules/pi-btw/extensions/btw.ts.
- Next: Keep sweeps read-only unless a fresh Feynman-owned repro or core-research PR appears; current main contains unreleased workbench commits after v0.3.5.

2026-07-07 00:53 EDT — check-new-issues-clean-main Copy Section

- Objective: Run the recurring Feynman intake sweep against live GitHub issues, PRs, contributor branches/forks, recent main workflows, release/npm state, package freshness, and local validation while preserving unrelated worktree changes.
- Checked: Live open issues stayed #185, #184, and #182; open PR list was empty; local main is aligned with origin/main at 54d08a3; latest main Publish and Release run 28835967900 succeeded at 54d08a3; latest GitHub release and npm package remain v0.3.5 / @companion-ai/[email protected]; runtime/package versions remain @earendil-works/[email protected], @companion-ai/[email protected], and [email protected]; the two most recently pushed public forks (founderqiang/feynman, ussdeveloper/feynman) are both behind main by three commits with zero ahead commits, and configured contributor refs are old/behind or non-actionable.
- Decisions: No queue-driven code changes were needed. #185 remains covered on main by bundling existing pi-btw in the core Pi package stack because it improves long-running research-loop steering without inventing a Feynman-owned interrupt protocol. #184 remains outside the AI-researcher product bar because it is a thesis-planning/support request, not a repo feature or defect. #182 remains deferred/external because Feynman delegates alpha auth to @companion-ai/alpha-hub, issue diagnostics point at alphaXiv/Clerk redirect/token handoff outside Feynman, and the current installed-tarball alpha status succeeds. No open PRs needed merge/port/reject/defer action.
- Freshness: Root and website have dependency drift only; root and website npm audit --omit=dev both found 0 vulnerabilities.
- Verified: npm test (585/585); npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings, 0 hints), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json with entryCount: 401, shasum dff26e588536c8184e30f2e39e208a47bea011c3; actual temp tarball smoke from /tmp/feynman-pack-smoke-PknUYQ/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list showing npm:pi-btw in Core, feynman alpha status, and runtime archive inspection for npm/node_modules/pi-btw/package.json plus npm/node_modules/pi-btw/extensions/btw.ts.
- Next: Keep sweeps read-only unless a fresh Feynman-owned repro or core-research PR appears; current main contains unreleased workbench commits after v0.3.5.

2026-07-06 EDT — workbench-light-theme-parity Copy Section

- Objective: Close the biggest visual 1:1 gap. Drove the installed Claude Science app live (authenticated via claude-science url) and captured its real project frame: it is a clean LIGHT UI (rgb(253,253,252) background, near-black text, blue accent), not the dark-green theme the workbench had. Owner decision: match Claude's light layout with Feynman green as the single accent, and simplify the frame chrome.
- Changed: Appended a light-theme override layer to workbench-web/src/styles.css that re-skins the frame surfaces (rail, conversation canvas, messages, generated tiles, composer, tab strip, files/side panels) to neutral light with --cs-* tokens and Feynman green (#2f6a3d) as the accent (links, active tab, selected session, send button). Hides the reference-absent chrome — top-bar status pills, model/session menus, and the context metric strip — to match Claude's quiet frame. Fixed the selected-session pill to a light-gray pill.
- Verified: Focused source-contract tests pass; full npm test (585/585, Node 24); build:workbench-web green; live headless render on /projects/workspace/frames/playwright shows white rail/conversation/composer, hidden metric strip, green accent, and no console errors, matching the captured Claude Science reference frame.
- Next: Tighten remaining details (composer column max-width/centering, generated-tile spacing) against the reference; regenerate stale dark-UI artifact thumbnails.

2026-07-06 EDT — workbench-center-tab-strip-parity Copy Section

- Objective: Finish the in-flight Claude Science parity slice that adds a Chat/Files tab strip to the workbench frame center pane, so Files can open in-place instead of only as a right-side panel.
- Changed: Added a CenterPane state (chat | files) and a .workspace-tab-strip nav under the frame header; the transcript+composer render only on the Chat tab, and the existing FilesPanel (factored out once as filesPanelElement and reused by the side panel) mounts in a .center-files-panel on the Files tab. Rail Files button and the files toggle now switch the center pane. New session / run navigation resets the pane to Chat.
- Verified: Full npm test (585/585) under Node 24; typecheck and build:workbench-web green; live headless render on /projects/workspace/frames/playwright confirmed both tabs present, Files tab shows the center files panel and hides the composer, Chat tab restores it, zero console errors.
- Next: Continue the visual 1:1 parity pass against the installed Claude Science app.

2026-07-06 12:44 EDT — check-new-issues-clean-main Copy Section

- Objective: Run the recurring Feynman intake sweep against live GitHub issues, PRs, contributor branches, recent main workflows, release/npm state, package freshness, and repo-local validation while preserving active worktree edits.
- Checked: Live open issues stayed #185, #184, and #182; open PR list was empty; origin/main stayed aligned with local main at fa26693; latest main Publish and Release run 28755882698 succeeded at fa26693; latest GitHub release and npm package remain v0.3.5 / @companion-ai/[email protected]; installed/runtime package versions remain @earendil-works/[email protected], @companion-ai/[email protected], and [email protected]; contributor refs were stale behind origin/main, had no ahead diff, or contained provider/platform/export/prompt/admin/docs churn rather than a fresh research-loop fix.
- Decisions: #185 remains locally covered by bundling existing pi-btw in the core Pi package stack because it improves long-running research-loop steering without inventing a Feynman-owned interrupt mechanism. #184 remains outside the AI-researcher product bar because it is a thesis-planning/support request, not a repo feature or defect. #182 remains deferred/external because Feynman delegates alpha auth to @companion-ai/alpha-hub, issue diagnostics point to alphaXiv/Clerk redirecting away before localhost receives code, and the current installed-tarball alpha status succeeds. No open PRs needed merge/port/reject/defer action. No new queue-driven code changes were needed in this run.
- Verified: npm test (585/585); npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; website npm run lint, npm run typecheck (0 errors, 0 warnings), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json with entryCount: 401, shasum cc7a11600c6ebf36481195626203769be3c52dcb; actual temp tarball smoke from /tmp/feynman-pack-smoke-dmOqSI/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, feynman packages list showing npm:pi-btw in Core, and feynman alpha status (Logged in to alphaXiv as Advait Paliwal); runtime archive inspection confirmed npm/node_modules/pi-btw/package.json and npm/node_modules/pi-btw/extensions/btw.ts.
- Note: one first archive-inspection helper hit ENOBUFS because it buffered the embedded runtime tarball in Node; a second tar-based inspection verified the archive paths directly.
- Next: Keep intake sweeps read-only unless a fresh Feynman-owned repro or core-research PR appears; the remaining dirty files are preserved active workbench/docs/package-stack edits plus append-only run notes.

2026-07-05 21:18 EDT — workbench-compact-composer-parity Copy Section

- Objective: Fix the live Claude Science parity mismatch where Feynman's frame composer stretched into a tall pale input slab with chunky light controls.
- Changed: The React workbench composer now opts out of grid stretching, renders as a compact dark input strip, uses a transparent textarea with light text, and keeps the composer action/send buttons at compact 32px dark/green sizes.
- Verified: Focused React/file-surface tests passed (17/17); root/workbench typecheck passed; npm run build:workbench-web passed with existing RDKit/3Dmol/patristic bundle warnings; headless browser verification on session-20260705210923-1cb3e7 measured composer height 52.9px instead of 304px, 32px controls, transparent textarea background, and no side panel; full npm test passed (585/585).
- Next: Continue the 1:1 workbench parity goal with the next live rendered mismatch.

2026-07-05 20:45 EDT — check-new-issues-clean-main Copy Section

- Objective: Run the recurring Feynman intake sweep against live GitHub issues, PRs, contributor branches, recent main workflows, release/npm state, package freshness, and repo-local validation while preserving active workbench edits.
- Checked: Live open issues stayed #182 and #184; open PR list was empty; origin/main is fa26693; latest main Publish and Release run 28755882698 succeeded at fa26693; latest GitHub release and npm package remain v0.3.5 / @companion-ai/[email protected]; installed/runtime package versions remain @earendil-works/[email protected] and @companion-ai/[email protected]; contributor refs were stale relative to current origin/main, had no ahead diff, or contained adjacent platform/admin/export/prompt churn rather than a new research-loop fix.
- Decisions: #182 remains deferred/external because Feynman delegates alpha auth to @companion-ai/alpha-hub, issue diagnostics still point to alphaXiv/Clerk redirecting to the landing page before localhost receives code, and the current installed-tarball alpha status succeeds. #184 remains outside the AI-researcher product bar because it is a thesis-planning/support request, not a repo feature or defect. No open PRs needed merge/port/reject/defer action. No queue-driven code changes were needed.
- Verified: npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; full npm test (585/585); root and website npm audit --omit=dev (0 vulnerabilities); website npm run lint, npm run typecheck (0 errors, 0 warnings), and npm run build (34 pages); git diff --check; npm pack --dry-run --json with entryCount: 401, shasum 047d3783178ab6ab5caa05d9c98b3cee005e28ff; actual temp tarball smoke from /tmp/feynman-pack-smoke-P1QWmm/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, and feynman alpha status.
- Next: Keep intake sweeps read-only unless a fresh Feynman-owned repro or core-research PR appears; the remaining dirty files are unrelated active workbench edits plus append-only run notes.

2026-07-05 16:49 EDT — check-new-issues-clean-main Copy Section

- Objective: Run the recurring Feynman intake sweep against live GitHub issues, PRs, contributor branches, recent main workflows, release/npm state, package freshness, and local validation without disturbing unrelated workbench edits.
- Checked: Live open issues stayed #182 and #184; open PR list was empty; refreshed origin/main now points at 0fd15dd; latest main Publish and Release run 28754199423 succeeded at 0fd15dd; latest GitHub release and npm package remain v0.3.5 / @companion-ai/[email protected]; installed runtime dependencies remain @earendil-works/[email protected] and @companion-ai/[email protected]; contributor refs were stale relative to origin/main or had no ahead diff.
- Decisions: #182 remains deferred/external because Feynman delegates alpha auth to @companion-ai/alpha-hub, the installed auth source owns the Clerk registration/localhost callback/token exchange flow, the issue evidence points to alphaXiv/Clerk redirecting away before localhost receives code, and current installed-tarball alpha status succeeds. #184 remains outside the AI-researcher product bar because it is a thesis-planning/support request, not a repo feature or defect. No PRs to merge, port, reject, or defer. No queue-driven code changes were needed.
- Verified: npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; full npm test (585/585); root npm audit --omit=dev (0 vulnerabilities); website npm run lint, npm run typecheck (0 errors, 0 warnings), npm run build (34 pages), and npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json with entryCount: 401, shasum 5ed1945fd2a13d3a46ad44a41319815b06c5fa53; actual temp tarball smoke from /tmp/feynman-pack-smoke-MewoZd/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, and feynman alpha status.
- Next: Keep intake sweeps read-only unless a fresh Feynman-owned repro or core-research PR appears; the remaining dirty files are unrelated active workbench edits plus append-only run notes.

2026-07-05 13:35 EDT — workbench-dark-main-surface-parity Copy Section

- Objective: Continue the Claude Science 1:1 workbench parity goal by moving the frame conversation surface from a light card-heavy canvas toward the reference dark project workspace.
- Changed: The React workbench conversation area now uses a dark green canvas, dark topbar/context strip borders and chips, dark assistant/user message surfaces, light transcript text, and a dark disabled-send state while keeping the composer input readable. The change is scoped to the in-frame workbench surface and leaves menus, launcher cards, and the underlying chat/artifact mechanics intact.
- Verified: Focused React/file-surface tests passed (17/17); root/workbench typecheck passed; npm run build:workbench-web passed with existing science-viewer bundle warnings; headless browser verification on session-20260705160452-ae55be showed conversation background rgb(32, 37, 31), topbar border rgb(52, 60, 50), title color rgb(245, 248, 238), context chip background rgb(42, 51, 40), assistant message background rgb(29, 35, 28), assistant text rgb(237, 244, 232), user message background rgb(34, 48, 32), composer border rgb(58, 66, 55), and readable composer text; architecture check passed with existing split-debt warnings; git diff --check passed; and full npm test passed (585/585).
- Next: Commit the focused dark main-surface slice, then continue with the next live rendered parity mismatch.

2026-07-05 13:26 EDT — workbench-dark-wide-rail-parity Copy Section

- Objective: Continue the Claude Science 1:1 workbench parity goal by matching the reference rail's wide dark project-pane structure while keeping Feynman's green identity.
- Changed: The React workbench grid now uses a responsive --rail-width up to 358px instead of a fixed 256px. The in-project rail uses a dark green surface, transparent large action rows, a divider under Files, dark hover/selection states, and lighter session text so project/session names truncate less aggressively and read closer to the Claude Science rail. Launcher/setup brand styles remain separate and intact.
- Verified: Focused React/file-surface tests passed (17/17); root/workbench typecheck passed; npm run build:workbench-web passed with existing science-viewer bundle warnings; headless browser verification on session-20260705160452-ae55be showed rail width 358px, rail background rgb(29, 35, 28), transparent 44px rail actions exactly New chat, Customize, Files, divider rgb(58, 66, 55), selected row background rgb(16, 21, 15), no project-card or brand-row, and main content starting at x=358; launcher verification still found brand-mark, brand-title, and brand-subtitle intact; architecture check passed with existing split-debt warnings; git diff --check passed; and full npm test passed (585/585).
- Next: Commit the focused dark/wide rail slice, then continue with the next live rendered parity mismatch.

2026-07-05 13:18 EDT — workbench-flat-project-header-parity Copy Section

- Objective: Continue the Claude Science 1:1 workbench parity goal by removing the extra card-like rail project summary that made the Feynman project rail denser and more decorated than the reference.
- Changed: The React workbench rail now uses one compact flat project header with the Feynman mark and active project name, then immediately flows into New chat, Customize, Files, and the session list. The old rounded project summary card and rail description copy are removed from the in-project rail only.
- Verified: Focused React/file-surface tests passed (17/17); root/workbench typecheck passed; npm run build:workbench-web passed with existing science-viewer bundle warnings; headless browser verification on session-20260705160452-ae55be showed projectCard: null, brandRow: null, rendered rail actions exactly New chat, Customize, Files, and the first action at y=72 under a 46px flat project header; architecture check passed with existing split-debt warnings; git diff --check passed; and full npm test passed (585/585).
- Next: Commit the focused header slice, then continue with the next live rendered parity mismatch.

2026-07-05 13:12 EDT — workbench-project-rail-parity Copy Section

- Objective: Continue the Claude Science 1:1 workbench parity goal by making the in-project rail match the reference project action structure.
- Changed: The React workbench rail now exposes only the primary project actions in reference order: New chat, Customize, and Files. Search remains available through the command palette/search surfaces, and notebook, compute, and memory remain available through their owned workbench surfaces instead of appearing as peer rail actions.
- Verified: Focused React/file-surface tests passed (17/17); root/workbench typecheck passed; npm run build:workbench-web passed with existing science-viewer bundle warnings; headless browser verification on session-20260705160452-ae55be showed rendered rail actions exactly New chat, Customize, Files, no side panel, shell class app-shell, and conversation width 924px at 1180px viewport; architecture check passed with existing split-debt warnings; git diff --check passed; and full npm test passed (585/585).
- Next: Commit the focused rail slice, then continue with the next live rendered parity mismatch.

2026-07-05 12:52 EDT — workbench-empty-frame-layout-parity Copy Section

- Objective: Continue the Claude Science 1:1 workbench parity goal by fixing the blank/new-frame layout mismatch found in the live Feynman route.
- Changed: The React workbench shell no longer opens Files by default for empty runs. The shell now uses two columns unless a side panel is present, grows to a third column only for active side panels on wide screens, and preserves full conversation width behind the fixed overlay side panel at narrower viewports. Artifact-bearing runs still auto-open the selected primary artifact.
- Verified: Live in-app browser checks on session-20260705160452-ae55be showed no side panel, no selected artifact, rail 224px, conversation 710px, and body width 934px. Live checks on session-20260705035324-621b20 still showed the side panel open with End-to-End Workbench Proof selected while the conversation stayed 710px instead of being squeezed to 278px. Focused React/file-surface tests passed (17/17); workbench web typecheck passed; npm run build:workbench-web passed with existing science-viewer bundle warnings; root typecheck passed; architecture check passed with existing split-debt warnings; git diff --check passed; and full npm test passed (585/585).
- Next: Continue with the next live rendered parity mismatch.

2026-07-05 12:41 EDT — check-new-issues-clean-main Copy Section

- Objective: Run the recurring Feynman intake sweep against live GitHub, package, release, workflow, contributor-branch, freshness, and local validation state.
- Checked: Live open issues stayed #182 and #184; open PR list was empty; recent main workflow runs were successful through e417a8c; latest GitHub release and npm package remain v0.3.5 / @companion-ai/[email protected]; installed runtime dependencies remain @earendil-works/[email protected] and @companion-ai/[email protected]; contributor branch diffs were behind current origin/main and did not contain a new core-research fix to port.
- Decisions: #182 remains deferred/external because the issue evidence points at the alphaXiv/Clerk redirect before Feynman can exchange a token, and the installed package still reports alphaXiv status successfully. #184 remains outside the AI-researcher product bar because it is a thesis-planning/support request, not a repo feature or defect. No PRs to merge, port, reject, or defer. No code changes were needed.
- Verified: npm run typecheck; npm run build with existing RDKit/3Dmol/patristic warnings; npm run architecture:check with existing split-debt warnings; full npm test (585/585); website npm run lint, npm run typecheck (0 errors), and npm run build (34 pages); root and website npm audit --omit=dev (0 vulnerabilities); git diff --check; npm pack --dry-run --json with entryCount: 401, shasum c15eb404a3594619fc1824e1943b60feb35914af; actual temp tarball smoke from /tmp/feynman-pack-smoke-8KRbQH/companion-ai-feynman-0.3.5.tgz passed for feynman --version, feynman --help, and feynman alpha status.
- Next: Keep queue read-only unless a fresh Feynman-owned repro or core-research PR appears; release state is unreleased main work after v0.3.5, with successful publish workflows but no newer version tag.

2026-07-05 04:18 EDT — html-annotation-overlay-parity Copy Section

- Objective: Close the reference HtmlAnnotationOverlay chunk with a Feynman-owned iframe annotation bridge.
- Changed: HTML artifact previews now inject a sandboxed annotation bridge, expose Annotate mode, capture clicked element selector/descriptor/text plus iframe geometry, paint saved selector badges, and route selected HTML elements through Feynman's owned artifact annotation/refinement path. Gap manifest screen/chunk status is now 52 done / 0 stub / 0 missing.
- Verified: Focused HTML annotation/source/React tests passed (21/21 across tests/workbench-files-surface.test.ts, tests/workbench-annotations.test.ts, and tests/workbench-react-shell.test.ts); root/workbench typecheck passed; root build passed with existing RDKit/3Dmol/large-chunk warnings; website typecheck passed (0 errors, 0 warnings); website build passed (34 pages); architecture check passed with existing split-debt warnings including science-database-variants.ts; and git diff --check passed. Rendered in-app browser smoke opened the packaged CRISPR seed design_report.html, verified the iframe has sandbox="allow-scripts", toggled Annotate mode, clicked the report heading inside the iframe, opened the artifact refinement panel with selector body > h1:nth-child(1), saved a smoke annotation, verified one saved annotation plus an iframe #1 badge, captured outputs/.plans/feynman-e2e-screenshots/07-html-annotation-overlay.png, then removed the smoke annotation and confirmed remainingSmoke: 0.
- Next: Continue on SQLite migration status stubs and full package verification.

2026-07-05 04:12 EDT — files-hosts-parity Copy Section

- Objective: Close the reference useFilesHosts hook with Feynman-owned Files host inventory.
- Changed: Files panel and full Files overlay now show a host selector for local workspace artifacts, SSH/BYOC compute hosts, and cloud buckets derived from Feynman's compute provider and credential-backed storage state. Gap manifest screen/chunk status is now 51 done / 1 stub / 0 missing.
- Verified: Focused Files/source/React tests passed (16/16 across tests/workbench-files-surface.test.ts and tests/workbench-react-shell.test.ts); root/workbench typecheck passed; root build passed with existing RDKit/3Dmol/large-chunk warnings; website typecheck passed (0 errors, 0 warnings); website build passed (34 pages); architecture check passed with existing split-debt warnings including science-database-variants.ts; and git diff --check passed.
- Next: Continue on the last real UI stub: HtmlAnnotationOverlay.

2026-07-05 04:10 EDT — project-section-status-parity Copy Section

- Objective: Close the reference ProjectSection chunk where Feynman's launcher and workbench rail already own the project behavior.
- Changed: Marked ProjectSection done in the gap manifest. Feynman owns project cards, project/session counts, new-project creation, project opening, seed workflow grouping, and project/run route navigation through the launcher and in-workbench rail. Gap manifest screen/chunk status is now 50 done / 2 stub / 0 missing.
- Verified: Focused project/session/source coverage passed (26/26 across tests/workbench-files-surface.test.ts, tests/workbench-new-sessions.test.ts, and tests/workbench-react-shell.test.ts); workbench web typecheck passed; and git diff --check passed.
- Next: Continue on the two remaining real UI stubs: HtmlAnnotationOverlay and useFilesHosts.

2026-07-05 04:09 EDT — text-preview-status-parity Copy Section

- Objective: Close the reference TextPreview and RemoteTextPreview chunks where Feynman's existing artifact inspector already owns the behavior.
- Changed: Marked TextPreview and RemoteTextPreview done in the gap manifest. Feynman's authenticated file preview path fetches workspace artifact text through /api/file, handles loading/truncation, routes rich formats to owned preview components, renders plain text in the artifact inspector, and captures keyboard/mouse selection for annotation/refinement. Left HtmlAnnotationOverlay open because iframe DOM-region annotation is not yet equivalent to the reference overlay. Gap manifest screen/chunk status is now 49 done / 3 stub / 0 missing.
- Verified: Focused source/React tests passed (16/16 across tests/workbench-files-surface.test.ts and tests/workbench-react-shell.test.ts); workbench web typecheck passed; and git diff --check passed.
- Next: Continue on the remaining real UI stubs: HtmlAnnotationOverlay, ProjectSection, and useFilesHosts.

2026-07-05 04:07 EDT — note-preview-modal-parity Copy Section

- Objective: Close the reference NotePreviewModal screen stub with a Feynman-owned note context preview.
- Changed: Existing artifact notes now include a Preview action that opens a read-only modal with note content, target type/name, session id, artifact path, timestamp, and Open artifact navigation. The modal uses Feynman's existing target-note and artifact state, with no reference-app runtime dependency. Updated public README, release notes, website docs, source guards, and the gap manifest; screen/chunk status is now 47 done / 5 stub / 0 missing.
- Verified: Focused source/memory/React tests passed (18/18 across tests/workbench-files-surface.test.ts, tests/workbench-memory.test.ts, and tests/workbench-react-shell.test.ts); root/workbench typecheck passed; root build passed with existing RDKit/3Dmol/large-chunk warnings; architecture check passed with existing split-debt warnings including science-database-variants.ts; website typecheck passed (0 errors, 0 warnings); website build passed (34 pages); and git diff --check passed.
- Next: Continue on the remaining preview/Files host UI stubs.

2026-07-05 04:05 EDT — reference-hook-status-parity Copy Section

- Objective: Close reference hook chunks that are already covered by Feynman-owned state and APIs, without hiding remaining behavior gaps.
- Changed: Marked useComputeProviders, useFrameMessages, and useOpenSessionInProject done in the gap manifest. Feynman already owns compute provider state/actions, durable frame message rows and authenticated state, and project/run/artifact navigation through the React route helpers. Left useFilesHosts open because the reference's unified local/SSH/cloud host picker is not yet implemented as a Files surface. Gap manifest screen/chunk status is now 46 done / 6 stub / 0 missing.
- Verified: Focused hook/status coverage passed (41/41 across tests/workbench-compute-provider-records.test.ts, tests/workbench-frame-messages.test.ts, tests/workbench-react-shell.test.ts, and tests/workbench.test.ts); git diff --check passed.
- Next: Implement the next real remaining UI stub instead of marking the Files-host picker done prematurely.

2026-07-05 04:03 EDT — cloud-storage-modal-parity Copy Section

- Objective: Close the reference CloudStorageModal and cloud-credential hook stubs with Feynman-owned storage UI and state.
- Changed: Customize > Storage now opens a Cloud storage modal with credential rows, provider/status badges, target details, configured/missing connection-reference feedback, Delete credential, and Go to Credentials. The modal reads Feynman's owned cloudCredentials and cloudExportTargets state and removes entries through the existing settings API instead of depending on a reference-app credential hook. Updated public README, release notes, website docs, source guards, and the gap manifest; screen/chunk status is now 43 done / 9 stub / 0 missing.
- Verified: Focused cloud export/source/React tests passed (18/18 across tests/workbench-cloud-export.test.ts, tests/workbench-files-surface.test.ts, and tests/workbench-react-shell.test.ts); root/workbench typecheck passed; root build passed with existing RDKit/3Dmol/large-chunk warnings; architecture check passed with existing split-debt warnings including science-database-variants.ts; website typecheck passed (0 errors, 0 warnings); website build passed (34 pages); and git diff --check passed.
- Next: Continue the active 1:1 parity goal on the remaining screen/migration stubs.

2026-07-05 03:59 EDT — note-modal-parity Copy Section

- Objective: Close the reference NoteModal screen stub with a Feynman-owned artifact note surface.
- Changed: Artifact actions now include Notes, which opens a modal with target context, existing note count, add/edit/delete controls, and Cmd/Ctrl+Enter save. The modal writes through Feynman's existing /api/notes path and target-note ledger, so notes stay attached to artifact/project/session context without any reference-app runtime dependency. Updated public README, release notes, website docs, source guards, and the gap manifest; screen/chunk status is now 41 done / 11 stub / 0 missing.
- Verified: Focused source/memory/React tests passed (18/18 across tests/workbench-files-surface.test.ts, tests/workbench-memory.test.ts, and tests/workbench-react-shell.test.ts); root/workbench typecheck passed; root build passed with existing RDKit/3Dmol/large-chunk warnings; architecture check passed with existing split-debt warnings including science-database-variants.ts; website typecheck passed (0 errors, 0 warnings) after rerunning it without the parallel content-store race; website build passed (34 pages); and git diff --check passed.
- Next: Continue the active 1:1 parity goal on the remaining screen/migration stubs from outputs/.plans/claude-science-gap-manifest.md.

2026-07-05 03:55 EDT — export-to-cloud-modal-parity Copy Section

- Objective: Close the reference ExportToCloudModal screen stub with a Feynman-owned artifact export surface.
- Changed: Artifact Cloud export now opens a modal instead of firing a hidden one-click action. The modal shows configured and missing cloud storage targets, lets the user choose a destination path, disables export until a configured target is selected, calls Feynman's existing /api/artifact/export-cloud endpoint, and records exports through the owned cloud-export audit log. Updated public README, release notes, website docs, source guards, and the gap manifest; screen/chunk status is now 40 done / 12 stub / 0 missing.
- Verified: Focused cloud export/source tests passed (18/18 across tests/workbench-files-surface.test.ts, tests/workbench-react-shell.test.ts, and tests/workbench-cloud-export.test.ts); root/workbench typecheck passed; root build passed with existing RDKit/3Dmol/large-chunk warnings; architecture check passed with existing split-debt warnings including science-database-variants.ts; website typecheck passed (0 errors); website build passed (34 pages); and git diff --check passed.
- Next: Continue the active 1:1 parity goal on the remaining screen/migration stubs from outputs/.plans/claude-science-gap-manifest.md.

2026-07-05 03:51 EDT — chat-stream-state-parity Copy Section

- Objective: Close the browser-proven core-loop gap where chat-written artifacts appeared in Workspace but the active run/project counters could remain stale at 0.
- Changed: The authenticated chat streaming endpoint now attaches a freshly rebuilt workbench state to final done and error SSE frames, and the React shell applies that state immediately. The final stream event now carries the updated artifact/project/run ownership after Pi writes files under outputs/, papers/, or notes/.
- Verified: Focused stream/server/client regression now writes outputs/stream-artifact.md during a streamed turn and asserts the final done SSE state includes that artifact under the active run and workspace project. Focused workbench tests passed (41/41 across tests/workbench.test.ts, tests/workbench-react-shell.test.ts, and tests/workbench-artifact-snapshots.test.ts); root/workbench typecheck passed; root build passed with existing RDKit/3Dmol/large-chunk warnings; website typecheck passed (0 errors); architecture check passed with existing split-debt warnings including science-database-variants.ts; and git diff --check passed.
- Next: Continue the active 1:1 parity goal on the remaining screen/migration stubs from outputs/.plans/claude-science-gap-manifest.md.

2026-07-05 04:34 EDT — variants-named-tool-parity Copy Section

- Objective: Close the installed reference variants exact-name gap while keeping Feynman Bio Tools standalone and Feynman-owned.
- Changed: Added exact variant query modes for get_variant, search_variants, gene_variants, gene_constraint, region_variants, liftover_variant, clinvar_variants, structural_variants, get_structural_variant, mitochondrial_variants, cadd_variant_score, cadd_position_scores, cadd_range_scores, clinvar_search, clinvar_get_records, clinvar_variant_by_rsid, dbsnp_get_rsids, and dbsnp_search_by_region. These route through owned gnomAD GraphQL, CADD REST, NCBI ClinVar E-utilities, NCBI dbSNP E-utilities, and NCBI Variation Services endpoint calls. Updated runtime tool guidance, README, release notes, website pages, command metadata, and the 1:1 gap manifest.
- Verified: Focused variants exact-name tests passed (1/1) across all eighteen names; full science-database tests passed (84/84); root/workbench typecheck passed; website lint/typecheck/build passed (34 pages); root build passed with existing RDKit/3Dmol/large-chunk warnings; architecture check passed with existing split-debt warnings and newly flagged science-database-variants.ts split debt; git diff --check passed; full npm test passed (581/581); and npm pack --dry-run --json passed with entryCount: 401, shasum df89bfee330715aa527c2572f9bc772e30ccdcb0.
- Next: Continue on non-Bio Tool parity gaps because active Bio Tool coverage is now 247 done / 0 stub / 0 missing.

2026-07-05 04:02 EDT — regulation-named-tool-parity Copy Section

- Objective: Close the installed reference regulation exact-name gap while keeping Feynman Bio Tools standalone and Feynman-owned.
- Changed: Added exact regulation query modes for encode_search_experiments, encode_search_biosamples, encode_list_files, encode_get_experiment, encode_get_file, encode_get_biosample, jaspar_get_matrix, jaspar_matrix_versions, jaspar_list_matrices, jaspar_list_species, jaspar_list_taxa, jaspar_list_collections, jaspar_list_releases, unibind_search_tfbs, unibind_get_dataset, and unibind_tfbs_in_region. These route through owned ENCODE REST, JASPAR REST, UniBind REST, and UCSC hub-backed endpoint calls. Updated runtime tool guidance, README, release notes, website pages, command metadata, and the 1:1 gap manifest.
- Verified: Installed reference regulation modules were inspected for exact names, payload shape, stable ENCODE projections, JASPAR catalog/version behavior, and UniBind dataset/region behavior. Official/current ENCODE REST, JASPAR API, UniBind genome-track, and UCSC Genome Browser API docs were checked for public endpoint shape. Focused regulation exact-name tests passed (1/1) across all sixteen names; full science-database tests passed (83/83); root/workbench typecheck passed; website lint/typecheck/build passed (34 pages); root build passed with existing RDKit/3Dmol/large-chunk warnings; architecture check passed with existing split-debt warnings only; git diff --check passed; full npm test passed (580/580); and npm pack --dry-run --json passed with entryCount: 401, shasum 014c0ec784c3b05e22a79c59f9af10bb64f2e46f.
- Next: Continue the exact named-tool parity run with the next manifest domain, variants.

2026-07-05 03:27 EDT — omics-archives-named-tool-parity Copy Section

- Objective: Close the installed reference omics-archive exact-name gap while keeping Feynman Bio Tools standalone and Feynman-owned.
- Changed: Added exact archive query modes for arrayexpress_search_experiments, arrayexpress_get_experiment, arrayexpress_get_experiment_files, arrayexpress_get_experiment_samples, geo_search_series, geo_get_series, metabolights_list_studies, metabolights_get_studies, metabolights_get_study_files, metabolights_search_data_files, mgnify_search_studies, mgnify_get_studies, mgnify_get_study_analyses, pride_search_projects, pride_get_projects, pride_search_project_proteins, and pride_find_projects_for_protein. These route through owned BioStudies, NCBI E-utilities, MetaboLights, MGnify v2, and PRIDE Archive endpoint calls. Updated runtime tool guidance, docs, website pages, command metadata, and the 1:1 gap trackers.
- Verified: Installed reference omics-archive modules were inspected for exact names, payload shape, sample/file/protein behavior, and parsers. Official/current BioStudies/ArrayExpress, NCBI E-utilities/GEO, MetaboLights, MGnify API v2, and PRIDE Archive docs plus live endpoint probes were checked for public endpoint shape. Focused omics-archive exact-name tests passed (1/1) across all seventeen names; full science-database tests passed (82/82); root/workbench typecheck passed; website lint/typecheck/build passed (34 pages); root build passed with existing RDKit/3Dmol/large-chunk warnings; architecture check passed with existing split-debt warnings only; git diff --check passed; full npm test passed (579/579); and npm pack --dry-run --json passed with entryCount: 400, shasum 40eac670a5f6418c9e69a5e32a30d3490c4b150f.
- Next: Continue the exact named-tool parity run with the next manifest domain, regulation.

2026-07-05 03:03 EDT — rna-named-tool-parity Copy Section

- Objective: Close the installed reference RNA/Rfam exact-name gap while keeping Feynman Bio Tools standalone and Feynman-owned.
- Changed: Added extensions/research-tools/science-database-rfam-exact.ts and exact Rfam query modes for get_family, accession_to_id, id_to_accession, get_seed_alignment, get_covariance_model, get_tree, get_sequence_regions, get_structure_mapping, and search_sequence. Family, alignment, model, tree, region, and structure modes use documented Rfam endpoints; sequence search uses the current documented Rfam batch submit/result flow. Updated runtime tool guidance, docs, website pages, command metadata, and the 1:1 gap trackers.
- Verified: Installed reference RNA/Rfam modules were inspected for exact names, payload shape, checksums, text capping, and parsers. Official Rfam API docs were checked for public endpoint shape. Focused Rfam exact-name tests passed (8/8 for the reference-parity file); full science-database tests passed (81/81); root/workbench typecheck passed; website lint/typecheck/build passed (34 pages); root build passed with existing RDKit/3Dmol/large-chunk warnings; architecture check passed with existing split-debt warnings only; full npm test passed (578/578); git diff --check passed; and npm pack --dry-run --json passed with entryCount: 399, shasum 937d1a61b92ce02550d56fe3cdace6cbf846fc03.
- Next: Continue the next exact named-tool parity domain.

2026-07-05 02:44 EDT — research-resources-named-tool-parity Copy Section

- Objective: Close the installed reference research-resource exact-name gap while keeping Feynman Bio Tools standalone and Feynman-owned.
- Changed: Added grantsgov as a built-in science database source and added exact research-resource query modes for search_antibodies, get_antibody, find_antibodies_by_catalog, get_antibody_registry_stats, and search_grants. Antibody Registry modes use the public SciCrunch API; Grants.gov uses the unauthenticated Search2 POST endpoint with keyword, opportunity number, ALN, agency, status, eligibility, funding category, and funding instrument filters. Updated runtime tool guidance, docs, website pages, command metadata, and the 1:1 gap trackers.
- Verified: Installed reference research-resource modules and Grants.gov client/spec code were inspected for exact names and payload shape. Official Antibody Registry OpenAPI and Grants.gov Search2 docs were checked for public endpoint shape. Focused research-resource exact-name tests passed (2/2); full science-database tests passed (80/80); root/workbench typecheck passed; website lint/typecheck/build passed (34 pages); root build passed with existing RDKit/3Dmol/large-chunk warnings; architecture check passed with existing split-debt warnings only; full npm test passed (577/577); git diff --check passed; and npm pack --dry-run --json passed with entryCount: 398, shasum f4e58ae1276c00cd64719d97d9086427c7210177.
- Next: Continue the exact named-tool parity run with the rna domain.

2026-07-05 02:43 EDT — protein-annotation-named-tool-parity Copy Section

- Objective: Close the installed reference protein-annotation Bio Tool domain while keeping Feynman standalone and avoiding any runtime dependency on ~/.claude-science.
- Changed: Added extensions/research-tools/science-database-protein-annotation.ts and exact query modes for get_domain_architecture, search_interpro_entries, get_interpro_entry, search_pfam_clans, get_pfam_clan, get_pfam_family_proteins, get_pfam_family_proteomes, get_protein_atlas_gene, search_protein_atlas, map_string_ids, get_string_network, get_string_similarity_scores, and get_string_best_similarity_hits. These route through owned InterPro/Pfam, Human Protein Atlas, and STRING endpoint calls inside feynman_science_database_search.
- Verified: Installed reference protein-annotation modules were used only as local reference structure; official InterPro, Human Protein Atlas, and STRING API docs were checked for endpoint shape. Focused protein-annotation exact-name tests passed (1/1), focused protein/public-atlas/reference/database tests passed (24/24), full science database tests passed (79/79), root/workbench typecheck passed, website typecheck passed (0 errors), root build passed with existing RDKit/3Dmol/large-chunk warnings, website lint and build passed (34 pages), architecture check passed with existing split-debt warnings only, git diff --check passed, full npm test passed (576/576), and npm pack --dry-run --json passed with entryCount: 398, shasum 8a355fae8ff28860d34cb18127486acc89824275.
- Next: Continue remaining Bio Tool stub domains from outputs/.plans/claude-science-gap-manifest.md.

2026-07-05 02:18 EDT — literature-named-tool-parity Copy Section

- Objective: Close the installed reference literature Bio Tool domain while keeping Feynman standalone and avoiding any runtime dependency on ~/.claude-science.
- Changed: Added exact OpenAlex and arXiv query modes to Feynman's owned Bio Tools. feynman_science_database_search now accepts openalex_search_works, openalex_get_work, openalex_citations, openalex_references, openalex_search_authors, openalex_get_author, openalex_venue_info, arxiv_search, and arxiv_get_papers, with reference-shaped snake_case records, DOI claimant accounting, arXiv category/date/sort windows, and batch duplicate/not-found accounting. Added focused regression tests, command metadata, README/release-note/website docs, and parity tracker updates.
- Verified: Installed reference literature modules were used only as local reference structure; official OpenAlex and arXiv API docs were checked for endpoint shape. Focused literature exact-name tests passed (1/1), focused literature/OpenAlex/database tests passed (8/8), full science database tests passed (78/78), root/workbench typecheck passed, website typecheck passed (0 errors), root build passed with existing RDKit/3Dmol/large-chunk warnings, website lint and build passed (34 pages), architecture check passed with existing split-debt warnings only after extracting arXiv and exact OpenAlex helpers, git diff --check passed, full npm test passed (575/575), and npm pack --dry-run --json passed with entryCount: 395, shasum a67f16a5c337083f4370e3fda5613146dc7acf10.
- Next: Continue remaining Bio Tool stub domains from outputs/.plans/claude-science-gap-manifest.md.

2026-07-05 01:58 EDT — human-genetics-named-tool-parity Copy Section

- Objective: Close the installed reference human-genetics Bio Tool domain while keeping Feynman standalone and avoiding any runtime dependency on ~/.claude-science.
- Changed: Added exact GWAS Catalog, eQTL Catalogue, and PheWeb/FinnGen PheWAS query modes to Feynman's owned Bio Tools. feynman_science_database_search now accepts gwas_associations_for_variant, gwas_associations_for_gene, gwas_associations_for_trait, gwas_search_traits, gwas_search_studies, gwas_get_study, gwas_get_variant, eqtl_list_datasets, eqtl_associations, phewas_instances, phewas_variant, phewas_finngen_gene, phewas_list_phenotypes, and phewas_search_phenotypes. Added the Feynman-owned pheweb source, focused regression tests, command metadata, README/release-note/website docs, and parity tracker updates.
- Verified: Installed reference mcp_human_genetics plus GWAS/eQTL/PheWeb helper modules were used only as local reference structure; public EBI GWAS Catalog v2, eQTL Catalogue API, PheWeb, and FinnGen PheWeb docs were checked for endpoint shape. Focused human-genetics tests passed (3/3), focused atlas/human-genetics tests passed (13/13), broader science database tests passed (77/77), full npm test passed (574/574), root/workbench typecheck passed, website typecheck passed (0 errors), root build passed with existing RDKit/3Dmol/large-chunk warnings, website lint and build passed (34 pages), architecture check passed with existing split-debt warnings only, git diff --check passed, and npm pack --dry-run --json passed with entryCount: 395, shasum 737d8378a8f8a5a2e7f8c6f238c9597d5fca6540.
- Next: Continue remaining Bio Tool stub domains from outputs/.plans/claude-science-gap-manifest.md.

2026-07-05 00:24 EDT — genomes-named-tool-parity Copy Section

- Objective: Close the installed reference genomes Bio Tool domain while keeping Feynman standalone and avoiding any runtime dependency on ~/.claude-science.
- Changed: Added extensions/research-tools/science-database-ensembl.ts with Feynman-owned Ensembl REST support for ensembl_lookup, ensembl_xrefs, ensembl_vep_variant, ensembl_homology, ensembl_sequence, and ensembl_overlap_region; extended the UCSC adapter with exact ucsc_list_tracks, ucsc_chrom_sizes, ucsc_track_data, ucsc_conservation, and ucsc_tfbs_clusters query names; and updated README, release notes, website docs, command metadata, Pi tool guidance, and parity trackers.
- Verified: Installed reference genome modules and public Ensembl/UCSC docs were checked for argument names and endpoint shape. Focused exact-name tests passed (2/2) for all eleven genome names; full science database tests passed (74/74); root/workbench typecheck passed; website typecheck passed (0 errors); root build passed with existing RDKit/3Dmol/large-chunk warnings; website lint and build passed (34 pages); architecture check passed with existing split-debt warnings only; git diff --check passed; full npm test passed (571/571); and npm pack --dry-run --json passed with entryCount: 394, shasum 8c05dccadde132d611d431205875c13958f44efd.
- Next: Continue to the next remaining Bio Tool stub domain from outputs/.plans/claude-science-gap-manifest.md.

2026-07-05 00:16 EDT — chat-artifact-run-project-ownership Copy Section

- Objective: Fix the live workbench parity gap where Pi chat-created artifacts appeared in Workspace with preview/provenance but not in the producing Run or Project scopes when the artifact slug differed from the chat frame id.
- Changed: Added explicit artifactPaths ownership to workbench runs, augmented runs from execution output paths and artifact snapshot producer ids, switched custom project/file-scope/header artifact counts to the same path-aware ownership rule, and documented the behavior in README, release notes, and the website workbench docs.
- Verified: Focused artifact snapshot, React shell, and architecture tests passed (19/19); full npm test passed (556/556); root/workbench typecheck passed; root build passed with existing RDKit/3Dmol/large-chunk warnings; website lint/typecheck/build passed (34 pages); architecture check passed with existing split-debt warnings only; git diff --check passed; and npm pack --dry-run --json passed with entryCount: 390, shasum 3a36f1019d05cee086a09b412452058303dcc82b. The rebuilt browser route for biology-evidence-map-2 / session-20260705035324-621b20 now shows ARTIFACTS 1, Run 1, Project 1, and the outputs/e2e-workbench-proof.md row in Run scope. Screenshot: outputs/.plans/feynman-e2e-screenshots/07-run-project-artifact-counts-fixed.png.
- Next: Continue only on concrete remaining 1:1 parity gaps found in real shipped science artifacts or reference-backed science workflow behavior.

2026-07-05 00:14 EDT — browser-e2e-workbench-proof Copy Section

- Objective: Prove the core Feynman workbench loop end to end in the running app before doing more connector breadth.
- Changed: Created proof screenshots under outputs/.plans/feynman-e2e-screenshots/ and added outputs/e2e-workbench-proof.md through a real Pi-backed chat turn.
- Verified: Fresh workbench launched on port 6190; browser flow created project biology-evidence-map-2, opened frame session-20260705035324-621b20, streamed a chat turn, wrote outputs/e2e-workbench-proof.md, opened it in Files, inspected Preview and Provenance, ran a Bash notebook cell in verification mode, and saw the artifact provenance update with Feynman notebook version, verified execution row, claim row, and VERIFICATION ... pass.
- Gap: The artifact attaches to Workspace discovery and artifact provenance/history, but active Run and Project artifact counters stayed at 0; next fix is active frame/project artifact attachment for chat-written files.
- Next: Fix the Run/Project artifact attachment gap, then rerun the browser proof.

2026-07-05 00:04 EDT — reference-gap-manifest Copy Section

- Objective: Stop one-gap-at-a-time discovery and create the full installed Claude Science reference-surface manifest required by the owner directive.
- Changed: Added outputs/.plans/claude-science-gap-manifest.md with screen chunks, migrations, Bio Tool domains/tools, license-deferred tools, skills, seed workflows, coarse status, and immediate next work.
- Verified: Generated directly from ~/.claude-science/runtime/0.1.15-dev.20260701.t220242.shaaa553de-release, including web-dist, drizzle/sqlite, mcp_bio/domains.json, mcp_bio/deferred.json, and skills, plus Feynman's local skills and fixtures/open-science-seeds. Manifest counts: 299 web assets, 112 JS chunks, 52 screen-like chunks, 96 migrations, 23 Bio Tool domains, 247 active Bio Tools, 14 license-deferred Bio Tools, 29 reference skills, and four seed workflow families.
- Next: Browser-prove the running workbench loop end to end before more connector breadth.

2026-07-04 23:58 EDT — kegg-link-conv-parity Copy Section

- Objective: Close the in-flight KEGG reference-tool gap while keeping the connector Feynman-owned, then return to the bulk-manifest/end-to-end directive.
- Changed: Added KEGG link:<targetDb> <ids> and conv:<targetDb> <ids> modes to feynman_science_database_search, including 10-id batching, two-column row normalization, operation/source/target/batch/request metadata, endpoint provenance, and missing-id reporting. Updated Pi prompt guidance, README, release notes, website homepage, website workbench guide, CLI command docs, command metadata, and parity trackers.
- Verified: Installed reference KEGG code and the official KEGG API manual were checked for /link, /conv, tab-delimited output, +-joined multi-entry calls, batching, request provenance, and missing-id behavior. Live Feynman tool smoke against real KEGG returned 58 pathway rows for link:pathway hsa:7157 hsa:672 and 2 NCBI GeneID conversion rows for conv:ncbi-geneid hsa:7157 hsa:672. Final gates passed: full npm test (555/555), root/workbench typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with split-debt warnings only, git diff --check, and npm pack --dry-run --json (entryCount: 389, shasum 1ae30d0843e83ff850251e58b7316875b0610b03).
- Next: Build the full reference-surface gap manifest and browser end-to-end proof before more connector breadth.

2026-07-04 23:41 EDT — OWNER DIRECTIVE: switch to bulk-port method Copy Section

- Directive (supersedes prior "Next" lines): stop the one-connector-per-slice grind; it is too slow. Keep the standalone boundary exactly as-is (Feynman-owned code, no ~/.claude-science runtime dependency).
- Do this instead: (1) build ONE full reference-surface gap manifest — every screen (web-dist chunk names), all 94 drizzle migrations, all 247 bio-tools, all 29 skills, all seed workflows — marked done/stub/missing; (2) bulk-port remaining bio-tools/schema/previews by category in a single sweep (generate the tools from a table off their shared HTTP+dispatch shape, do not hand-write each), running the full gate ONCE at the end; (3) prove the whole app loop END-TO-END in the browser — create project → chat/stream run → produce artifact → open provenance/history → run a verification check — screenshotting each step and reporting what works in the running app vs only in tests.
- Priority: whole app loop working 1:1 end-to-end FIRST; specialist bio-tool long tail AFTER. Do not spend another slice on a single preview/connector format.
- Next: build the gap manifest, then run the first bulk-port sweep; record results here and in outputs/.plans/claude-science-1to1.md.

2026-07-04 23:34 EDT — panglaodb-marker-source Copy Section

- Objective: Continue science-tool parity by porting PanglaoDB as a Feynman-owned no-login single-cell marker source instead of relying on the reference runtime.
- Changed: Added panglaodb to feynman_science_database_search, tool schema, runtime prompt context, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, command metadata, and parity trackers. extensions/research-tools/science-database-panglaodb.ts now downloads or reads the frozen PanglaoDB marker TSV, checksum-verifies the gzip by default, parses marker rows, and supports cell:, markers:, gene:, synonym lookup, options, species, organ, canonical-marker, sensitivity, and specificity filters. The first implementation briefly pushed science-database-longtail.ts over the architecture split threshold, then was corrected by moving PanglaoDB into its own module.
- Verified: Installed reference panglaodb_markers code and public PanglaoDB marker pages were checked for TSV URL, checksum behavior, marker rows, options, reverse lookup, 8,286 associations, 178 cell types, 4,679 gene symbols, 29 tissues, and 27 Mar 2020 update. Live Feynman tool smoke returned 8286 total rows, 49 canonical human T-cell marker rows, and first returned genes BATF3, BRAF, and CCL20 from the real PanglaoDB gzip. Final gates passed: root/workbench typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with split-debt warnings only and no new long-tail warning, git diff --check, full npm test (554/554), and npm pack --dry-run --json (entryCount: 389, shasum 435760c36e61387ec964e2c1bcf8f917f34b020d).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 22:56 EDT — ketcher-sketch-format-preview Copy Section

- Objective: Close the reference Ketcher format loop so Feynman-owned KET/RXN/CDXML chemistry artifacts created by chat tools open as first-class workbench science previews.
- Changed: Added .ket, .rxn, .cdxml, and .cxsmiles to the scanner previewable file table, content-type/language mapping, React artifact classifier, and molecule preview parser. KET previews now summarize Ketcher atom/bond nodes, RXN previews summarize reaction member molecules, CDXML previews summarize ChemDraw atom/bond nodes, and CXSMILES previews follow the SMILES parser. The RDKit preview now reports that Ketcher-only formats should open in Ketcher instead of attempting a bad RDKit parse, while the Ketcher editor receives raw KET/RXN/CDXML content. Updated README, release notes, website workbench docs, website release notes, command metadata, and parity trackers.
- Verified: Focused preview/editor/backend tests passed (24/24) for chemistry sketcher creation, KET/RXN/CDXML/CXSMILES classification and parsing, backend KET artifact edit/snapshot behavior, and React artifact helper contracts. Final gates passed: root/workbench typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with split-debt warnings only, git diff --check, full npm test (553/553), and npm pack --dry-run --json (entryCount: 388, shasum 478d3f5a9ac51faf7aa31de749b3c20e64f4a6a3).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 19:42 EDT — ketcher-chemistry-sketcher Copy Section

- Objective: Close the reference-app chemistry MCP gap where Feynman had Ketcher artifact editing but no chat-callable, Feynman-owned sketcher seed tool mirroring the reference open_sketcher shape.
- Changed: Added feynman_open_chemistry_sketcher in extensions/research-tools/chemistry-sketcher.ts. The tool accepts KET, RXN, Molfile, or SMILES seeds, prefers KET when present, writes an editable workspace artifact under outputs/chemistry-sketches/, and returns artifact path/format/mime metadata for the local Ketcher editor. The Customize connector catalog now marks Ketcher Chemistry as a configured built-in science workbench tool. Updated README, release notes, website workbench docs, website release notes, command metadata, and parity trackers.
- Verified: Installed reference Ketcher MCP server was inspected for its open_sketcher tool, UI resource, accepted seed formats, KET preference, save metadata, and supported extensions. Public Ketcher docs were checked for browser molecule/reaction editing and supported file formats. Final gates passed: focused chemistry/settings tests (6/6), root/workbench typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with split-debt warnings only, full npm test (553/553), and npm pack --dry-run --json (entryCount: 388, shasum d913c79d96722e1555335eff60bf067f645e43e7).
- Next: Run final git diff --check, then continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes.

2026-07-04 09:18 PDT — org-database-reference-ledger-envelopes Copy Section

- Objective: Close the remaining product-structure gap where Feynman's state coverage map had reference-shaped ledgers that were not yet physical tables in the owned org database.
- Changed: Added src/workbench/org-database-ledgers.ts and wired it into src/workbench/org-database.ts so ~/.feynman/orgs/<org_uuid>/feynman-workbench.db creates compact table envelopes for every remaining reference-shaped workbench ledger already owned in Feynman state. The envelope tables cover agents, bundled-agent settings, agent-skill assignments, custom skills/prompts, custom MCP servers/assignments, directory attachments, OAuth tokens, user secrets, Anthropic key rows, cloud credentials, setup decisions, marketplace rows, skill license assents, use-intent declarations, user agents, events, notifications, queued user messages, session seen marks, session concurrency, compaction archives, frame branch archives, frame system prompts, frame backfill poison, artifact dependencies, content snapshots, host grants, host call log, safety feedback, compute usage, compute pending terminations, poller leases, transcript annotations, and session claims. Updated README, release notes, website workbench docs, website release notes, and parity trackers.
- Verified: Focused org database tests passed (2/2) for physical table presence across the full reference coverage map, seeded event/session-claim rows, payload preservation, active-org database placement, and no .claude-science/operon-cli path coupling. Final gates passed: focused path/data-root/org-db/settings/resource tests (22/22), root/workbench typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with split-debt warnings only, git diff --check, full npm test (551/551), and npm pack --dry-run --json (entryCount: 387, shasum 338b28e19ded8e1f1c9568ad1d4b91eca1df71f9).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 08:25 PDT — org-database-spine Copy Section

- Objective: Close the product-structure gap where Feynman had an active org folder but no Feynman-owned org database mirror like the reference app's durable control-plane database.
- Changed: Added ~/.feynman/orgs/<org_uuid>/feynman-workbench.db via src/workbench/org-database.ts, with reference-shaped projects, frames, frame_messages, artifacts, artifact_versions, execution_log, verification_checks, memories, notes, annotations, frame_read_cursors, artifact_folders, compute_providers, mcp_tool_grants, memory_categories, routine_schedules, managed_endpoints, and capability_settings tables plus feynman_state_payloads for Feynman-specific fields. The served workbench refreshes the database from Feynman's own state. Updated README, release notes, website configuration/workbench docs, website release notes, and parity trackers to describe the owned org database.
- Verified: Focused extended org database tests passed (2/2) for schema metadata, table names, row counts, payload preservation, active-org database placement, extended control-plane rows, and no .claude-science/operon-cli path coupling. Final gates passed: focused path/data-root/org-db/settings/resource tests (22/22), root/workbench typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full npm test (551/551), and npm pack --dry-run --json (entryCount: 386, shasum 005f89772e47e7b2393d1647189f3b9d24d4b638).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 07:42 PDT — app-org-home-spine Copy Section

- Objective: Close the product-structure gap where Feynman had a ~/.feynman home but did not yet mirror Claude Science's active-org/app-home spine.
- Changed: Added Feynman-owned active org support in src/config/paths.ts: ~/.feynman/active-org.json, ~/.feynman/orgs/<org_uuid>/, and preservation of existing reference-shaped org manifests. Moved default workbench app data from the previous home-level ~/.feynman/workbench/workspaces/<workspace-id>/ path into ~/.feynman/orgs/<org_uuid>/workbench/workspaces/<workspace-id>/, added per-workspace manifests plus an org-level workspaces.json index, and kept first-access migration from both legacy home-level workbench state and checkout-local .feynman/workbench records. Updated README, release notes, website configuration/workbench docs, website release notes, and parity trackers to describe the org-scoped home.
- Verified: Installed Claude Science home was checked for active-org.json and orgs/<org_uuid>/operon-cli.db. Focused path/data-root tests passed (14/14), broader path/settings/resource tests passed (19/19), and final gates passed: root/workbench typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full npm test (548/548), and npm pack --dry-run --json (entryCount: 385, shasum d787072c9f65f287ff5a94c811aafaf18d07b7ee).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 07:07 PDT — pubmed-workflow-parity Copy Section

- Objective: Continue Claude Science 1:1 science-tool parity by replacing Feynman's shallow PubMed keyword search with a Feynman-owned adapter matching the reference PubMed MCP workflow modes.
- Changed: Added extensions/research-tools/science-database-pubmed.ts with existing PubMed ESearch/ESummary search plus EFetch XML article metadata, PMC ID Converter PMID/PMCID/DOI conversion, ELink related articles and PMC links, Europe PMC-backed PMC full-text routing with bounded section snippets, PubMed/PMC copyright and license status, and ECitMatch citation lookup. Routed source: "pubmed" through the dedicated adapter, added focused tests, and updated README, website docs/homepage/release notes, CLI command docs, command metadata, Settings resources, runtime context, Pi tool prompt guidance, and parity trackers.
- Verified: Installed reference mcp_pubmed exposed search_articles, get_article_metadata, convert_article_ids, find_related_articles, get_full_text_article, get_copyright_status, and lookup_article_by_citation. Official NCBI E-utilities docs were checked for ESearch, ESummary, EFetch, ELink, and ECitMatch; official PMC ID Converter docs were checked for ids, idtype, PMID/PMCID/DOI conversion, and multi-ID behavior; Europe PMC REST docs were checked for search and /{id}/fullTextXML. Focused PubMed plus shared science database tests passed (7/7); a stale workbench prompt assertion was updated to protect the richer PubMed mode list and its focused context test passed (5/5). Final gates passed: root typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full npm test (543/543), and npm pack --dry-run --json (entryCount: 385, shasum 66d927c9f6d7cfd150d976c7edb61d4654e59938).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 06:25 PDT — chembl-molecular-pharmacology-parity Copy Section

- Objective: Continue Claude Science 1:1 science-tool parity by replacing Feynman's shallow ChEMBL molecule/target/assay search with a Feynman-owned adapter matching the reference chemistry MCP modes.
- Changed: Added extensions/research-tools/science-database-chembl.ts with legacy ChEMBL entity search plus compound name search, SMILES similarity/substructure search, drug indication and warning lookup, calculated ADMET properties, ligand-target bioactivity filters, mechanism records, and target/gene/organism filters. Routed source: "chembl" through the dedicated adapter, added focused tests, and updated README, website docs/homepage/release notes, CLI command docs, command metadata, Settings resources, workbench runtime context, Pi tool prompt guidance, and parity trackers.
- Verified: Installed reference mcp_chembl exposed compound_search, drug_search, get_admet, get_bioactivity, get_mechanism, and target_search. Public ChEMBL web-service docs were checked for molecule, drug indication, drug warning, mechanism, target, activity, similarity, substructure, filter syntax, only, and order_by support. Focused tests passed (7/7). Live smokes returned imatinib CHEMBL941, ADMET properties for CHEMBL941, ABL1 bioactivity against CHEMBL1862 with IC50=38nM and pChEMBL=7.42, mechanism id 304 with action type INHIBITOR, leukemia drug indication row for CHEMBL1096882 with black-box warning summaries, and target CHEMBL1862 with gene symbol ABL1. Final gates passed: root typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with existing split-debt warnings only after splitting the ChEMBL regression into tests/science-database-chembl.test.ts, git diff --check, full npm test (542/542), and npm pack --dry-run --json (entryCount: 383, shasum 1c8377d30cb37b09b5a65c4f642953b984bd7017).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 06:00 PDT — openfda-drugsfda-parity Copy Section

- Objective: Continue Claude Science 1:1 science-tool parity by replacing Feynman's shallow openFDA label/event/recall search with a Feynman-owned adapter matching the reference drug-regulatory MCP modes.
- Changed: Added extensions/research-tools/science-database-openfda.ts with FDA label, adverse-event, recall, structured label filter, Drugs@FDA application detail/search, application count, statistics, pharmacologic-class, and generic-equivalent active-ingredient-set modes. Routed source: "openfda" through the dedicated adapter, added focused tests, and updated README, website docs/homepage/release notes, CLI command docs, command metadata, Pi tool prompt guidance, and parity trackers.
- Verified: Installed reference mcp_drug_regulatory exposed search_drug_applications, get_drug_application, count_drug_applications, get_drug_statistics, list_pharmacologic_classes, get_generic_equivalents, and search_drug_labels. Public openFDA Drugs@FDA and label docs were checked for application/product/submission/openfda sections, searchable fields, query syntax, and {term,count} aggregation rows. Focused tests passed (16/16). Live smokes returned application NDA020503, Keytruda application BLA125514, Keytruda sponsor count MERCK SHARP DOHME, pharmacologic class Corticosteroid Hormone Receptor Agonists [MoA], Advil generic-equivalent active-ingredient sets, and Tylenol oral-label row 015a6179-bacb-452d-b594-4de628ddc11d. Final gates passed: focused science tests (16/16), root typecheck, website lint, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full npm test (541/541), and npm pack --dry-run --json (entryCount: 382, shasum 839239dd94e224603913471ae6fabe9f007ed584).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 04:31 PDT — clinical-trials-parity Copy Section

- Objective: Continue Claude Science 1:1 science-tool parity by replacing Feynman's shallow ClinicalTrials.gov search with a Feynman-owned adapter matching the reference clinical-trials MCP modes.
- Changed: Added extensions/research-tools/science-database-clinical-trials.ts with general study search, direct NCT details, sponsor-specific programs, eligibility filters with ClinicalTrials.gov age-unit normalization, investigator/contact discovery from overall officials, responsible parties, and site contacts, and endpoint summaries across trial outcome measures. Routed source: "clinicaltrials" through the dedicated adapter, added focused tests, and updated README, website docs/homepage/release notes, CLI command docs, command metadata, Pi tool prompt guidance, and parity trackers.
- Verified: Installed reference mcp_clinical_trials exposed analyze_endpoints, get_trial_details, search_by_eligibility, search_by_sponsor, search_investigators, and search_trials. Public ClinicalTrials.gov v2 endpoints were checked for /studies, /studies/{nctId}, query., filter., fields, countTotal, and /version. Focused tests passed (11/11). Live smokes returned detail record NCT04280705, melanoma eligibility rows with brain-metastases criteria, phase-3 melanoma endpoint summaries, Merck sponsor rows (totalCount: 9), and Rosenberg investigator rows from overallOfficials. Final gates passed: root typecheck, website typecheck (0 errors), root build with existing RDKit/3Dmol/large-chunk warnings, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full npm test (536/536), and npm pack --dry-run --json (entryCount: 381, shasum 002ff0af57cbfcc8d9c56409dccf15a02d84a3ce).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes.

2026-07-04 02:17 PDT — app-data-root Copy Section

- Objective: Close the product-structure gap where Feynman had a home ~/.feynman folder but still treated checkout-local .feynman/workbench as the primary app state store.
- Changed: Added src/workbench/data-root.ts with deterministic per-workspace app data roots under ~/.feynman/workbench/workspaces/<workspace-id>/, legacy .feynman/workbench migration on first access, and shared stored-path resolution. Moved workbench settings, chat sessions, uploads, memory, artifact annotations/actions/trash, transcript annotations, safety feedback, read cursors, onboarding profile, project rows, OAuth token/pending stores, notebook execution logs, environment action logs, managed Python/R environment roots, Modal CLI/job paths, artifact snapshots, cloud-export logs, compute pending-terminate rows, endpoint timestamp probes, Pi-side connector/context settings readers, and Settings/Storage resource cards onto the shared app-data root. Research artifacts still remain in outputs/, papers/, and notes/.
- Verified: Focused app-data/workbench regression passed (59/59) after moving stale fixtures to the app-data root and canonicalizing symlinked workspace paths. Final gates passed: root typecheck, root build, website lint, website typecheck (0 errors), website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full npm test (530/530), and npm pack --dry-run --json (entryCount: 379, shasum e90b924e32a5668fb061674e536be180fb9a1e40).
- Next: Continue remaining Claude Science parity gaps from the current reference/seed probes.

2026-07-04 01:58 PDT — zinc-source Copy Section

- Objective: Continue science-tool parity by turning the existing ZINC Settings preset into an executable Feynman-owned CartBlanche22/ZINC source instead of a reference-shaped placeholder.
- Changed: Added zinc to feynman_science_database_search. The source submits form-encoded CartBlanche22 tasks, polls /search/result/<task>, caps response reads, canonicalizes short ZINC IDs, supports ZINC ID lookup, SMILES exact/analog search with dist/adist, supplier catalog-code lookup, random screening-set samples, and 3D tranche-location metadata when current records expose a tranche code. Settings/Customize now marks ZINC as a configured built-in Feynman Bio Tools source, and the Pi prompt context, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers describe the owned ZINC path.
- Verified: The installed reference mcp_zinc module, public ZINC/CartBlanche search pages, and live CartBlanche submit/poll behavior were checked. Focused database/context/settings tests passed (17/17). Live Feynman adapter smoke for id:ZINC12 returned ZINC000000000012, one zinc20 record, SMILES O=C(CS@@C(c1ccccc1)c1ccccc1)NO, 75 supplier catalog rows, source counts, and tranche properties. Final gates passed: root typecheck, website lint, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, full npm test (530/530), git diff --check, public product/source reference-leakage scan, stale wording scan, and npm pack --dry-run --json (entryCount: 378, shasum 670050ec1f7595b7094d0429f91f18205046e866).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference and seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 01:26 PDT — europepmc-fulltext Copy Section

- Objective: Continue science-tool parity by porting the Claude Science-shaped Europe PMC full-text path into Feynman's owned feynman_science_database_search tool instead of relying on the reference runtime.
- Changed: Added Europe PMC full-text mode behind the existing europepmc source. Queries such as fulltext:PMC5815332, pmid:29456894, fulltext pmid=..., and supported article URLs now resolve availability through Europe PMC /search with resultType=core, fetch /{PMCID}/fullTextXML only for open-access PMCID records, extract title, abstract, section inventory, bounded section snippets, figure/table captions, and reference counts, and report explicit retrieved, not_open_access, no_pmcid, xml_not_available, not_found, invalid_id, or not_processed statuses without returning raw XML. Updated tool prompts, runtime context, Settings/Customize resource copy, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers.
- Verified: The installed reference europepmc_fulltext module, Europe PMC RESTful API docs, and rOpenSci Europe PMC docs were checked for PMCID/PMID availability, Open Access full-text XML, section extraction, and non-OA behavior. Focused database/context/settings tests passed (18/18). Live Feynman adapter smokes returned retrieved for fulltext:PMC5815332 and pmid:29456894, resolved PMID 29456894 to PMCID PMC5815332, extracted 6 sections, 6 figures, 3 tables, and 52 references, and preserved /search plus /fullTextXML endpoint provenance. Final gates passed: root typecheck, website lint, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (528/528), npm pack --dry-run --json (entryCount: 377, shasum b5a9c25f963cd072d0c7149c3a34f79f91706bfe), public product/source reference-leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 01:01 PDT — unibind-source Copy Section

- Objective: Continue science-tool parity by porting UniBind as a Feynman-owned no-login direct TF-DNA interaction and TFBS region source instead of relying on the reference runtime.
- Changed: Added unibind to the feynman_science_database_search adapter, tool schema, runtime prompt context, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers. UniBind now searches TF/cell-line/JASPAR datasets, resolves exact dataset detail/model rows with BED/FASTA/plot URLs, and fetches bounded UCSC hub-backed TFBS region rows for Robust or Permissive collections while preserving source endpoints and hub URLs.
- Verified: The installed reference module, UniBind public genome-track documentation, and UCSC REST API contract were checked for dataset/detail/hub-region behavior. Focused database/context/settings tests passed (24/24). Live tool smoke returned 968 CTCF datasets, exact CTCF dataset ENCSR000AUE.A549_lung_carcinoma.CTCF with 57900 peaks and one DAMO model, and a Robust hg38 chr17:7661779-7687546 GATA3 region scan with 1949 TFBS rows scanned, 18 GATA3 rows, and first row ENCSR000EWS_MCF-7_GATA3_MA0037.3. Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (525/525), npm pack --dry-run --json (entryCount: 376, shasum 232a6e80233c0b6a93dc52520c6bedb09942bc16), and public product/source reference-leakage scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 00:42 PDT — openalex-source Copy Section

- Objective: Continue science-tool parity by porting OpenAlex as a Feynman-owned credential-aware literature/citation-graph source instead of relying on the reference runtime.
- Changed: Added openalex to the feynman_science_database_search adapter, tool schema, runtime prompt context, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers. OpenAlex now searches works, resolves W-id and DOI work detail through the DOI claimant filter route, returns incoming citations and outgoing references, searches and resolves authors and sources/venues, reports open-access status, reconstructs abstracts only for declared open licenses, redacts API keys from provenance/errors, and returns structured openalex_key_required rate-limit diagnostics when OPENALEX_API_KEY is missing.
- Verified: Official OpenAlex docs and installed reference modules were checked for works/authors/sources, API-key/rate-limit, citation/reference traversal, DOI claimant resolution, and source/author ID contracts. Focused database/context/settings tests passed (24/24). Live no-key tool smoke returned W3161425918 for CRISPR base editing, W2064815984 detail and DOI-filter resolution for 10.1126/science.1231143, 15549 incoming citations, 32 outgoing references, author A5067184382 for Jennifer Doudna search, source S106963461 for Nature Biotechnology, and structured openalex_key_required for rate-limit. Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (524/524), npm pack --dry-run --json (entryCount: 375, shasum bea248aa0664c8325ddf75002779b8137c4cfa52), public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-04 00:23 PDT — intake-sweep-clean-queue Copy Section

- Objective: Run the check-new-issues intake sweep against live GitHub/package/runtime state while preserving the dirty workbench/science-tools tree.
- Checked: Local main is still two commits ahead of origin/main with the existing dirty workbench/science-tools changes preserved. Live GitHub has open issues #184 and #182, zero open PRs, latest main workflow run Publish and Release 28343487961 succeeded at cb5fa56, latest GitHub release is v0.3.5 with four native assets, npm latest is @companion-ai/[email protected], bundled Pi latest/current is 0.80.3, and @companion-ai/alpha-hub remains 0.1.3.
- Decisions: #184 remains a support/research-topic issue outside Feynman's AI-researcher product bar. #182 remains deferred/externally blocked absent a fresh Feynman-owned repro; the current package still delegates alpha login/status through alpha-hub. No open PRs existed. Contributor branch origin/fix/deepresearch-local-model-warning remains already absorbed by local warning behavior and tests; other contributor branches were rejected/deferred as admin/export/provider/platform churn rather than core research-loop fixes.
- Verified: npm run typecheck, npm run build, npm run architecture:check, full npm test (523/523), git diff --check, root and website npm audit --omit=dev, website lint/typecheck/build, npm pack --dry-run --json (entryCount: 375, shasum d0919d30bb22de57f0a388d290ebe00aa1b8f944), actual temp tarball pack, and disposable installed-tarball smoke for feynman --version, feynman --help, and feynman alpha status passed.
- Next: Keep #184 as manual GitHub support if desired; keep #182 deferred until alphaXiv/Clerk/alpha-hub behavior changes or a new local repro points at Feynman code.

2026-07-04 00:09 PDT — antibody-registry-source Copy Section

- Objective: Continue science-tool parity by porting Antibody Registry as a Feynman-owned no-login reagent/RRID source instead of relying on the reference runtime.
- Changed: Added antibodyregistry to the feynman_science_database_search adapter, tool schema, runtime prompt context, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers. Antibody Registry now searches antibody RRIDs, resolves AB/RRID detail records, performs catalog-number lookup with vendor filtering, lists vendors, and returns registry statistics with endpoint provenance.
- Verified: Installed reference modules, Antibody Registry public pages/OpenAPI, RRID guidance, and live Antibody Registry service behavior were checked for FTS search, detail, catalog, vendor, and stats contracts. Focused database/context/settings tests passed (35/35). Live tool-level smoke returned TP53 RRID:AB_3717446, AB_330944 detail, catalog 9205 as RRID:AB_330944, vendor rows from 5814 registered vendors, and registry stats of 3186152 antibodies with last update 2026-07-03. Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (523/523), npm pack --dry-run --json (entryCount: 374, shasum f9c91eb2d9e9fa68d93ba752ac7ddb149022f2ed), public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 23:26 PDT — cellguide-source Copy Section

- Objective: Continue science-tool parity by porting CellGuide as a Feynman-owned no-login cell-type source instead of relying on the reference runtime.
- Changed: Added cellguide to the feynman_science_database_search adapter, tool schema, runtime prompt context, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers. CellGuide now searches Cell Ontology cell types, resolves CL ids, returns validated descriptions, computational and canonical marker genes, tissue occurrence rows, and CELLxGENE source collections with snapshot and endpoint provenance.
- Verified: Installed reference modules, the public CellGuide surface, public marker-gene docs, and live CellGuide service behavior were checked for snapshot, metadata, marker, source-collection, and tissue-mapping contracts. Focused database/context/settings tests passed (34/34). Live tool-level smoke returned T cell CL:0000084, CellGuide snapshot 1764612212, computational/canonical marker rows, 165 source collections, and 56 tissue mappings from the public CellGuide service. Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (522/522), npm pack --dry-run --json (entryCount: 373, shasum faf45078c3f655672662287aa0e501876137bbf0), public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 23:16 PDT — ucsc-source Copy Section

- Objective: Continue science-tool parity by porting UCSC Genome Browser as a Feynman-owned no-login genomics source instead of relying on the reference runtime.
- Changed: Added ucsc to the feynman_science_database_search adapter, tool schema, runtime prompt context, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers. UCSC now lists assemblies, searches track metadata, returns chromosome sizes, fetches bounded genomic region track rows while preserving UCSC truncation state, computes conservation score summaries, and exposes ENCODE TFBS cluster rows with endpoint provenance.
- Verified: Official UCSC REST API docs, installed reference modules, and live UCSC service behavior were checked for assembly, track search, chromosome-size, bounded track-data, conservation, and TFBS-cluster contracts. Focused database/context/settings tests passed (33/33). Live tool-level smoke returned hg38 chr17 size 83257441, TP53 knownGene rows with UCSC truncation flagged, phyloP100way conservation scores over chr17:7676150-7676170, and ClinVar track-search metadata from the UCSC REST API. Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (521/521), npm pack --dry-run --json (entryCount: 373), public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 22:50 PDT — metabolights-source Copy Section

- Objective: Continue science-tool parity by porting MetaboLights as a Feynman-owned no-login metabolomics source instead of relying on the reference runtime.
- Changed: Added metabolights to the long-tail feynman_science_database_search adapter, tool schema, runtime prompt context, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers. MetaboLights now lists public MTBLS study accessions, fetches public study metadata, returns study-folder file listings, and supports public data-file listings by accession/pattern with endpoint provenance.
- Verified: Official MetaboLights public pages and the EBI MetaboLights utility surface were checked for repository scope, public study listing, metadata/file usage, and ISA-Tab public-study workflows. Focused database/context/settings tests passed (32/32). Live tool-level smoke returned MTBLS1 study metadata, MTBLS1 folder listings, a valid empty public *.mzML data-file listing, and public accession list metadata from the EBI MetaboLights service. Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (520/520), npm pack --dry-run --json (entryCount: 372), public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 22:32 PDT — biomart-source Copy Section

- Objective: Continue science-tool parity by turning the existing BioMart Settings preset into an executable Feynman-owned no-login source instead of a reference-shaped placeholder.
- Changed: Added extensions/research-tools/science-database-biomart.ts and routed biomart through feynman_science_database_search. BioMart now lists Ensembl mart registry rows, datasets, common/all attributes, filters, and constrained gene/data table rows with BioMart completion-stamp checks and endpoint provenance. Updated the tool schema, runtime prompt context, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers.
- Verified: Installed reference modules and live Ensembl martservice probes were checked for registry, dataset, attribute/filter, and TSV data-query contracts. Focused database/context/settings tests passed (31/31). Live tool-level smoke returned TP53 as ENSG00000141510 plus registry row ENSEMBL_MART_ENSEMBL. Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (519/519), npm pack --dry-run --json (entryCount: 372), public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 21:59 PDT — gwas-catalog-source Copy Section

- Objective: Continue science-tool parity by porting a stable no-login human-genetics source from the reference bio-tool surface while keeping Feynman Bio Tools standalone.
- Changed: Added gwascatalog to extensions/research-tools/science-database-public-atlases.ts and routed it through feynman_science_database_search. GWAS Catalog now returns curated association rows by rsID, mapped gene, EFO id, or EFO trait; trait rows by text search; and study rows by GCST accession or PubMed id. Updated the tool schema, workbench runtime prompt guidance, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers.
- Verified: Official/public docs and the installed reference module were checked for the GWAS Catalog v2 REST API surface. Focused database/context/settings tests passed (23/23). Live tool-level smoke returned one record each from GWAS association search (101326235), GWAS trait search (MONDO_0956975), and GWAS PMID study search (GCST90103431). Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (517/517), npm pack --dry-run --json (entryCount: 371), public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 21:11 PDT — public-atlas-regulatory-sources Copy Section

- Objective: Continue science-tool parity by adding more stable no-login public sources from the reference bio-tool surface while keeping Feynman Bio Tools fully Feynman-owned.
- Changed: Added extensions/research-tools/science-database-public-atlases.ts and routed openfda, proteinatlas, and eqtlcatalogue through feynman_science_database_search. openFDA returns drug label, adverse-event, and recall/enforcement records; Human Protein Atlas returns gene, synonym, Ensembl, UniProt, and tissue-expression fields; eQTL Catalogue returns v3 association, study, and dataset rows. Updated the tool schema, workbench runtime prompt guidance, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers.
- Verified: Official/public docs were checked for openFDA, Human Protein Atlas, and eQTL Catalogue API surfaces. Focused database/context/settings tests passed (21/21). Live tool-level smoke returned one record each from openFDA (008ee85b-5cac-45a6-a857-a828f8125175), Human Protein Atlas (ENSG00000141510), and eQTL Catalogue (chr17_6690037_T_G). Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (515/515), npm pack --dry-run --json (entryCount: 371), public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 20:25 PDT — ebi-structural-interactions-sources Copy Section

- Objective: Continue science-tool parity by adding more no-login public EBI sources from the installed reference bio-tool catalog while keeping Feynman Bio Tools standalone.
- Changed: Added extensions/research-tools/science-database-ebi-structural.ts and routed chebi, complexportal, intact, and emdb through feynman_science_database_search. ChEBI returns compound accessions, formula/mass/structure identifiers, synonyms, and ontology detail records; Complex Portal returns CPX accessions, species, participant accessions, and complex metadata; IntAct returns interaction accessions, participants, MI scores, detection methods, and PubMed evidence; EMDB returns cryo-EM map accessions, resolution, fitted PDB ids, release dates, and map metadata. Updated the tool schema, runtime prompt guidance, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, website release docs, and parity trackers.
- Verified: Official/public docs were checked for IntAct, ChEBI, EMDB, and Complex Portal API surfaces. Focused database/context/settings tests passed (18/18). Live tool-level smoke returned one record each from ChEBI (CHEBI:759292), Complex Portal (CPX-6093), IntAct (EBI-1562402), and EMDB (EMD-77042). Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, git diff --check, full test suite (512/512), npm pack --dry-run --json (entryCount: 370), public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 19:56 PDT — reference-longtail-science-sources Copy Section

- Objective: Continue Claude Science science-tool parity by adding concrete no-login public sources from the installed reference bio-tool catalog while keeping the runtime Feynman-owned.
- Changed: Added extensions/research-tools/science-database-longtail.ts and routed alphafold, arrayexpress, jaspar, mgnify, and mygene through the existing feynman_science_database_search tool. AlphaFold DB returns UniProt-linked predicted structure records and PDB/CIF/PAE links; ArrayExpress/BioStudies returns migrated functional-genomics studies; JASPAR returns transcription-factor matrix records; MGnify returns metagenomics study/biome/ENA metadata; MyGene.info returns gene annotation ids and summaries. Updated the tool schema, Pi prompt guidance, runtime context, Settings/Customize connector catalog, README, release notes, website homepage, website workbench guide, and parity trackers.
- Verified: Official/public docs were checked for AlphaFold DB API access, JASPAR API, MyGene query service, BioStudies/ArrayExpress migration/API, and MGnify REST API. Focused database/context/settings tests passed (14/14). Live tool-level smoke returned one record each from AlphaFold DB (AF-P05067-F1), ArrayExpress/BioStudies (E-GEOD-17155), JASPAR (MA0106.1), MGnify (MGYS00006825), and MyGene.info (TP53). Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, full test suite (508/508), npm pack --dry-run --json (entryCount: 369), git diff --check, public-doc reference leakage scan, and stale-gate wording scan. GWAS Catalog was deferred in that slice because the first endpoint probes returned 404/406 before the later v2 contract check.
- Next: Keep looking for concrete remaining no-login reference sources or specialist workflow gaps. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 19:12 PDT — reference-artifact-viewer-parity Copy Section

- Objective: Close the reference bundle's remaining media/document artifact viewer gap while keeping previews implemented in Feynman-owned React code.
- Changed: Expanded artifact kind classification and workbench previews for audio, video, XLSX spreadsheets, Jupyter notebooks, and LaTeX/TeX files. Spreadsheet previews parse bounded workbook sheets with JSZip plus fast-xml-parser; notebook previews summarize kernels, cells, outputs, and source snippets; LaTeX previews summarize sections, equations, citations, labels, bibliography commands, and source. Added a shared text-preview fetch policy so binary/media/XLSX panes use download or media URLs instead of the text preview endpoint. Updated scan/file-type handling, React artifact inspector components, preview styling, source tests, README, release notes, website docs, and parity trackers.
- Verified: The installed reference bundle was checked for separate audio, video, spreadsheet, notebook, and LaTeX preview chunk names. Focused React/source tests passed (18/18) for preview classification, fetch policy, parsers, and source/CSS ownership. Rendered browser smoke in a disposable workspace opened XLSX, IPYNB, LaTeX, audio, and video artifacts with zero overflow, zero console errors, and zero failed responses; screenshots were written under outputs/playwright/feynman-artifact-preview-*.png. Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, full test suite (505/505), npm pack --dry-run --json (entryCount: 368), git diff --check, public-doc reference leakage scan, and stale-gate wording scan.
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 18:13 PDT — frame-backfill-poison-parity Copy Section

- Objective: Close the Claude Science frame_backfill_poison structural gap while keeping Feynman's default state honest when no frame backfill failures exist.
- Changed: Added src/workbench/frame-backfill-poison.ts, expanded workbench ledger/state types with frameBackfillPoison, and expose frame-scoped backfill health rows through /api/state. The ledger reads Feynman's own .feynman/workbench/frame-backfill-poison.json when present, accepts both reference-shaped snake-case and Feynman camel-case fields, filters rows to live frame ids, and returns an empty array for clean workspaces. Added tests/workbench-reference-table-coverage.test.ts so every audited reference table maps to a Feynman-owned WorkbenchState key. Updated README, release notes, website homepage copy, website release notes, the Science Workbench guide, and parity trackers to mention frame backfill health records.
- Verified: The installed Claude Science DB and migration were checked for frame_backfill_poison; the local reference table currently has zero rows and defines frame_id, fail_count, terminal, reason, and updated_at. Focused frame/workbench tests passed (27/27) for persisted row normalization, live-frame filtering, empty API default, and existing frame/frame-message behavior; focused reference-table coverage tests passed (3/3). Final gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, full test suite (504/504), npm pack --dry-run --json (entryCount: 368, including dist/workbench/frame-backfill-poison.js), and git diff --check.
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 17:40 PDT — project-metadata-parity Copy Section

- Objective: Close the Claude Science projects metadata gap while keeping Feynman's project rows derived from owned workspace project, run, artifact, and upload-frame state.
- Changed: Expanded WorkbenchProject and project derivation with local user id, upload-frame id linkage, context, memory-enabled state, created timestamps, updated timestamps, run slugs, artifact paths, session counts, and artifact counts. Custom project context now appears as reference-shaped project context while the chat prompt still reads the stored Feynman project file. Updated README, release notes, website homepage copy, website release notes, the Science Workbench guide, and the parity trackers to mention project metadata and upload-frame linkage.
- Verified: The installed Claude Science DB was checked for projects; local reference rows expose id, name, description, context, created/updated timestamps, user id, uploads frame id, and memory-enabled state. Focused project/frame/React tests passed (27/27) for project metadata, upload-frame linkage, created timestamps, custom project context, and typed React fixtures. Full gates passed: root typecheck, website typecheck (0 errors), root build, website build (34 pages), architecture check with existing split-debt warnings only, full test suite (503/503), npm pack --dry-run --json (entryCount: 367), and git diff --check.
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 17:14 PDT — frames-ledger-parity Copy Section

- Objective: Close the Claude Science frames structural gap while keeping Feynman's frame spine derived from owned projects, chat sessions, artifact runs, and upload areas.
- Changed: Added src/workbench/frames.ts, expanded workbench ledger/state types with frames, and expose first-class frame rows through /api/state. Rows include root/parent frame identity, project id, agent/delegate names, conversation type, status, bounded input/output/context JSON, model and compute settings, artifact references, timestamps, root sequence, and source ownership. Updated README, release notes, website homepage copy, website release notes, the Science Workbench guide, and the parity trackers to mention frame records.
- Verified: The installed Claude Science DB was checked for frames; the local reference DB exposes agent and uploads conversation types with parent/root ids, project ids, agent/delegate names, task summaries, hidden flags, root sequence, token/cost columns, and timestamps. Focused frame/workbench tests passed (27/27) for session-derived frames, artifact-run frames, upload frames, structured JSON payloads, frame-message linkage, and authenticated /api/state exposure. Final gates passed: npm run typecheck, website npm --prefix website run typecheck, npm run build, website npm --prefix website run build, npm run architecture:check, git diff --check, full npm test (503/503), and npm pack --dry-run --json (366 files, including dist/workbench/frames.js).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 16:18 PDT — frame-messages-parity Copy Section

- Objective: Close the Claude Science frame_messages structural gap while keeping Feynman's chat transcript state derived from owned workbench session files.
- Changed: Added src/workbench/frame-messages.ts, expanded workbench ledger/state types with frameMessages, and expose one row per persisted chat turn through /api/state. Rows include frame id, message index, structured message JSON with _uuid, role, text content, status, creation timestamp, Feynman message metadata, and bounded tool-event payloads. Updated README, release notes, website homepage copy, website release notes, the Science Workbench guide, and the parity trackers to mention frame message rows.
- Verified: The installed Claude Science DB was checked for frame_messages; the local reference DB currently has 592 rows and stores frame_id, idx, and JSON msg_json with _uuid, role, and content blocks. Focused frame-message/workbench tests passed (25/25) for direct state derivation, structured JSON shape, tool-event payloads, and authenticated /api/state exposure. Final gates passed: npm run typecheck, website npm --prefix website run typecheck, npm run build, website npm --prefix website run build, npm run architecture:check, full npm test (501/501), and npm pack --dry-run --json (365 files, including dist/workbench/frame-messages.js).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 15:52 PDT — safety-feedback-parity Copy Section

- Objective: Close the Claude Science safety_feedback structural gap while keeping Feynman's review-feedback state tied to owned review requests and bounded context.
- Changed: Added src/workbench/safety-feedback.ts, expanded workbench ledger/state types with safetyFeedback, and record one review feedback row per frame/user/type when the existing workbench Request review action runs. Rows include root frame id, local user id, feedback type, optional model, reviewer response id, reason, bounded context snapshot, creation timestamp, and review-request source. Updated README, release notes, website homepage copy, website release notes, the Science Workbench guide, and the parity trackers to mention review feedback rows.
- Verified: The installed Claude Science DB and migration were checked for safety_feedback; the local reference table currently has zero rows. Focused safety-feedback/review tests passed (3/3) for direct review requests, uniqueness by frame/user/type, bounded context snapshots, secret scan assertions, and authenticated /api/state exposure. Final gates passed: npm run typecheck, website npm --prefix website run typecheck, npm run build, website npm --prefix website run build, npm run architecture:check, git diff --check, full npm test (499/499), and npm pack --dry-run --json (364 files, including dist/workbench/safety-feedback.js).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 15:23 PDT — poller-lease-parity Copy Section

- Objective: Close the Claude Science poller_lease structural gap while keeping Feynman's compute polling state truthful and derived from owned runtime state.
- Changed: Added src/workbench/poller-leases.ts, expanded workbench ledger/state types with pollerLeases, and derive provider * compute-polling lease rows from active compute jobs and pending compute termination records. Updated README, release notes, website homepage copy, website release notes, the Science Workbench guide, and the parity trackers to mention compute poller lease rows.
- Verified: The installed Claude Science DB and migration were checked for poller_lease; the local reference DB currently has one provider * lease row. Focused compute lifecycle tests passed (2/2) for active local compute and pending Modal termination lease exposure. Final gates passed: npm run typecheck, website npm --prefix website run typecheck, npm run build, website npm --prefix website run build, npm run architecture:check, git diff --check, full npm test (497/497), and npm pack --dry-run --json (363 files, including dist/workbench/poller-leases.js).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 14:58 PDT — setup-decisions-parity Copy Section

- Objective: Close the Claude Science contact_email_decisions and credential_ask_decisions structural gap while keeping Feynman's setup state standalone and secret-safe.
- Changed: Added src/workbench/setup-decision-ledgers.ts, expanded workbench ledger/state types with contactEmailDecisions and credentialAskDecisions, and derive public scientific API contact-email consent from NCBI_EMAIL/ENTREZ_EMAIL/CROSSREF_MAILTO plus provider credential readiness from Feynman's redacted settings/env/Pi-auth credential records. Updated README, release notes, website homepage copy, website release notes, the Science Workbench guide, and the parity trackers to mention setup decision rows.
- Verified: The installed Claude Science DB and migrations were checked for contact_email_decisions and credential_ask_decisions; both local reference tables currently have zero rows. Focused setup decision tests passed (2/2) for direct state, authenticated /api/state exposure, contact-email de-duplication, accepted/pending credential decisions, and secret-redaction assertions. Final gates passed: focused regression bundle (5/5), npm run typecheck, website npm --prefix website run typecheck, npm run build, website npm --prefix website run build, npm run architecture:check, git diff --check, full npm test (497/497), and npm pack --dry-run --json (362 files, including dist/workbench/setup-decision-ledgers.js).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 14:27 PDT — routine-schedules-parity Copy Section

- Objective: Close the Claude Science routine_schedules structural gap while preserving Feynman's honest /watch contract: a recurring routine exists only when scheduling tooling is actually available.
- Changed: Added src/workbench/routine-schedules.ts, expanded workbench ledger/state types with routineSchedules, and derive watch routine rows from durable outputs/.plans/<slug>.md watch plans plus outputs/<slug>-baseline.md baselines. Rows include root frame id, owner, label, JSON tick payload, cadence, enabled/blocked state, next due timestamp, last baseline result, and plan/baseline paths. Updated README, release notes, website homepage copy, website release notes, and the Science Workbench guide to mention watch routine state.
- Verified: The installed Claude Science DB and migration were checked for routine_schedules; the local reference table currently has zero rows. Focused routine schedule tests passed (2/2) for direct state and authenticated /api/state exposure. Final gates passed: npm run typecheck, website npm --prefix website run typecheck, npm run build, website npm --prefix website run build, npm run architecture:check, git diff --check, full npm test (495/495), and npm pack --dry-run --json (361 files, including dist/workbench/routine-schedules.js).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 13:59 PDT — skill-source-license-parity Copy Section

- Objective: Close the Claude Science marketplace_sources and skill_license_assents structural gap while keeping Feynman's skill catalog Feynman-owned and local.
- Changed: Added src/workbench/marketplace-ledgers.ts, expanded workbench ledger/state types with marketplaceSources and skillLicenseAssents, and derive a pinned Feynman Science Skill Pack source plus per-skill license-assent rows from Feynman's local skills//SKILL.md catalog and package license. Updated README, release notes, website homepage copy, website release notes, and the Science Workbench guide to mention skill source/license state without introducing an external marketplace runtime dependency.
- Verified: The installed Claude Science DB and migrations were checked for marketplace_sources and skill_license_assents. Focused skill-ledger tests passed (2/2) for direct state and authenticated /api/state exposure. Final gates passed: npm run typecheck, website npm --prefix website run typecheck, npm run build, website npm --prefix website run build, npm run architecture:check, git diff --check, full npm test (493/493), and npm pack --dry-run --json (360 files, including dist/workbench/marketplace-ledgers.js).
- Next: Continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 13:27 PDT — use-intent-and-docs-parity Copy Section

- Objective: Close the Claude Science use_intent_declarations structural gap and make the public README/website/docs describe the standalone Feynman science workbench rather than only the terminal CLI.
- Changed: Added src/workbench/use-intent-declarations.ts, expanded workbench ledger/state types with useIntentDeclarations, and derive onboarding-backed intent rows for field, goal, workflow, task, specialist, compute default, tools, bottlenecks, permissions, Feynman Bio Tools connector suggestions, and seed workflow suggestions. Updated the root README, RELEASES.md, website homepage, website command reference, setup/quickstart/install docs, release docs, docs sidebar, and a new Science Workbench guide to describe feynman serve, Feynman Bio Tools, redacted credential availability, onboarding intent context, and the standalone no-reference-runtime boundary.
- Verified: Focused workbench new-session and secret-ledger tests passed (11/11) after the use-intent implementation. Final gates passed: npm run typecheck, website npm --prefix website run typecheck, npm run build, website npm --prefix website run build, npm run architecture:check, git diff --check, full npm test (493/493), and npm pack --dry-run --json (359 files). Rendered website smoke captured outputs/playwright/feynman-website-workbench-docs.png and outputs/playwright/feynman-website-home-mobile.png; the built HTML contains the new workbench route, sidebar link, feynman serve command reference, Feynman Bio Tools copy, standalone boundary text, and corrected Node engine range.
- Next: Finish the gate sweep and then continue only on concrete remaining 1:1 parity gaps found by reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 06:32 PDT — session-activity-ledger-parity Copy Section

- Objective: Close the Claude Science events/notifications/queued_user_messages/session_seen_marks structural gap while keeping the activity ledger Feynman-owned and research-scoped.
- Changed: Added src/workbench/session-activity.ts, src/workbench/summary.ts, state arrays for events, notifications, queuedUserMessages, sessionSeenMarks, and sessionActivity, plus summary counters for activity, notifications, queued messages, and unread activity. The launcher Research queue now surfaces unread/queued/running/failed session activity alongside plan and compute cards.
- Verified: The installed Claude Science DB was checked for the reference tables, and the local reference bundle was checked for queued-user-message and notification rendering paths. Focused session-activity/read-cursor/React-source tests passed. Fresh-server API smoke returned 15 events, 13 notifications, 0 queued user messages, 1 seen mark, and 25 session activity items. Browser smoke rendered five visible Unread session activity cards, zero console errors, zero failed responses, and no horizontal overflow (1440/1440, queue 1074/1074). Final gates passed: npm run typecheck, npm run build, npm run architecture:check, git diff --check, full npm test (464/464), and npm pack --dry-run (331 files).
- Next: Continue only on the next concrete 1:1 parity gap from reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 06:12 PDT — session-claims-ledger-parity Copy Section

- Objective: Close the Claude Science session_claims/verification-check claim-linkage gap while keeping the claim ledger Feynman-owned and research-scoped.
- Changed: Added src/workbench/claims.ts, state.claims, summary.claimCount, deterministic claimIds on verification checks, artifact metadata claim export, and a Claims section in the artifact Provenance tab. Explicit Claim:, Finding:, Conclusion:, and Verified: markers in research Markdown become structured claim records, and verification checks merge into the same ledger.
- Verified: The installed Claude Science DB was checked for session_claims and verification-check claim linkage. Focused claim/state/UI tests passed. Fresh-server API smoke returned 10 claims, 10 checks, and summary.claimCount: 10. Browser smoke opened outputs/reference-audit/verification-matrix.md, rendered two Claims rows with zero console errors, zero failed responses, and no horizontal overflow (1440/1440, panel 432/432). Final gates passed: npm run typecheck, npm run build, npm run architecture:check, git diff --check, full npm test (463/463), and npm pack --dry-run (329 files).
- Next: Continue only on the next concrete 1:1 parity gap from reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 06:00 PDT — memory-notes-screen-parity Copy Section

- Objective: Close the Claude Science MemoryScreen/NoteModal/NotePreviewModal gap while keeping memory and notes Feynman-owned and standalone.
- Changed: Added .feynman/workbench/memory.json as the local workbench memory store, authenticated /api/memory and /api/notes mutation routes, memories and notes in workbench state, memory resource counts in Settings/Customize, and a React Memory rail panel. The panel saves profile/project/session/artifact/category scoped memory rows, saves target notes for the active session or artifact, shows saved-row metadata, and deletes records without using ~/.claude-science at runtime.
- Verified: The installed Claude Science DB and bundle were checked for notes, memories, memory_categories, MemoryScreen, NoteModal, and NotePreviewModal. Focused memory/resource tests passed. Browser smoke on the seed workflow route saved a scoped session memory plus a session target note, verified both through /api/state, removed both through /api/memory and /api/notes, confirmed no smoke strings remained in .feynman/workbench/memory.json, measured no horizontal overflow (1440/1440, panel 460/460), recorded zero console errors, and captured outputs/playwright/feynman-memory-notes-panel.png. Final gates passed: npm run build, npm run architecture:check, git diff --check, full npm test (462/462), and npm pack --dry-run (328 files).
- Next: Continue only on the next concrete 1:1 parity gap from reference or seed-workflow probes. Hosted NVIDIA ESMFold execution remains credential-gated until NVIDIA_API_KEY exists locally.

2026-07-03 — composer-reference-mentions-parity Copy Section

- Objective: Close the Claude Science-style composer affordance gap so the React workbench can reference project artifacts, sessions, and commands directly from chat.
- Changed: Added a Feynman-owned composer mention model and UI. Typing or clicking @ opens artifact suggestions, # opens session suggestions, and / opens command/skill suggestions from the real workbench state. Suggestions insert the concrete artifact path, session slug, or executable command. Command ranking now prioritizes resource names and command strings over incidental description matches. Mobile workbench routes now open chat-first instead of letting the default Files side panel cover the composer.
- Verified: Focused React shell tests passed (15/15) with new composer helper coverage. Desktop browser smoke on the seed-workflow route inserted @outputs/open-science-seeds/example_enzyme_engineering/plddt.npy, #example_crispr_screen, and /lit, with zero browser errors and no horizontal overflow. Mobile browser smoke at 390x740 confirmed the side panel is closed by default, the suggestion menu fits the viewport, the composer tool row wraps above the textarea, and no horizontal overflow occurs. Full gates passed: npm run typecheck, npm run build through npm pack --dry-run, npm run architecture:check, git diff --check, full npm test (454/454), and npm pack --dry-run. Screenshots: outputs/playwright/feynman-composer-mentions.png and outputs/playwright/feynman-composer-mentions-mobile.png.
- Next: Continue only on concrete remaining 1:1 parity gaps; hosted NVIDIA ESMFold remains credential-gated until NVIDIA_API_KEY exists.

2026-07-03 — numpy-tensor-artifact-preview-parity Copy Section

- Objective: Close the Claude Science-style tensor artifact gap for Feynman's packaged enzyme-engineering seed workflow while keeping tensor parsing and rendering inside Feynman-owned code.
- Changed: Added .npy and .npz artifact content types, routed them through authenticated binary downloads instead of UTF-8 text previews, added a React tensor preview using npyjs and jszip, and rendered array cards with dtype/shape/order metadata, bounded stats, vector plots, matrix heatmaps, archive member lists, and sample values.
- Verified: Focused tensor/workbench tests passed (37/37). Full gates passed: npm run typecheck, npm run build through npm pack --dry-run, npm run architecture:check, git diff --check, full npm test (453/453), and npm pack --dry-run with the packaged seed .npy/.npz artifacts included. Browser smoke opened the Feynman-owned is621_esmfold.npz and plddt.npy seed artifacts, rendered NPZ tensor preview | 4 arrays and NPY tensor preview | 1 array, verified four NPZ array cards, heatmap/vector geometry, correct binary content types, no page-level horizontal overflow, and zero console/page/request failures. Screenshots: outputs/playwright/feynman-tensor-npz-preview.png and outputs/playwright/feynman-tensor-npy-preview.png.
- Next: Continue only on concrete remaining 1:1 parity gaps; hosted NVIDIA ESMFold remains credential-gated until NVIDIA_API_KEY exists.

2026-07-03 — open-science-genome-browser-parity Copy Section

- Objective: Close the Claude Science-style genome/variant artifact viewer gap while keeping Feynman standalone and library-backed.
- Changed: Added [email protected] and wired VCF/BED/GFF previews to an embedded IGV.js genome browser inside the existing artifact inspector. Feynman now infers loci from the selected artifact, mounts IGV through an empty imperative stage to avoid React/IGV DOM ownership conflicts, keeps parsed rows/stat cards underneath for provenance, and widens the Files side panel for genome/molecule/structure artifacts so scientific viewers are not cramped.
- Verified: Focused React shell tests passed (13/13) with VCF/BED/GFF/GenBank track inference coverage. Browser smoke on a disposable workspace opened outputs/variants.vcf at /projects/workspace/frames/variants, rendered IGV 3.8.4 | VCF at chr1:100000-100001, confirmed IGV shadow-DOM controls, panel width 640px, stage width 585px, no page-level horizontal overflow, hidden stage overflow, and zero console/page/request failures. Expected IGV warning was limited to unindexed tiny VCF preview loading. Screenshots: outputs/playwright/feynman-igv-genome-preview.png and outputs/playwright/feynman-igv-stage.png. Full gates passed: npm run typecheck, npm run build, npm run architecture:check, git diff --check, full npm test (452/452), and npm pack --dry-run with dist/workbench-web/assets/igv-*.js included.
- Next: Continue only on remaining concrete 1:1 parity gaps; hosted NVIDIA ESMFold remains credential-gated until NVIDIA_API_KEY exists.

2026-07-03 — open-science-model-endpoint-parity Copy Section

- Objective: Close the Claude Science-style model-endpoint control-plane gap while keeping Feynman standalone and Feynman-owned.
- Changed: Added feynman_model_endpoint_call, an executable Pi tool for NVIDIA BioNeMo/NIM-style scientific model calls. Hosted ESMFold uses NVIDIA_API_KEY; self-hosted/local AlphaFold2 NIM accepts an endpointUrl. Endpoint responses now save under outputs/model-endpoints with a provenance sidecar, and Settings/runtime context expose the tool as the NVIDIA BioNeMo NIM model endpoint path.
- Verified: Focused endpoint/settings/context/chat tests passed (12/12), npm run typecheck passed, and a real local HTTP smoke through the registered tool wrote PDB/provenance artifacts. Full gates passed: npm run build, npm run architecture:check, git diff --check, full npm test (452/452), and npm pack --dry-run with extensions/research-tools/model-endpoints.ts included. Browser smoke on fresh server 127.0.0.1:6188 verified Customize exposes NVIDIA BioNeMo NIM, feynman_model_endpoint_call, and outputs/model-endpoints, with no console/page/network failures and no horizontal overflow; screenshot outputs/playwright/feynman-model-endpoint-settings.png. The local environment has no NVIDIA_API_KEY, so hosted NVIDIA ESMFold execution remains unverified instead of falsely claimed.
- Next: Keep hosted NVIDIA execution marked credential-gated until NVIDIA_API_KEY exists, then run one hosted ESMFold smoke.

2026-07-03 — open-science-reference-connector-parity Copy Section

- Objective: Close the remaining no-login Claude Science bio-tool source gap while keeping Feynman standalone and Feynman-owned.
- Changed: Added built-in feynman_science_database_search sources for PubChem, BindingDB, STRING, KEGG, Rhea, and Rfam; exposed them in Feynman Bio Tools and the Settings/Customize connector catalog; promoted Chemistry, RNA, and Structures & Interactions presets to executable built-ins where appropriate.
- Verified: Focused source/settings tests passed for the six new sources and connector catalog exposure. Live Feynman-tool smoke succeeded against PubChem aspirin, BindingDB uniprot:P35355 cutoff=100, STRING TP53,BRCA1 species=9606 score=700, KEGG find:compound aspirin, Rhea glucose, and Rfam RF00005. npm run typecheck, npm run build, npm run architecture:check, git diff --check, npm pack --dry-run, and full npm test passed (449/449).
- Next: Continue compute/runtime/provider parity; hosted NVIDIA NIM execution stays unverified until NVIDIA_API_KEY exists.

2026-07-03 — open-science-seed-fixture-parity Copy Section

- Objective: Close the Claude Science seed-workflow parity gap without leaving Feynman dependent on ~/.claude-science or ignored workspace outputs.
- Changed: Added package-owned fixtures/open-science-seeds with the four workflow families, included fixtures/ in the package manifest, added a startup sync that materializes missing seed files into outputs/open-science-seeds, and preserved existing workspace edits by skipping files that already exist.
- Verified: The fixture inventory has 83 artifacts across CRISPR screen (20), enzyme engineering (28), extremophile protein (19), and immunotherapy scRNA-seq (16). npm test -- --test-name-pattern="seed fixture|seed workflows" ran the repo harness and passed (446/446).
- Next: Continue 1:1 parity on remaining science connector/tool depth or long-tail artifact action states while NVIDIA hosted execution waits on NVIDIA_API_KEY.

2026-07-02 19:17 PDT — intake-sweep-open-184 Copy Section

- Objective: Run the check-new-issues intake sweep against live GitHub/package/runtime state while preserving the existing dirty React workbench tree.
- Checked: Local main is still one commit ahead of origin/main at 6c84b24 with the existing dirty workbench/package slice preserved. Live GitHub has open issues #184 and #182, zero open PRs, latest main workflow run Publish and Release 28343487961 succeeded at cb5fa56, latest GitHub release is v0.3.5 with four native assets, npm latest is @companion-ai/[email protected], Pi latest/current is 0.80.3, and @companion-ai/alpha-hub remains 0.1.3.
- Decisions: #184 is a user research-topic support request, not a repo defect or feature to port. #182 remains deferred/externally blocked because evidence points to alphaXiv/Clerk OAuth redirect behavior before Feynman/alpha-hub receives a callback, while unauthenticated alphaXiv search remains available. No open PRs were available to merge or port. Contributor branch origin/fix/deepresearch-local-model-warning is not an open PR and its core warning behavior is already present in the local dirty tree with tests, so no additional port was made.
- Verified: npm run typecheck, npm run build, npm run architecture:check, git diff --check, root npm audit --omit=dev, website npm audit --omit=dev, full npm test (431/431), npm pack --dry-run, and a disposable installed-tarball smoke from /tmp/feynman-pack-smoke-ZWjC2U/companion-ai-feynman-0.3.5.tgz running feynman --help and feynman packages --help passed. Package freshness checks found only non-security drift in root and website dependencies.
- Next: Keep #184 as non-product GitHub support unless someone wants to answer it manually; keep #182 deferred until alphaXiv/Clerk OAuth redirect behavior changes or alpha-hub ships a supported auth alternative.

2026-07-02 08:58 PDT — react-shell-streaming-chat Copy Section

- Objective: Move the React/Vite workbench shell from blocking chat submission toward Claude Science's live research-chat loop with streamed assistant text and visible tool progress.
- Researched: Rechecked the installed Claude Science runtime bundle at ~/.claude-science/runtime/0.1.0-dev.20260630.t160235.sha2e3e6f9-release/web-dist/assets/, confirming the shell modules MessageBubble, useFrameMessages, ProjectControlPlane, FilesOverlay, and ArtifactTile. Rechecked the local Claude Science SQLite frame message store, which now has 592 frame messages; seeded tool-use blocks include generate_plan, manage_environments, skill, and bash with user-facing descriptions such as Planning scRNA-seq immunotherapy response analysis, Listing envs for scanpy availability, and Downloading GSE120575 supplementary files.
- Changed: The React shell composer now uses /api/chat/message/stream instead of blocking /api/chat/message, parses SSE frames, streams assistant deltas into the transcript, merges streamed tool events into the latest assistant message, lets follow-up text steer a running Pi turn through /api/chat/message/steer, and exposes a Stop control backed by /api/chat/abort. Stream parsing and assistant tool merging now live in workbench-web/src/stream.ts with direct tests, and npm run typecheck now includes workbench-web/tsconfig.json so TSX is covered by the normal gate.
- Verified: Temporary prompt-executor server http://127.0.0.1:54812/app-shell/projects/active-plans/frames/open-science-workbench?token=react-stream-smoke streamed Streamed React shell reply: stream a quick verification update into the React transcript and rendered the tool row Run verification notebook complete with zero console warnings/errors; screenshot outputs/playwright/feynman-react-shell-stream-smoke.png. npm run typecheck, npm run build:workbench-web, npm run build, npm run architecture:check, git diff --check, focused React/workbench tests (25/25), and full npm test passed (417/417).
- Next: Continue React shell parity on artifact preview/open actions, Files overlay behavior, Customize mutations, notebook/compute panes, and annotation/refinement flows before switching /projects/... to React.

2026-07-02 08:39 PDT — open-science-workbench-react-shell Copy Section

- Objective: Stop growing the crowded string-rendered workbench shell and start the Claude Science-shaped React/Vite app shell on top of the existing Feynman/Pi APIs.
- Researched: Rechecked the live Claude Science product page, OpenCode's desktop/app package split, and Conductor's React/Vite dashboard structure. The reference direction is a backend-backed app shell with a narrow project/session rail, central chat, explicit Files/Customize surfaces, pane-local scroll, artifact state, and provenance rather than an always-expanded dashboard.
- Changed: Added workbench.vite.config.ts, workbench-web/, React/Vite/lucide dependencies, a build:workbench-web build step, authenticated /app-shell/... static serving through src/workbench/static-shell.ts, and tests/workbench-react-shell.test.ts. The React shell reads /api/state, opens real workbench chat sessions, sends messages through /api/chat/message, shows project/session rail, central transcript/composer, Files artifact panel, and Customize resource panel. The rail caps at six visible sessions plus an overflow count and hides its scrollbar chrome.
- Verified: Fresh server http://127.0.0.1:51274/app-shell/projects/active-plans/frames/open-science-workbench?token=cxf8y2kVEXs0PJs3Zjpv1WGORRRtWyfc measured default viewport 1280x720, no document overflow, bodyOverflow:hidden, rail 256x720, conversation 678.4x720, side panel 345.6x720, six visible session rows, 10 more sessions, session-list overflow hidden, and zero console warnings/errors. Mobile 390x740 measured no document overflow, hidden rail, overlay side panel, and zero warnings/errors. Screenshots: outputs/playwright/feynman-react-shell.png and outputs/playwright/feynman-react-shell-no-rail-scroll.png. npm run build:workbench-web, npm run build, npm run typecheck, npm run architecture:check, focused shell/UI tests, and full npm test passed (416/416).
- Next: Continue migrating the default /projects/... surface to the React shell only after stream handling, artifact preview actions, Files overlay parity, and Customize mutations reach feature parity with the existing workbench.

2026-07-02 08:00 PDT — open-science-workbench-density-framework Copy Section

- Objective: Re-anchor the crowded active frame to the installed Claude Science app and choose the durable UI framework direction instead of continuing ad hoc template sprawl.
- Researched: Launched the installed /Applications/Claude Science.app through a fresh claude-science url, captured launcher/project screenshots, and inspected the bundled Vite web app modules plus local SQLite schema. The reference structure is a sparse project launcher, narrow project/session rail, central conversation, explicit Files/Customize/Workspace surfaces, pane-local scrolling, and artifact/provenance drawers rather than a document page with every surface visible at once.
- Changed: Collapsed the active rail session list to the active session plus six recent rows with a quiet overflow count, preserving session navigation while removing the all-history rail dump. Recorded the framework decision: keep Feynman's Pi/workbench backend, but move durable UI work toward a React/Vite app shell rather than growing string-rendered HTML and global CSS.
- Verified: Fresh server http://127.0.0.1:64584/projects/active-plans/frames/open-science-workbench?token=O0GFnV3ygqfjrLo1TihaZt0T3mbft-LI measured no document overflow, body overflow hidden, rail 196x720, central chat 1084x720, transcript 878x523.4 with hidden scrollbar chrome, hidden right pane by default, hidden model/config chips by default, seven visible session rows, 9 more sessions, and zero console errors. Screenshot: outputs/playwright/feynman-patched-collapsed-rail.png. Focused workbench UI/new-session tests passed (7/7), npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (415/415).
- Next: Run the full gate, then start the React/Vite shell migration in slices around project rail, chat transcript, composer, artifact viewer, Files overlay, and Customize settings without changing the Pi-backed API contract.

2026-07-02 07:34 PDT — open-science-workbench-gnomad-and-rail-cleanup Copy Section

- Objective: Continue the Claude Science parity pass by adding the installed app's gnomAD-style variant source and removing the remaining crowded rail/search chrome from the active frame.
- Researched: Rechecked the public Claude Science page and stored installed-app screenshots. The reference frames Claude Science as a workbench around scientific tools, database connections, compute, reproducible artifacts, and provenance, with a light current-project/session rail rather than an all-project dashboard inside the project view. Re-read the installed Claude Science gnomAD client/query source, which uses the public gnomAD GraphQL API, gnomad_r4, and a longer request timeout.
- Changed: Added gnomad to the built-in feynman_science_database_search source set for rsID search, direct variant allele-frequency lookup, and gene constraint lookup; updated runtime prompt/settings resources/tests for gnomAD; tightened the active frame rail to the current project only, hid the rail filter box in the compact frame shell, fixed session-list horizontal overflow, narrowed the rail to 196px, and capped the chat/composer column to 880px so the screen reads as chat-first instead of dashboard-wide.
- Verified: Browser smoke on http://127.0.0.1:6174/projects/active-plans/frames/open-science-workbench?token=JjwtbTyutG_ANMCEMJlq21OnR9dvBOmn measured default columns 196px 1084px, visible project rows ["Active Plans"], search input display:none, document overflow 0/0, session list scrollbarWidth:none with no horizontal overflow, hidden right pane, and screenshots outputs/playwright/feynman-open-science-workbench-claude-rail-fixed.png plus outputs/playwright/feynman-open-science-workbench-claude-rail-fixed.json. Split mode measured workspace-open artifact-view-open, columns 196px 546.406px 537.594px, right tabs/tab panel/artifact strip/preview tabs hidden, preview scrollbar chrome hidden, and screenshot outputs/playwright/feynman-open-science-workbench-claude-rail-split.png. Focused UI/database/settings/context tests passed (15/15), npm run typecheck passed, full npm test passed (415/415), and git diff --check passed.
- Next: Continue with exact PDF renderer glyph anchoring, deeper variant annotation flows, and NVIDIA hosted execution once credentials exist.

2026-07-02 07:11 PDT — open-science-workbench-artifact-view-and-gtex Copy Section

- Objective: Continue correcting the active Open Science Workbench frame toward Claude Science's control-plane structure and add more no-setup science sources from the installed reference app.
- Researched: Rechecked the installed Claude Science project view screenshot and current Feynman route. The reference keeps the default frame as rail + conversation, then uses the right side as an intentional selected-artifact viewer; Feynman's explicit artifact Open path still showed the Files browser, tabs, artifact tabs, and preview stacked together, which made the split state crowded.
- Changed: Made frame/project navigation leave the artifact viewer closed and unselected by default; tightened sidebar session rows to one-line 32px rail items with hidden scrollbar chrome; made explicit artifact selection open the split viewer; added an artifact-view-open mode that hides the right-pane tab/file-browser chrome so the selected artifact gets the whole right pane; expanded feynman_science_database_search with GTEx tissue-expression lookup and QuickGO UniProt GO-annotation lookup; updated runtime prompt, Customize connector presets, and tests for the twenty built-in read-only science sources.
- Verified: Restarted the local server at http://127.0.0.1:6174/?token=8DGNU6J1WVLjPmwV0tn2M530nGxXyla9. Browser metrics for /projects/active-plans/frames/open-science-workbench show default workspaceOpen:false, artifactViewOpen:false, two columns 204px 1236px, right pane display:none, session row height 32, and session scrollbar none; after clicking the artifact Open button, metrics show workspaceOpen:true, artifactViewOpen:true, columns 204px 631.203px 604.797px, right pane rows 960px, and right tabs/tab panel/artifact tabs/preview tabs all hidden. Screenshots: outputs/playwright/feynman-open-science-workbench-artifact-mode-default.png and outputs/playwright/feynman-open-science-workbench-artifact-mode-split.png. Focused tests passed (15/15), full npm test passed (415/415), npm run typecheck passed, and git diff --check passed.
- Next: Continue with gnomAD/variant catalogs and exact PDF renderer glyph anchoring without reopening the default frame into a crowded workspace pane.

2026-07-02 06:47 PDT — open-science-workbench-collapse-and-specialty-bio Copy Section

- Objective: Fix the visibly crowded active Open Science Workbench frame and continue moving the chat tool layer toward Claude Science's bundled scientific database behavior.
- Researched: Rechecked the live installed Claude Science project control plane, which uses a project rail, central research chat, generated artifact tray, and right artifact preview for useful selected artifacts; rechecked Feynman's current rendered route and found the right artifact/workspace column was being served from stale server CSS and, when open, defaulted to a long plan artifact that made the route feel like a scroll-heavy document pane instead of a chat.
- Changed: Made the desktop right workspace truly on-demand by defaulting the workbench frame to the project rail plus chat column and only adding the right column when workspace-open is active. Added extensions/research-tools/science-database-specialty.ts and wired feynman_science_database_search to six Claude Science-style public bio sources: OLS, ENCODE, InterPro, GEO, PRIDE, and Reactome, with stable ids/source URLs/provenance returned through the same Pi tool contract.
- Verified: Restarted the local server on http://127.0.0.1:6174/?token=wrj4sU01wZGHTJx5fipIgcWxlhlCqDOL; the active frame screenshot outputs/playwright/feynman-open-science-workbench-after-restart.png shows the crowded right pane gone on first load, and served HTML contains the two-column default plus body.workspace-open three-column override. Captured Claude Science dashboard/project references at outputs/playwright/claude-science-reference-dashboard.png and outputs/playwright/claude-science-reference-project-direct.png. Focused tests passed (7/7), npm run typecheck passed, and full npm test passed (415/415).
- Next: Continue functional parity on GTEx/QuickGO/variant catalogs, better artifact-selection defaults for frame routes, and exact PDF renderer glyph anchoring without reintroducing always-on dashboard chrome.

2026-07-02 06:24 PDT — open-science-workbench-claude-column-frame Copy Section

- Objective: Replace the crowded active frame with a Claude Science-shaped research workbench structure and keep expanding no-setup science sources.
- Researched: Used the installed Claude Science runtime/page evidence already captured for projects/frames/chat/artifact history, then rechecked the live Feynman route and the current Pi/workbench code path before patching.
- Changed: Reworked the active frame into a persistent desktop project rail, full-height chat column, and right artifact inspector; restored a compact topbar/drawer structure for mobile; made Files open the full overlay from the visible rail; split Markdown preview rendering/styles out of oversized preview modules; and expanded the built-in database tool to bioRxiv, medRxiv, UniProt, RCSB PDB, and Ensembl in addition to the existing seven sources.
- Verified: Fresh server http://127.0.0.1:6174/projects/active-plans/frames/open-science-workbench?token=b3R6bfbeh5Y9ubiNzoVlV73qy6vgoPmX measured no desktop/mobile document overflow, desktop columns 204px / 573.6px / 662.4px, visible Markdown preview, Files overlay 1440x904, mobile chat under the 390x80 topbar with overlap 0, and zero browser console/request failures. Live API smoke returned records from UniProt, RCSB PDB, Ensembl, bioRxiv, and medRxiv. git diff --check, npm run typecheck, npm run build, npm run architecture:check, focused tests, and full npm test passed (414/414).
- Next: Continue parity on pathway/variant sources such as gnomAD, GTEx, ENCODE, and Reactome, plus exact PDF renderer glyph anchoring.

2026-07-02 05:27 PDT — open-science-workbench-frame-layout-correction Copy Section

- Objective: Fix the active Open Science Workbench frame feeling crowded/broken by correcting the Claude-style chat/artifact split layout.
- Researched: Reused the installed Claude Science app/runtime evidence for the quiet chat-first frame with secondary Files/Workspace surfaces; remeasured the live Feynman route before patching and found the transcript was only 222px tall inside a 743px conversation card because the frame grid still reserved an empty second row.
- Changed: Made the transcript own the full middle column, hid nonessential topbar version/refresh chrome, removed the visible State kicker, widened the desktop Workspace drawer to 720px, structured the drawer file controls, hid the redundant drawer grid/list toggle, and made mobile preview actions wrap.
- Verified: Fresh server http://127.0.0.1:6174/projects/active-plans/frames/open-science-workbench?token=GCh6fz2gmA_zyZcjE7NGkMoWIeEClacJ measured desktop/mobile closed/open layouts with no document overflow and zero console errors; desktop transcript is now 1014x741, Workspace drawer is 720x924, and mobile drawer preview controls fit in 361px. Screenshots saved under outputs/playwright/open-science-workbench-layout-*.png. npm run typecheck, npm run build, npm run architecture:check, git diff --check -- src/workbench/ui-style-frame.ts, and full npm test passed (413/413).
- Next: Continue parity on deeper specialty science database execution and exact PDF renderer glyph/page anchoring.

2026-07-02 00:51 PDT — open-science-workbench-read-cursors Copy Section

- Objective: Close the Claude Science frame read-cursor gap so long research frames remember the last read transcript message across reloads.
- Researched: Re-opened the installed Claude Science migration 0055_frame_read_cursors.sql, which stores root_frame_id, message_uuid, message_index, and updated_at.
- Changed: Added a local .feynman/workbench/read-cursors.json store, WorkbenchFrameReadCursor state, authenticated /api/read-cursor, per-message transcript ids, unread/current labels, first-unread jump behavior, and a Mark read action that persists the current frame cursor.
- Verified: Focused read-cursor/files tests passed (4/4); npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (407/407). Rebuilt in-app browser smoke on http://127.0.0.1:6174/projects/workspace/frames/open-science-workbench?token=ncHp5CGU6uIcN_Wk1PPkZKzBeX_EQuEW showed 2 new messages, clicked Mark read, reloaded, verified Current, verified the saved cursor at messageIndex: 1 / messageCount: 2, and recorded zero browser errors.
- Next: Continue parity on richer PDF text-selection/page-rect anchoring and live science database/tool connector execution.

2026-07-02 00:32 PDT — open-science-workbench-media-annotations Copy Section

- Objective: Close the Claude Science figure/PDF annotation gap by making image and PDF artifacts markable with coordinates that Pi can use in follow-up chat.
- Researched: Re-opened the public Claude Science page and the installed local app bundle. The reference product promises plain-language figure iteration, artifact history, protein/genomic/chemical/PDF renderers, reviewer checks, persistent kernels, databases, skills, and connectors. The installed bundle uses unified annotations records, image point/region overlays, PDF text-selection annotations with page/rect metadata, and HTML element overlays.
- Changed: Extended Feynman artifact annotations with anchorKind, page/line fields, selection prefix, and percent x/y/width/height geometry. Image and PDF previews now expose an Annotate control, click/drag point-or-region capture, saved numbered badges/boxes, annotation target summaries, API persistence, and prompt injection of anchor type/page/coordinates so the Pi-backed chat sees the selected scientific artifact region.
- Verified: Focused annotation/files tests passed (6/6); npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (405/405). Rebuilt in-app browser smoke on a throwaway workbench at http://127.0.0.1:51355/projects/workspace/frames/figure?token=IfCJ1XQX2eRpINetxYqzr366VMgrmjlC dragged an image region, created Image region x=20.1%, y=21.9%, w=45.8%, h=35.2%, saved a revision note, verified one saved region box on the image preview, verified .feynman/workbench/annotations.json stored percent geometry, recorded zero browser errors, and captured /tmp/feynman-media-annotation-rebuilt-smoke.png.
- Next: Continue parity on persistent read cursors, richer PDF text-selection/page anchoring, and live science database/tool connectors.

2026-07-02 00:08 PDT — open-science-workbench-refinement-apply Copy Section

- Objective: Match Claude Science's artifact refinement loop where selected text can produce a model suggestion, preview the replacement as a diff, and apply the edit back into the artifact with version history.
- Researched: Re-opened the installed Claude Science runtime and bundle. AnnotationRefinementPanel calls annotations/suggestEdit, renders Ask/Edit, Generating suggestion, Diff/Full, an editable suggestion textarea, and Apply; ArtifactTile then calls annotations/applyEdit and swaps to the returned artifact version with carried annotations.
- Changed: Replaced the direct-chat refinement edit path with authenticated /api/artifact/refinement/suggest and /api/artifact/refinement/apply routes. Feynman now validates the selected text and offsets against the current artifact, asks the workbench/Pi prompt executor for a JSON suggestion, renders a Claude-style suggestion card with word diff/full modes and editable replacement text, and applies only the selected span through the existing snapshot/version writer.
- Verified: Focused artifact/files tests passed (7/7); npm run typecheck, npm run build, npm run architecture:check, and full npm test passed (404/404). In-app browser verification on the real 6174 workbench opened the artifact preview and confirmed the selected-text panel exposes Editing selection, Save note, Ask, and Edit. A second in-app browser smoke used a throwaway server at http://127.0.0.1:64727/?token=KLI24zZSqpfkJ3UEoY_Dx_kbZmAO39Ay, generated a fake model suggestion, displayed the diff/apply state, clicked Apply, verified outputs/apply.md changed to include the sample-size caveat, and verified before/after snapshots under .feynman/workbench/artifact-snapshots/.
- Next: Continue parity on persistent read cursors, richer PDF/image region annotations, and live science-specific tool/database connectors.

2026-07-01 23:43 PDT — open-science-workbench-artifact-edit Copy Section

- Objective: Match Claude Science's editable artifact viewer by turning Feynman's right artifact pane into a real inline text editor with auditable save/version behavior.
- Researched: Re-read the installed Claude Science bundle modules for EditableTextPreview, EditableMarkdownPreview, ArtifactTile, and AnnotationRefinementPanel. Claude's editor swaps text/markdown previews into a focused textarea with original/edited content state; the refinement panel calls a suggestion path and shows Apply after an edit suggestion. Feynman's existing artifact snapshot/version code already had the correct local history spine for this behavior.
- Changed: Added authenticated artifact edit read/save APIs, a backend text-artifact edit module limited to tracked outputs/, papers/, and notes/ artifacts, before/after snapshot recording on every changed save, and a green Feynman-styled Edit content action in the artifact menu. The content tab now opens a textarea editor with Save changes and Cancel, refreshes the preview after saving, and records the result in the existing Versions tab for diff/restore.
- Verified: Focused edit/files UI tests passed (5/5); npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (402/402). Fresh Playwright smoke on a throwaway workbench opened outputs/smoke.md, used Edit content, loaded the real file body through /api/artifact/edit, saved revised text, verified the file bytes, verified .feynman/workbench/artifact-snapshots/workbench-edit.jsonl, opened the Versions tab, recorded zero browser errors, and captured /tmp/feynman-artifact-edit-smoke.png.
- Next: Continue parity on model-generated suggestion/apply diffs, read cursors, and richer PDF/image region annotations.

2026-07-01 23:31 PDT — open-science-workbench-refinement-panel Copy Section

- Objective: Match Claude Science's plain-language artifact/figure iteration flow by turning selected artifact text into an anchored refinement interaction instead of only a manual annotation form.
- Researched: Re-opened the public Claude Science page, which names figure iteration in plain language, reproducible artifact history, scientific renderers, reviewer checks, persistent kernels, and compute/database integration as the product bar. Drove the installed Claude Science Example project, opened a generated report artifact, and inspected the local bundle modules imported by text/PDF previews. AnnotationRefinementPanel-BlsUc42k.js renders Editing selection, a selected-passage preview, a Describe the edit you'd like... textarea, Ask, Edit, generated suggestion, and Apply; the PDF preview shows an Annotate popover on selected text and passes anchored text/rect metadata. The SQLite migrations show Claude moved from transcript/file annotations into a unified annotations table keyed by project, target kind/key, label index, checksum, and JSON body.
- Changed: Added a focused workbench refinement client and style module. Selecting text inside an annotatable artifact preview now opens a sticky Editing selection panel over the preview, preserves the selected anchor and start/end offsets, accepts an edit instruction, enables Save note, Ask, and Edit, saves revision annotations through the existing authenticated annotation API, and sends Ask/Edit prompts through the existing in-app Pi chat stream so the refinement stays attached to the active research frame.
- Verified: Focused annotation/files UI tests passed (5/5); npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (399/399). Fresh Playwright smoke on a throwaway workbench at http://127.0.0.1:6215/?token=refine-smoke selected responder signal is strong, opened the refinement panel, saved Add a sample-size caveat before making the response claim., verified the Annotations tab row, verified .feynman/workbench/annotations.json stored the anchor plus startOffset: 30 and endOffset: 56, recorded zero browser errors, and captured /tmp/feynman-refinement-panel-smoke.png. Refreshed the visible local server on port 6174 and verified http://127.0.0.1:6174/projects/verification/frames/reference-audit?token=sEs1AdjRRwW1qHX6ckWlJ4QWAZvmrQ1X opens the Editing selection panel from selected text in outputs/reference-audit/handoff.md, with zero browser errors and screenshot /tmp/feynman-live-refinement-panel.png.
- Next: Continue parity on direct editable artifact contents, suggestion/apply diffs, Claude-style read cursors, and richer PDF/image region annotations.

2026-07-01 23:17 PDT — open-science-workbench-cloud-export Copy Section

- Objective: Match Claude Science's artifact Export to Cloud action with a real credential-backed flow instead of a disabled placeholder.
- Researched: Drove the installed local Claude Science Example project and clicked Export to Cloud; with no cloud credentials it opened Settings → Storage with No cloud storage configured and Go to Credentials. Read the installed app bundle modules for ExportToCloudModal, CloudStorageModal, and useCloudCredentials; the reference supports credential selection, bucket selection, destination path, provider credential tests, and a no-secrets credential model.
- Changed: Added workbench cloud export target discovery from credential references, exposed targets in WorkbenchState, updated the Storage settings card, added authenticated /api/artifact/export-cloud, implemented real file:///absolute-path exports plus aws s3 cp and gcloud storage cp/gsutil cp execution paths, wrote .feynman/workbench/cloud-exports.jsonl audit records, enabled the artifact menu action, and added a green Feynman-styled export modal with the Claude-style empty state and Go to Credentials path.
- Verified: Focused cloud/artifact/files tests passed (6/6); npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (399/399). Fresh Playwright smoke on a throwaway workbench at http://127.0.0.1:6214/?token=cloud-smoke opened the artifact menu, confirmed Export to Cloud was enabled, exported outputs/alpha.md to a configured file:// target, verified the copied file contents, recorded zero browser errors, and captured /tmp/feynman-cloud-export-smoke.png. Refreshed the visible local server on port 6174 and verified http://127.0.0.1:6174/projects/verification/frames/reference-audit?token=6InrvzybxhndI__VaLGgZdu4x-sEBgC- shows the enabled action and the no-storage modal with zero browser errors, captured at /tmp/feynman-live-cloud-export-menu.png.
- Next: Continue parity on editable artifact/version flows, Claude-style read cursors, and annotation refinement drawers.

2026-07-01 22:53 PDT — open-science-workbench-artifact-actions Copy Section

- Objective: Match Claude Science's artifact preview action menu with real local actions instead of placeholder preview chrome.
- Researched: Re-drove the installed local Claude Science Example project and captured the artifact menu at /tmp/claude-science-probe-artifact-menu.png. The reference menu exposes Star, Hide, View in context, Provenance, Copy link, Rename, Export Metadata, Export to Cloud, and Delete from the preview's More actions button.
- Changed: Added a persisted artifact-action store under .feynman/workbench/artifact-actions.json, applied starred/renamed/hidden/deleted state during workspace scans, exposed hidden/deleted action records in state, added authenticated /api/artifact/action, and wired the right preview plus Files overlay menus to Star/Unstar, Hide, Rename, soft Delete, Unhide, and Restore. Delete moves the artifact into .feynman/workbench/artifact-trash/ instead of destroying it, and the Files overlay now has a Hidden & trash recovery source.
- Verified: Focused artifact/files UI tests passed (4/4); npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (397/397). Fresh Playwright smoke on a throwaway workspace at http://127.0.0.1:6212/projects/workspace/frames/alpha?token=KF0HeeBmYSmGDFjkEbtxu7o9wD1kb1Mk verified the full action menu text, starred outputs/alpha.md, renamed it through the browser prompt, hid it, deleted outputs/beta.md through the confirm flow, confirmed the file moved to workbench trash, recorded zero browser errors, and captured /tmp/feynman-artifact-actions-smoke.png. A second throwaway Playwright smoke at http://127.0.0.1:6213/projects/workspace/frames/alpha?token=MRRyHatMiGQBaMv5VT_YpkJHsAEkAuLh opened Files → Hidden & trash, unhid outputs/alpha.md, restored outputs/beta.md, verified both artifacts returned to visible state, recorded zero browser errors, and captured /tmp/feynman-archive-restore-smoke.png.
- Next: Continue parity on editable artifact/version flows, Claude-style read cursors, annotation refinement drawers, and cloud-export endpoint configuration.

2026-07-01 22:34 PDT — open-science-workbench-files-overlay Copy Section

- Objective: Match Claude Science's dedicated file-browser surface so the left rail Files control opens a full-height browse/inspect flow instead of only swapping the right-side tab.
- Researched: Continued from the installed Claude Science bundle/live-app evidence for FilesOverlay, FileBrowserPane, persistent right preview actions, and the frame-level Files rail.
- Changed: Added a focused Files overlay client and style module plus static shell markup. The overlay reuses the existing artifact/upload/file-card model, supports session/project source switching, search, grid/list layout, import, artifact selection, right-preview synchronization, selected-file details, and actions for open preview, provenance, download, copy link, and metadata JSON. The left-rail Files button and Files-pane Expand button now open the overlay while preserving the existing side preview.
- Verified: Focused workbench UI tests passed (2/2); npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (395/395). Fresh Playwright smoke on http://127.0.0.1:6211/projects/workspace/frames/reference-audit?token=mJHzzXZpKjB5YkJSaLDF0okdRGYfffQr opened the Files overlay from the left rail, switched list mode, searched verification, selected outputs/reference-audit/verification-matrix.md, confirmed the preview title and five overlay actions, closed the overlay, recorded zero browser errors, and captured /tmp/feynman-files-overlay-smoke.png.
- Next: Continue parity on persistent frame read state, richer file annotations/drawers, and Claude-style message/read cursors.

2026-07-01 22:26 PDT — open-science-workbench-transcript-tools Copy Section

- Objective: Match Claude Science's conversation-level execution trace, where tool runs appear as grouped transcript cards with step chips, command/code context, and collapsible output instead of a flat debug dump.
- Researched: Reused the installed Claude Science live-app audit and screenshots showing tool-group-header, tool-chip, BASH/ENV code cards, and Show output disclosures embedded in the chat while the right file preview remains visible.
- Changed: Added focused transcript tool-event client and style modules that override the existing flat renderer without growing the 1200-line main client. Tool events now render a group header, per-step status chips, normalized tool kind badges, code/environment cards from existing Pi inputs/details, output disclosures, and existing connector approval cards.
- Verified: Focused workbench UI tests passed (2/2); npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (395/395). Fresh Playwright smoke on http://127.0.0.1:6211/projects/workspace/frames/reference-audit?token=eRkiuEWztANZV4qXzLsghL0sRBJ9dyFU injected only an in-memory chat session, verified 3 transcript tool events, 3 code cards, 3 output toggles, zero browser errors, and captured /tmp/feynman-transcript-tool-events-final.png.
- Next: Continue parity on exact Claude-style file overlay/actions and persistent frame messaging/read state.

2026-07-01 22:05 PDT — open-science-workbench-artifact-tray-overflow Copy Section

- Objective: Match Claude Science's generated-artifact tray behavior where a long artifact set shows several cards plus a +N more card that opens the full file surface.
- Changed: Added a focused artifact-tray override module that keeps five visible generated artifact cards, adds a +N more overflow card for larger runs, and routes that card to the Files pane. Added a small dashed-card style and static bundle coverage without growing the already-large main client module.
- Verified: Focused workbench UI tests passed (2/2); npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed. Fresh Playwright smoke on http://127.0.0.1:6211/projects/workspace/frames/reference-audit?token=NG5xpAXqxzwdL07GTGJ4V3qm_mmQp0j0 verified 5 visible tray cards, a +17 more overflow card, click-through to the Files tab, 22 rendered file cards, zero browser errors, and screenshot /tmp/feynman-turn-tray-more-smoke.png. Full npm test passed (395/395).
- Next: Continue parity on exact Claude-style file overlay/actions.

2026-07-01 22:00 PDT — open-science-workbench-inline-artifacts Copy Section

- Objective: Match Claude Science's inline generated-file affordance where artifact filenames in assistant messages are direct file anchors, not only separate tray or Files-pane entries.
- Changed: Added a focused message-artifact renderer that detects known artifact paths and filenames from the active run/project, renders them as safe inline file chips in transcript message bodies, and routes clicks through the existing artifact preview path. Added a compact green chip style and static bundle coverage.
- Verified: Focused workbench UI tests passed (8/8); npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed. Fresh Playwright smoke on http://127.0.0.1:6211/?token=dZ7xAfZh8aPSWNqFX9KM953EVptxlvrw injected an in-memory transcript message mentioning outputs/.plans/open-science-workbench.md and open-science-workbench.md, verified two inline artifact refs, clicked one, confirmed the preview title became Open Science Workbench, recorded zero browser errors, and captured /tmp/feynman-message-artifact-ref-smoke.png. Full npm test passed (395/395).
- Next: Continue parity on exact Claude-style file overlay/actions.

2026-07-01 21:54 PDT — open-science-workbench-activity-pane Copy Section

- Objective: Close the Claude Science frame-activity gap by making the active research frame browseable as messages, tools, files, plan steps, and review events instead of scattering that state across separate panes.
- Researched: Re-drove the installed local Claude Science project view and extracted its active project snapshot. The reference frame showed grouped tool chips, generated artifact cards, reviewer status, inline file references, and a persistent right preview working together as one session surface.
- Changed: Added an Activity tab to the right science pane, backed by a focused client module and style module. The pane builds one chronological frame model from chat messages, tool events, Pi/execution records, generated artifacts, uploads, plan steps, and review checks, with filters for All, Messages, Tools, Files, Plan, and Review plus artifact-opening links.
- Verified: Focused workbench UI tests passed (8/8); npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed. Fresh Playwright smoke on http://127.0.0.1:6211/?token=kw85w811IijZKfmp4-sDZzkT1raNeF5T opened the workspace frame, switched to Activity, verified 10 events across Messages/Tools/Files/Plan filters, recorded zero browser errors, and captured /tmp/feynman-activity-smoke.png. Full npm test passed (395/395).
- Next: Continue parity on richer artifact reference chips and exact Claude-style file overlay/actions.

2026-07-01 21:41 PDT — open-science-workbench-file-import Copy Section

- Objective: Turn the Files pane into a real research intake surface so users can import session evidence, inspect it, download it, and remove it without hiding the capability behind the composer plus menu.
- Changed: Added a visible Import control to the Files toolbar, made uploaded files render as actionable upload cards, added upload preview/download/remove handling in a focused client script, exposed a session-bound authenticated /api/chat/attachment/download route, kept upload previews in the right preview pane, and split attachment API coverage into tests/workbench-attachments.test.ts to keep tests/workbench.test.ts below the architecture hard cap.
- Verified: Focused workbench/import tests passed (31/31); npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed; full npm test passed (395/395). Fresh Playwright smoke on http://127.0.0.1:6211/?token=DyD7POAc5Y8BE_iWvZDDqxi1suW_CN33 created a throwaway project, clicked the visible Files Import button, uploaded import-smoke.csv, verified preview text, downloaded exact uploaded bytes through /api/chat/attachment/download, removed the upload card, measured the search box at 72px after the toolbar fit fix, captured /tmp/feynman-files-import-smoke.png, and removed the temporary project/session/upload files.
- Next: Continue parity on turn-level artifact opening and denser live activity trace.

2026-07-01 21:28 PDT — open-science-workbench-project-create Copy Section

- Objective: Close the Claude Science project-creation gap so the dashboard can create a real research project and immediately open a chat frame instead of showing a disabled placeholder.
- Researched: Drove the installed local Claude Science app through its dashboard New project flow. The reference modal has Name, Description, and Agent Context; the description is shown in the project list and is not included in the agent prompt, while agent context is included in every project agent prompt.
- Changed: Added persisted custom workbench projects under .feynman/workbench/projects.json, included custom projects in scanned state/project rails, added authenticated /api/project/new, created an initial blank chat session for each new project, added a Claude-style dashboard modal in Feynman's green workbench UI, wired the client flow through state/URL/session rendering, and injected only project name plus agent context into Pi prompts.
- Verified: Focused workbench tests passed (10/10); npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed; full npm test passed (395/395). Fresh Playwright smoke on http://127.0.0.1:6211/?token=S-tfIKiPXkoABTK5IEQqRM8JnPyvXkoM clicked New project, filled all three reference fields, created a custom project, verified /api/state project/session rows and agent context, captured /tmp/feynman-new-project-smoke.png, and removed the temporary smoke project/session files.
- Next: Continue parity on turn-level artifact opening, import/attachment affordances, and denser live activity trace.

2026-07-01 18:30 PDT — open-science-workbench-managed-environments Copy Section

- Objective: Close the Claude Science environment-management gap by turning runtime discovery into real Python/R create/install actions for notebook work.
- Researched: Re-read the installed Claude Science local runtime and transcript evidence for manage_environments(mode="list"), manage_environments(mode="create", name="scanpy", packages=[...]), manage_packages(mode="install", ...), execution conda_env, and environment_snapshot behavior.
- Changed: Added /api/notebook/environment, persisted feynman.notebookEnvironmentAction.v1 records under .feynman/workbench/environment-actions.jsonl, created project-local Python venv and R library paths under .feynman/workbench/environments/, made Python execution prefer the managed venv when present, made R kernels/processes inherit the managed library through R_LIBS_USER, and added a Notebook-pane Managed environment form with Create/Install controls and managed-runtime/action metadata.
- Verified: Focused managed-environment tests passed (3/3), full npm test passed (381/381), and npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed. Fresh server http://127.0.0.1:6188/?token=TWJPoamvuIZP7am9-mo5T3-6jtR4Bhd6 created the managed Python venv, ran an isolated Python notebook cell through /Users/advaitpaliwal/Companion/Code/feynman/.feynman/workbench/environments/python-venv/bin/python, and recorded that executable/version in the environment snapshot. Playwright smoke verified the Notebook UI Create path, managed Python row, no console errors, and screenshot /tmp/feynman-managed-env-click-smoke.png.
- Next: Add live compute job lifecycle controls: queued/running state, cancel/terminate/retry, and pending terminate records for long-running local/cloud jobs.

2026-07-01 18:16 PDT — open-science-workbench-runtime-inventory Copy Section

- Objective: Make notebook runtime/kernel state visible in the workbench the way Claude Science exposes environment status and frame kernels.
- Changed: Added first-class environments and kernels to workbench state. Environment records now expose Python, managed R/Rscript, and Bash command source, executable, version, modes, session/execution counts, and lockfile snapshot counts. Kernel records expose persisted session kernel ids, active process state, runtime source, executable/version, and latest execution metadata. The Notebook pane now shows live session kernels above the runtime catalog, with compact cards that keep active state visible in the split pane.
- Verified: Full npm test passed (378/378); npm run typecheck and npm run build passed after the final UI filter/layout fix. Fresh rebuilt server http://127.0.0.1:6187/?token=science-runtimes-20260701c ran a real managed R session cell, printed 42, and reported active kernel session:runtime-parity-smoke:r on /Users/advaitpaliwal/.claude-science/conda/envs/r/bin/R with R version 4.5.3 (2026-03-11). Playwright/Chrome verified the active R kernel renders above the runtime catalog and saved /tmp/feynman-notebook-final-runtimes.png.
- Next: Add managed environment create/install actions for Python/R notebook runtimes, matching the manage_environments behavior observed in the installed Claude Science transcripts.

2026-07-01 17:27 PDT — open-science-workbench-r-session-kernel Copy Section

- Objective: Close the persistent-kernel parity gap where Feynman had session kernels for Python/Bash but R cells still fell back to isolated process mode.
- Changed: Added a persistent R notebook kernel using a long-lived R --vanilla --slave process, global-environment evaluation, per-cell completion markers, bounded stdout/stderr capture, timeout shutdown, and session kernel ids like session:<session>:r. Runtime environment probes now tolerate missing runtime stdout, so absent R/Rscript reports as unavailable context instead of crashing environment capture.
- Verified: Focused tests/workbench-r-kernel.test.ts passes with a fake R process proving variables persist across cells and notebook records keep session:r-memory:r. Full npm test passed (377/377). npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed after splitting the R test out of tests/workbench.test.ts. Fresh server HTML contains the R language option, Session kernel runtime option, and Modal cloud runtime option. Local machine still has no R/Rscript, so live R execution is unverified here until R is installed.
- Next: Keep provider work focused on real science jobs and NVIDIA only when NVIDIA_API_KEY is present.

2026-07-01 17:05 PDT — open-science-workbench-modal-notebook Copy Section

- Objective: Close one provider execution-depth gap by making Modal a real Notebook runtime mode instead of only a credential/status card.
- Researched: Re-read the repo's skills/modal-compute/SKILL.md, which scopes Modal to bounded research experiments when the modal CLI is available. Rechecked Modal docs for modal run, App, local_entrypoint, Image.debian_slim, and current local-data guidance. Local machine has ~/.modal.toml and Python/pip; latest PyPI Modal is 1.2.6.
- Changed: Added a Modal notebook execution bridge. Python cells can now use executionMode: "modal", which writes an auditable Modal app script under .feynman/workbench/modal-jobs/, runs modal run <script>, parses a result marker for remote stdout/stderr/exit code, records Modal cloud provenance, and keeps generated scripts local for audit. The Notebook runtime selector now includes Modal cloud for Python cells. Missing Modal CLI records a notebook error instead of pretending a cloud job ran. Installed a managed local Modal CLI at .feynman/workbench/modal-venv/bin/modal, and Compute diagnostics now prefer that managed CLI when present. Modal cells also expose FEYNMAN_MODAL_ARTIFACT_DIR so bounded cloud-produced files under outputs/, papers/, or notes/ can be returned to the local artifact/version/snapshot pipeline.
- Verified: Full npm test passed (376/376), including the Modal artifact-return assertion. npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed. The managed Modal CLI reports modal client version: 1.2.6. Fresh server /api/state on http://127.0.0.1:6184 returned 43 connectors, managed Modal CLI diagnostics, and NVIDIA available; server-rendered HTML contains the Modal cloud notebook runtime option. A real Modal cloud cell completed through /api/notebook/execute with stdout feynman modal quiet smoke 2026-07-01 and Modal app URL https://modal.com/apps/companion/main/ap-D5yRyW2a7m1cX9h2CVXFj3. A second real Modal cloud smoke from a temporary workspace wrote outputs/modal-artifact-smoke.md, returned it locally, produced one snapshot, and completed at https://modal.com/apps/companion/main/ap-w3udlvpyi4uV3QuhcVO9df.
- Next: Use Modal for a bounded research/replication job that produces a real science artifact; implement NVIDIA hosted NIM calls once NVIDIA_API_KEY is present.

2026-07-01 16:17 PDT — open-science-workbench-environment-lockfiles Copy Section

- Objective: Continue Claude Science-style provenance by making notebook environment snapshots record concrete package/environment lockfile fingerprints, not only OS/runtime/resource context.
- Changed: feynman.workbenchEnvironmentSnapshot.v1 now includes environmentFiles for detected package manifests and lockfiles, with path, kind, size, checksum, and updated time. The snapshot detects root Node/Python/R/Conda manifests and lockfiles plus the bundled Pi runtime manifest/lockfile under .feynman/npm/. The artifact Environment tab now renders those files in a compact provenance block beside the producer runtime, while raw JSON details remain available for audit.
- Verified: Focused workbench context tests passed (3/3), focused workbench/settings/server tests passed (30/30), and full npm test passed (375/375). npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed. Fresh server /api/state on http://127.0.0.1:6184 returned the expected groups and 43 connectors, with Modal configured and NVIDIA available. A non-mutating snapshot probe in the real workspace captured package.json, package-lock.json, .feynman/npm/package.json, and .feynman/npm/package-lock.json with checksums.
- Next: Pick one executable provider action for the next slice: Modal notebook job submission, NVIDIA hosted NIM calls, or connector OAuth handshake.

2026-07-01 16:09 PDT — open-science-workbench-provider-credentials Copy Section

- Objective: Continue the Claude Science parity work by making the cloud/model provider cards reflect real local credential state instead of generic available placeholders.
- Researched: Checked Modal's official config/token docs (https://modal.com/docs/reference/modal.config, https://modal.com/docs/reference/cli/token) and NVIDIA's official API-key docs (https://docs.nvidia.com/nemo/retriever/26.5.0/extraction/api-keys/). Local runtime check found ~/.modal.toml present, no MODAL_TOKEN_ID/MODAL_TOKEN_SECRET env pair, no NVIDIA_API_KEY, and no installed modal CLI/Python module.
- Changed: Modal compute and credential resources now detect either the env token pair or ~/.modal.toml, show the detected credential source without exposing values, and keep cloud execution labeled as waiting on a Modal runtime adapter. NVIDIA BioNeMo/NVIDIA API resources now use NVIDIA_API_KEY diagnostics consistently and keep self-hosted/local NIM endpoints routed through custom connectors or credential refs.
- Verified: Focused workbench/settings tests passed (3/3), including deterministic env-backed Modal/NVIDIA assertions. npm run typecheck, npm run build, npm run architecture:check, and git diff --check passed. Fresh authenticated /api/state on http://127.0.0.1:6184 returned Modal compute/credential as configured via ~/.modal.toml, NVIDIA BioNeMo/NVIDIA API as available, and the 43 connector resources from the science catalog slice. The in-app browser automation bridge exposed no usable browser globals after restart, so this slice is API/state/test verified rather than click-smoked.
- Next: Implement the actual cloud execution adapter only after the provider action is scoped: Modal notebook job submission, NVIDIA hosted NIM calls, or connector OAuth handshake.

2026-07-01 16:02 PDT — open-science-workbench-science-catalog Copy Section

- Objective: Respond to the Claude Science parity critique by making the Feynman workbench feel like an in-app Pi research chat with a science connector/control plane, not a generic resource dashboard.
- Researched: Re-used the installed Claude Science local app observations for Settings > Connectors, including Featured/Directory/Organization sections, BioMart's visible tool list, Remote/Local connector forms, OAuth/header/env fields, permissions, and the modal page structure. Re-read Pi 0.80.3 RPC/session/extension evidence already captured for persistent chat, commands, packages, and MCP-like tool bridges.
- Changed: Connector resources now include connector kind and tool metadata. Feynman exposes a Claude Science-shaped science connector catalog with 20 Featured, 6 Directory, and 9 Organization presets, while keeping executable Pi packages and custom connectors separate and honest as configured/package-backed rows. Customize now has a Settings-style sidebar grouped into Capabilities and Workspace, breadcrumb/back chrome, connector list/search/filter, connector detail pages with tool permission previews, and Remote/Local add screens using the existing persisted connector model. The transcript now shows a pending Pi session strip before the first turn so the central surface reads as a Pi-backed chat frame immediately. Split connector client and style code into focused modules to keep architecture guard green.
- Verified: npm run typecheck, npm run build, npm run architecture:check, git diff --check, focused workbench/settings tests (26/26), and full npm test passed (374/374). Fresh authenticated /api/state on http://127.0.0.1:6184 returned 43 connector resources: Featured 20, Directory 6, Organization 9, Configured packages 5, Optional packages 2, Project extensions 1; BioMart is a Featured available preset with list_marts, list_datasets, list_common_attributes, list_all_attributes, list_filters, get_data, get_translation, and batch_translate. The in-app browser bridge could load and screenshot the current app route, but its click context reset/timed out before a post-split connector-modal click smoke; interactive connector behavior remains covered by state/API and existing settings handlers.
- Next: Add provider-backed OAuth/cloud connection flows where a supported local CLI/API path exists, then enrich environment snapshots with package/environment lockfiles.

2026-07-01 15:17 PDT — issue-sweep-workbench-clean-repeat Copy Section

- Objective: Run the recurring Feynman AI researcher intake sweep from the actual dirty local main checkout, preserving unrelated workbench/package changes and making no GitHub writes.
- Checked: Local main is still one commit ahead of origin/main at local 6c84b24, with the existing dirty workbench/package slice preserved. Live GitHub still has open issue #182 only, zero open PRs, and latest main workflow run Publish and Release 28343487961 succeeded at cb5fa56. Latest GitHub release remains v0.3.5 with four release assets; npm latest remains @companion-ai/[email protected]; local/package Pi remains 0.80.3; @companion-ai/alpha-hub remains 0.1.3.
- Decisions: No product code change was needed. Issue #182 stays deferred because the issue still reports old CLI 0.2.17 plus a later 0.3.4/alpha-hub 0.1.3 trace where alphaXiv/Clerk redirects to the landing page before Feynman/alpha-hub receives a callback code; this machine's source feynman alpha status succeeds, and no fresh current-version logged-out callback trace proves a Feynman-owned defect. Open PR classification is empty. Contributor refs remain non-actionable: pr4fork/main has no commits ahead, origin/fix/deepresearch-local-model-warning is a stale local-model warning branch, and sampled fork branches are Overleaf/admin export, provider/runtime bypasses, Windows/platform changes, fork docs, architecture notes, or fork-specific parallel-tool extensions outside the narrow research-loop bar.
- Package freshness: Root and website production audits found 0 vulnerabilities. Remaining root drift is non-security (@clack/prompts, @types/node, fast-xml-parser, posthog-node); website drift is non-security Astro/React/Tailwind/ESLint/UI-tooling drift. No drift maps to an open research-loop defect.
- Verified: npm run architecture:check; focused workbench/runtime tests (49/49); full npm test (374/374); npm run typecheck; npm run build; website npm run lint; website npm run typecheck; website npm run build (33 pages); root and website npm audit --omit=dev; source feynman alpha --help; source feynman alpha status; git diff --check; npm pack --dry-run (172 files, package size 52.5 MB); and temp installed-tarball smoke passed after correcting the archive path assertion. The installed tarball printed 0.3.5, rendered help, and its runtime archive contains @companion-ai/[email protected] plus @earendil-works/pi-coding-agent, pi-ai, pi-agent-core, and pi-tui at 0.80.3.
- Next: Keep watching #182 for a fresh current-version logged-out OAuth callback trace. Preserve the still-dirty workbench/package slice unless explicitly asked to publish it.

2026-07-01 13:16 PDT — open-science-workbench-sse-connectors Copy Section

- Objective: Close the remaining custom connector transport gap by making legacy SSE MCP connectors executable from the in-app Pi chat.
- Researched: Re-read installed Pi 0.80.3 SDK/extension/session docs, MCP SDK 1.29.0 SSE client/server transport source, and the live local Claude Science runtime/log/SQLite evidence. Claude Science runs a daemon-backed research chat surface with project frames, messages, custom MCP servers, agent assignments, tool grants, and lazy pooled MCP connectors over Streamable HTTP and stdio; MCP SDK SSE uses a GET event stream, an endpoint event, POSTed JSON-RPC messages, and response message events.
- Changed: feynman_connector_tools and feynman_connector_call now execute transport: "sse" connectors through the same approval-gated bridge as Streamable HTTP and local stdio. The bridge opens the SSE stream, enforces same-origin endpoint resolution, posts initialize/list/call JSON-RPC to the server-provided endpoint, resolves pending responses from event-stream messages, cleans up pending requests on close, and updates runtime prompt/context/settings diagnostics to describe SSE as executable.
- Verified: Focused connector tests now cover Streamable HTTP, SSE, local stdio, grants, skip approvals, specialist assignments, excluded tools, and helper/env parsing. npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test passed (374/374). Fresh in-app browser smoke on http://127.0.0.1:6182/projects/verification/frames/reference-audit?token=M5eEiSEaQXSy0e66JLDwosfr1FjShUlg added a temporary SSE connector, verified the Customize > Connectors card and executable runtime diagnostic, captured /tmp/feynman-sse-connector-smoke.png, and cleaned settings back to zero custom connectors/grants/domains.
- Next: Add provider-backed OAuth/cloud connection flows where a supported local CLI/API path exists, then enrich environment snapshots with package/environment lockfiles.

2026-07-01 13:02 PDT — open-science-workbench-connector-assignments Copy Section

- Objective: Close the Claude Science connector attachment gap by making custom connectors specialist-aware and able to hide selected MCP tools from chat execution.
- Researched: Re-read installed Pi 0.80.3 RPC/SDK/extension docs and the local Claude Science SQLite/runtime evidence. Claude Science stores MCP servers separately from mcp_agent_assignments, with excluded_tools on the assignment; its customize skill describes connector access by profile plus per-connector excluded tools after connector resolution.
- Changed: Custom connector settings now persist assignedSpecialists and bare-name excludedTools. The feynman_connector_tools and feynman_connector_call Pi tools accept the active specialist, report not_assigned connectors, omit excluded tools from discovery, and reject excluded or wrong-specialist calls before any HTTP/local MCP execution or approval request. Runtime prompts, sanitized context, connector diagnostics, and the Customize connector form now expose the assignment/exclusion policy. Fixed Customize panel rendering so its tab body, long connector form, and resource sections reserve layout height instead of overlapping.
- Verified: npm run typecheck, npm run build, npm run architecture:check, git diff --check, focused workbench connector/settings/context/UI tests, and full npm test passed (373/373). Fresh in-app browser smoke on http://127.0.0.1:6182/projects/verification/frames/reference-audit?token=vovodDnZeOXaR-cCg9J7nA4JEoUCMV2t verified the real Customize Connectors tab, Assigned specialists and Excluded tools fields, no form/resource overlap, and clean connector-panel geometry.
- Next: Add SSE connector transport, then provider-backed OAuth/cloud connection flows.

2026-07-01 12:42 PDT — open-science-workbench-chat-approvals Copy Section

- Objective: Move connector ask approvals from Settings-only review into the actual chat transcript, matching the installed Claude Science approval-card flow more closely.
- Researched: Re-read Pi 0.80.3 extension docs, JSON event stream docs, package metadata, and permission-gate examples. Inspected the installed Claude Science approval/runtime assets for pending_input_requests, mcp_tool connector cards, Connector kind labels, allow/deny controls, and skip-server semantics.
- Changed: Transcript tool events now render a connector approval card when a Pi connector-call error carries a connector:<connector-id>:<tool-name> scope. The card shows connector, tool, scope, input arguments, Allow, Block, and Allow connector actions. All actions write to the existing permissionGrants settings collection, and Settings mutations now re-render the transcript so chat and Settings share one approval state.
- Verified: npm run typecheck, npm run build, and git diff --check passed after the final UI polish. The full Node test harness passed earlier in the slice (372/372). Fresh-server in-app browser smoke verified the pending card, Allow exact grant, Allow connector exact-plus-wildcard grants, visible card geometry/screenshot with no overlap, suppression of the raw connector error output above the card, and cleanup back to the original settings/session files.
- Next: Add SSE connector transport, then agent-specific connector assignment/exclusion and provider-backed OAuth/cloud connection flows.

2026-07-01 11:36 PDT — open-science-workbench-local-stdio-connectors Copy Section

- Objective: Close the next Claude Science connector parity gap by making local command MCP connectors executable from the in-app Pi chat, matching the installed Claude Science local MCP launcher shape.
- Researched: Re-read the MCP SDK stdio transport and the installed Claude Science local MCP launcher at ~/.claude-science/runtime/0.1.0-dev.20260630.t212931.sha2bc1ac8-release/mcp-servers/bio-tools/run_server.py; Claude Science launches local MCP servers over stdio, while Pi 0.80.3 still needs app-owned extension tools for MCP execution.
- Changed: Extended feynman_connector_tools and feynman_connector_call to support transport: "local" connectors. The extension now validates local commands, spawns them in the workspace, speaks LF-delimited MCP JSON-RPC over stdin/stdout, captures bounded stderr, parses connector env lines, closes child processes, and keeps the existing explicit allow grant gate before execution. Runtime prompt/context/settings diagnostics now describe Streamable HTTP and local command connectors as executable.
- Verified: Focused connector tests prove local stdio discovery, allowed tools/call, env parsing, and grant enforcement before local spawn. npm run typecheck; npm run build; npm run architecture:check; git diff --check; full npm test (371/371) all passed. Restarted the real built workbench on PID 61886 at http://127.0.0.1:6174/projects/verification/frames/reference-audit?token=connector-bridge-20260701; browser smoke verified the chat composer, temporary local connector card with executable local command diagnostics, temporary allowed grant card, zero console errors, and cleanup back to zero custom connectors/grants.
- Next: Add SSE connector transport, then UI approval cards for ask grants and agent-specific connector assignments/exclusions.

2026-07-01 11:24 PDT — open-science-workbench-connector-execution Copy Section

- Objective: Close the next Claude Science parity gap by making saved custom connectors executable from the in-app Pi chat instead of only visible as prompt/settings context.
- Researched: Rechecked Anthropic's current Claude Science page for connectors, skills, scientific databases, traceable artifacts, compute, and internal API/ELN/pipeline integrations. Re-read the installed Claude Science runtime/database evidence for custom_mcp_servers, mcp_tool_grants, mcp_agent_assignments, MCP app tiles, connector attachment/exclusion APIs, and host.mcp(...) as the reference connector execution surface. Re-read Pi 0.80.3 README, extension docs, dynamic-tool examples, RPC/session launch path, and security notes; Pi has no built-in MCP, and extensions are the supported path for app-owned tool integrations.
- Changed: Added feynman_connector_tools and feynman_connector_call to the bundled research-tools Pi extension. Streamable HTTP MCP connectors now run the MCP initialize, initialized notification, tools/list, and tools/call JSON-RPC sequence; connector calls require an explicit allow grant for connector:<connector-id>:<tool-name> or connector:<connector-id>:* before any network request. Header helpers can provide request headers without printing or storing secret values. Runtime prompts, sanitized context diagnostics, settings diagnostics, and the Permissions placeholder now describe the executable bridge instead of the old "adapter needed" boundary.
- Verified: Targeted connector tests prove tool discovery, allowed tool calls, MCP session headers, grant enforcement before network execution, and header-helper parsing. npm run typecheck; npm run build; npm run architecture:check; git diff --check; full npm test (370/370) all passed. Fresh rebuilt-server browser smoke on http://127.0.0.1:6174/projects/verification/frames/reference-audit verified the rendered workbench frame, temporary Streamable HTTP connector card with feynman_connector_tools/feynman_connector_call runtime text, temporary allowed permission-grant card, zero browser console errors, and cleanup back to zero custom connectors/grants.
- Next: Add local stdio and SSE connector transports, UI approval cards for ask grants, and agent-specific connector assignments/exclusions.

2026-07-01 11:09 PDT — open-science-workbench-review-action Copy Section

- Objective: Fix the composer Request review action so the workbench behaves more like Claude Science's in-frame reviewer instead of pasting review instructions into chat.
- Researched: Re-drove installed Claude Science and confirmed its composer Request review starts a reviewer child frame from the chat surface. Re-read Pi 0.80.3 RPC, prompt-template, extension, and session docs; Pi RPC prompt expands prompt templates and the package prompts/review.md command is available as /review <artifact>.
- Changed: Added a first-class workbench review request path. The authenticated /api/chat/review/request route selects the primary review artifact, submits /review <artifact> through the existing persisted workbench chat/Pi path, records the transcript/tool event, and refreshes workbench state. The composer plus-menu action now calls that route, shows an in-chat reviewing state, and targets the active run's primary output artifact rather than the side-pane selection.
- Verified: npm run typecheck; npm run build; npm run architecture:check; git diff --check; focused workbench/review tests; full npm test (367/367); and a rebuilt-server in-app browser smoke with a fixture Pi executor. Browser verification opened Verification, clicked composer Request review, and confirmed the transcript contained /review outputs/scaling-laws.md, not notes/scaling-laws-verification.md; the fixture reply rendered in chat and the composer input stayed empty. Restarted the real local workbench on http://127.0.0.1:6174/projects/verification/frames/reference-audit?token=QxvLzneQw5haG_sqC0HsRZYfoUicATPg.
- Next: Build the MCP/package/extension execution adapter for saved custom connectors and explicit grant enforcement.

2026-07-01 10:43 PDT — open-science-workbench-runtime-context Copy Section

- Objective: Respond to the "chat inside it" critique by making the in-app Pi chat aware of the same configured science resources that the Claude Science-shaped Customize surface exposes.
- Researched: Re-read installed Pi 0.80.3 RPC, SDK, settings, package, security, usage, and extension docs. Pi docs confirm this version intentionally has no built-in MCP; app-owned capabilities need to flow through prompts, extensions, packages, or external adapters. Rechecked installed Claude Science SQLite/runtime evidence for frame_messages, MCP server/grant tables, cloud credentials, compute providers, memory categories, artifact environment snapshots, execution logs, and provenance panes.
- Changed: Added a shared workbench runtime context layer that formats custom connectors, credential env refs, grants, domains, compute hosts, and memory categories into normal chat prompts without secret values. Added a bundled Pi tool, feynman_workbench_context, so Pi can inspect sanitized workbench resources during a turn. Notebook executions now persist feynman.workbenchEnvironmentSnapshot.v1 records that include OS/runtime/resource context, and connector diagnostics now state the real bridge plus the remaining MCP adapter boundary.
- Verified: npm run typecheck; npm run build; npm run architecture:check; git diff --check; focused runtime-context tests; full npm test (366/366); and fresh rebuilt-server in-app browser smoke on http://127.0.0.1:6174/projects/verification/frames/reference-audit. Browser verification opened the real project frame/transcript, opened Customize, selected Connectors, verified the temporary runtime-context connector card plus feynman_workbench_context bridge diagnostic, saw zero console errors, then removed the temporary connector and confirmed customConnectors: 0.
- Next: Build the MCP/package/extension execution adapter for saved custom connectors and explicit grant enforcement.

2026-07-01 09:50 PDT — open-science-workbench-settings-control-plane Copy Section

- Objective: Respond to the Claude Science parity critique by making the Customize surface a real science-app settings/control plane instead of a generic resource-card drawer.
- Researched: Re-drove the installed Claude Science local app and confirmed its Settings sections: Skills, Connectors, Specialists, Memory, Compute, Network, Permissions, Credentials, Storage, Usage, and General. Re-read Pi 0.80.3 docs for RPC embedding, package sources/filtering, project trust, extension execution, settings, usage, and the no-built-in-sandbox boundary. Rechecked current OpenCode and Conductor references for the relevant control-plane cues: multi-session/local desktop agent UX, provider credentials, isolated/parallel agent work, event/dashboard visibility, and settings/env surfaces.
- Changed: Replaced the workbench Customize resource grouping with Claude Science-shaped sections while keeping Feynman semantics. Skills now include prompt templates in the Skills tab; Connectors are grouped by configured/core/optional/project extensions; Memory, Compute, Network, Permissions, Credentials, Storage, Usage, and General are populated from local Pi/Feynman state, package manifests, web-access status, environment-variable presence, artifact/session counts, runtime versions, and trust/package boundaries. The UI now renders subsection headings inside each Settings tab.
- Verified: API state returned the 11 Settings groups with counts 33/8/4/3/6/6/5/10/5/3/4. Headless Chrome smoke on the live local workbench verified the rendered modal tabs, Network/Credentials/Storage content, zero console errors, and zero tab/card overflow; screenshot /tmp/feynman-settings-claude-science-structure.png. npm run typecheck, npm run build, npm run architecture:check, git diff --check, focused workbench tests (27/27), and full npm test (361/361) passed.
- Next: Add deeper custom connector/tool-grant mutation paths and real credential connection flows rather than read-only inventory cards.

2026-07-01 08:09 PDT — issue-sweep-workbench-clean-repeat Copy Section

- Objective: Run the recurring Feynman AI researcher intake sweep from the actual dirty local main checkout while preserving unrelated workbench/package changes and making no GitHub writes.
- Checked: Local main is one commit ahead of origin/main at 6c84b24 with the existing dirty workbench/package slice preserved. Live GitHub has open issue #182 only, zero open PRs, and latest main workflow run Publish and Release 28343487961 succeeded at cb5fa56. Latest GitHub release remains v0.3.5 with release assets; npm latest remains @companion-ai/[email protected]; local/package Pi remains 0.80.3; @companion-ai/alpha-hub remains 0.1.3.
- Decisions: No product code change was needed. Issue #182 stays deferred because the latest issue/comment evidence still points to alphaXiv/Clerk redirect behavior before Feynman/alpha-hub receives a callback code, this machine's source feynman alpha status succeeds, and no fresh current-version logged-out callback trace proves a Feynman-owned defect. Open PR classification is empty. Contributor refs remain non-actionable: pr4fork/main has no commits ahead, origin/fix/deepresearch-local-model-warning is one stale local-model warning commit, and sampled forks remain Overleaf/admin export, provider/runtime, Windows/platform, fork docs, or fork-specific extension work outside the narrow research-loop bar.
- Package freshness: Root and website production audits found 0 vulnerabilities. Remaining root drift is non-security (@clack/prompts, @types/node, fast-xml-parser, posthog-node); website drift is non-security Astro/React/Tailwind/ESLint/UI-tooling drift. No drift maps to an open research-loop defect.
- Verified: npm run architecture:check; focused workbench/runtime tests (39/39); full npm test (352/352); npm run typecheck; npm run build; website npm run lint; website npm run typecheck; website npm run build (33 pages); root and website npm audit --omit=dev; source feynman alpha --help; source feynman alpha status; git diff --check; npm pack --dry-run (159 files, package size 52.4 MB); and temp installed-tarball smoke passed. The installed tarball printed 0.3.5, rendered help, and its runtime archive contains @companion-ai/alpha-hub plus @earendil-works/pi-coding-agent, pi-ai, pi-agent-core, and pi-tui.
- Next: Keep watching #182 for a fresh current-version logged-out OAuth callback trace. Preserve the still-dirty workbench/package slice unless explicitly asked to publish it.

2026-07-01 00:41 PDT — open-science-workbench-kernel-notebook Copy Section

- Objective: Respond to the "chat inside it" / insufficient-research critique by replacing the artifact-list Notebook pane with a Pi-backed code-cell surface closer to Claude Science's kernel notebook.
- Researched: Re-read installed Pi 0.80.3 RPC, SDK, and session-format docs plus the current Feynman workbench execution scanner. Reused the installed Claude Science bundle evidence for KernelNotebookPane, useExecutionLog, ProvenancePane, and execution-log/verification-check schemas: Claude Science centers notebook cells on execution records with code, output, language, environment, files written, and review context.
- Changed: Made the right-pane Notebook tab prefer real execution records with extracted Pi code over artifact cells; each rendered cell now shows a bracketed cell index, language/environment/source id, status, code, output, details, and read/wrote artifact links. Artifact notebook rows remain as the fallback/file trail. Added a focused notebook stylesheet and wired it into the workbench style bundle.
- Verified: Focused tests/workbench.test.ts passed (18/18); npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test (345/345) passed. A headless Chrome CDP smoke against a throwaway Pi JSONL workspace confirmed kernel-notebook-pane rendered with one Pi-backed Python code cell, output Saved outputs/producer-result.md, file read/write links, and zero visible-overflow elements. Screenshot: /tmp/feynman-kernel-notebook.png.
- Next: Add direct kernel/code execution from the notebook surface or composer, then promote verification checks and artifact versions into structured records rather than best-effort scans.

2026-07-01 00:23 PDT — open-science-workbench-producer-context Copy Section

- Objective: Respond to the Claude Science parity critique by making selected artifacts show the producer code, producer messages, and producer environment/details from real Pi session data instead of generic workspace scan text.
- Researched: Re-read installed Pi 0.80.3 session-format, RPC, SDK, extension, AgentSession, RPC event, and SessionManager docs/source. Verified Pi session JSONL entries store assistant toolCall arguments, toolResult content/details, bash execution messages, and stable toolCallId correlation. Reused the installed Claude Science public/product and local-app evidence that artifact history is organized around exact code, environment, conversation/messages, execution, and review.
- Changed: Extended workbench tool events to preserve Pi tool names, input arguments, result details, and error state; derived execution records directly from Pi session JSONL files by correlating assistant tool calls with tool results; attached producer code, producer messages, details, language, environment, and artifact links to execution records; added a selected-artifact Messages tab; and made the Code and Environment tabs prefer linked producer records before falling back to local content/workspace metadata.
- Verified: Focused tests/workbench.test.ts passed (18/18), including a new Pi JSONL producer fixture; npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test (345/345) passed. A live Chrome/Playwright smoke against a throwaway workbench workspace confirmed preview tabs include Messages, producer code renders for outputs/producer-result.md, producer messages include Saved outputs/producer-result.md, the environment pane shows Pi session details including Python 3.12 and tool-code, and the artifact Execution tab renders 2 rows. Screenshot: /tmp/feynman-producer-tabs.png.
- Next: Add richer notebook/code-cell execution surfaces and structured verification checks equivalent to Claude Science's kernel notebook and reviewer panes.

2026-06-30 22:17 PDT — open-science-workbench-execution-log Copy Section

- Objective: Close the next Claude Science parity gap by giving Feynman a frame-level execution ledger and selected-artifact producer links.
- Researched: Re-read installed Pi 0.80.3 session/RPC/SDK/extension docs for prompt, steer, abort, queued messages, JSONL session entries, tool lifecycle events, and AgentSession event subscriptions. Queried the installed Claude Science SQLite schema for execution_log, verification_checks, artifacts, artifact_versions, artifact_dependencies, frames, and frame_messages, then confirmed seeded artifact versions carry extracted code and metadata while execution/verification tables are empty in the sample DB.
- Changed: Added typed WorkbenchExecutionRecord state, split execution scanning into src/workbench/execution.ts, derived execution events from local artifact writes plus persisted workbench/Pi chat session messages/tool events/timeline entries, linked events to artifact paths when the artifact is explicitly named, added a right-pane Execution tab, and added a selected-artifact Execution preview tab.
- Verified: npm run typecheck, focused tests/workbench.test.ts (17/17), npm run build, npm run architecture:check, and git diff --check passed. In-app browser smoke against http://127.0.0.1:49921/projects/verification/frames/reference-audit confirmed the right Execution pane renders 29 events, the artifact Execution tab renders 21 rows for the selected artifact, preview tabs include Execution, right tabs include Execution, and a layout geometry check found zero row overlap or overflow across 50 visible execution rows.
- Next: Add richer notebook/code-cell execution surfaces equivalent to Claude Science's kernel notebook pane, then promote environment snapshots and verification checks from best-effort local scans into structured records.

2026-06-30 22:02 PDT — open-science-workbench-science-previews Copy Section

- Objective: Use the installed Claude Science app as the reference and move Feynman toward functional parity for scientific artifact previews.
- Researched: Opened the running Claude Science app from a fresh nonce URL, drove the dashboard, Example project, Files overlay, CSV artifact split view, and IS621 PDB artifact route. Inspected the local Claude Science runtime bundle and SQLite DB to identify frame/artifact routes, content types, artifact version storage paths, and preview chunks for CSV, FASTA, PDB, PDF, image, genome, sequence, structure, molecule, notebook, provenance, and execution-log surfaces.
- Changed: Added typed Feynman workbench previews for CSV/TSV tables with row/column metadata, FASTA sequence cards with residue counts, PDB structure previews with style controls plus canvas rotate/zoom/pan behavior, and inline image/PDF rendering through the existing safe download endpoint. Extended scanner/content-type/language handling for FASTA, PDB, and TSV while preserving /api/file as text-only for binary media.
- Verified: Focused tests/workbench.test.ts (16/16), npm run typecheck, npm run build, npm run architecture:check, git diff --check, and full npm test (343/343) passed. Browser smoke against a temporary workbench workspace confirmed PDB structure controls and canvas (/tmp/feynman-science-pdb-preview.png), CSV table rendering (/tmp/feynman-science-csv-preview.png), and FASTA sequence rendering (/tmp/feynman-science-fasta-preview.png). Claude Science reference screenshots were saved at /tmp/claude-science-frame-current.png, /tmp/claude-science-files-overlay.png, /tmp/claude-science-csv-preview.png, and /tmp/claude-science-pdb-current.png.
- Next: Build the frame-level execution log and artifact-producing-turn links from Pi tool events and Feynman artifact writes, then expose structured environment snapshots and verification checks.

2026-06-30 21:47 PDT — open-science-workbench-live-chat-controls Copy Section

- Objective: Close the immediate "chat inside it" gap by making the workbench composer behave like a live research frame while a Pi-backed turn is still running.
- Researched: Drove the installed Claude Science dashboard/frame/artifact split view, inspected its local runtime bundle and SQLite tables for frames/messages/artifacts/execution/provenance, and re-read installed Pi 0.80.3 RPC/SDK/session docs for prompt, steer, abort, queue, session state, and streaming events.
- Changed: Kept the composer input enabled during active Pi runs, changed Send to Queue while running, added Stop, wired queued messages through Pi RPC steer, wired Stop through Pi RPC abort, preserved queued transcript messages across stream writes, and mapped aborted Pi turns to a stopped chat state instead of a generic error.
- Verified: npm run typecheck, focused tests/workbench.test.ts (16/16), npm run build, npm run architecture:check, git diff --check, full npm test (343/343), and a headless Chrome smoke with a delayed executor passed. The smoke confirmed running-state controls (Queue, visible Stop, enabled input) and clean reset after completion; screenshot saved at /tmp/feynman-live-chat-running.png.
- Next: Add Claude Science-style scientific artifact previewers and deeper execution/provenance surfaces from Pi tool events, Feynman artifact writes, and verification records.

2026-06-30 21:31 PDT — intake-sweep-workbench-packaging-fix Copy Section

- Objective: Run the recurring Feynman AI researcher intake sweep against the actual dirty local tree while preserving unrelated workbench/package changes.
- Checked: Live GitHub queue still has open issue #182 only, zero open PRs, latest main workflow run Publish and Release success at cb5fa56, latest release v0.3.5, npm latest @companion-ai/[email protected], alpha-hub latest 0.1.3, and Pi latest/current 0.80.3. Contributor refs remain stale or outside the research-loop bar: local-model warning, Overleaf/admin export, provider/runtime forks, Windows/platform work, fork docs, and fork-specific parallel-tool extension work.
- Decision: Keep issue #182 deferred because the thread still points to alphaXiv/Clerk redirect behavior before Feynman can exchange a token, this machine's feynman alpha status succeeds, and no current-version Feynman-owned callback trace was added. No PR was open to classify beyond an empty PR queue.
- Changed: Fixed the dirty workbench package gate by keeping generated plan mutation ownership in src/workbench/plan.ts and ensuring server/tests import that module instead of treating chat as the plan owner. No GitHub writes, pushes, merges, closes, or comments were performed.
- Verified: npm run architecture:check, focused tests/workbench.test.ts (16/16), full npm test (343/343), npm run typecheck, npm run build, website npm run lint, website npm run typecheck, website npm run build (33 pages), root and website npm audit --omit=dev, source feynman alpha --help, source feynman alpha status, git diff --check, npm pack --dry-run, and temp installed-tarball smoke passed. The installed tarball printed 0.3.5, rendered help, and its runtime archive contains Pi coding-agent, pi-ai, pi-agent-core, pi-tui, and alpha-hub package entries.
- Next: Keep watching #182 for a fresh logged-out OAuth callback trace on current Feynman/alpha-hub; preserve the still-dirty local workbench slice unless explicitly asked to publish it.

2026-06-30 21:29 PDT — open-science-workbench-generated-plan Copy Section

- Objective: Make the workbench behave more like Claude Science's science-frame planning loop by turning "Plan next step" into a real generated plan artifact with approval and step-status mutation.
- Researched: Re-read Pi 0.80.3 SDK/RPC/session/extension docs and the installed Claude Science app/database/bundle evidence for generate_plan, update_step_status, plan approval UI, artifact versions, execution logs, verification checks, and scientific artifact panes.
- Changed: Added typed feynman.workbenchPlan.v1 JSON plans in outputs/.plans/<session>.workbench-plan.json, plan scanning through /api/state, authenticated plan generate/approve/reject/step-update APIs, visible approval and step controls in the transcript/right-pane Plan UI, and split the plan lifecycle into src/workbench/plan.ts so chat/session persistence stays separate.
- Verified: npm run typecheck, focused tests/workbench.test.ts (16/16), npm run build, npm run architecture:check, git diff --check, and full npm test (343/343) passed. Headless Chrome UI smoke on a temporary workspace generated a plan, rendered the approval bar, approved it, completed the first step, confirmed persisted JSON had plan status running and first-step status complete, and saved /tmp/feynman-workbench-generated-plan-smoke.png.
- Next: Connect Pi/Feynman tool events and artifact writes into a frame-level execution log, then add richer scientific previewers and real skills/connectors/compute management.

2026-06-30 21:07 PDT — open-science-workbench-plan-status Copy Section

- Objective: Move the workbench closer to Claude Science's science-frame workflow by making plan/status state visible while chat remains active inside the research session.
- Researched: Reused the installed Claude Science evidence from the project surface, View plan flow, plus menu, and plan/status tool counts, then mapped the slice to Feynman's existing outputs/.plans, notebook cells, verification artifacts, provenance sidecars, and Pi-backed chat state.
- Changed: Added a Plan right-pane tab, a transcript Execution plan card, and plus-menu actions for View plan, Your files, Plan next step, Request review, Save as skill, and Attach from files. The plan model is derived from real selected-run artifacts across plan, evidence, synthesis, verification, and provenance states. Split right-pane rendering into ui-client-panes.ts and split agent/plan styles into focused modules so the workbench did not add new architecture-size warnings.
- Verified: npm run typecheck, focused tests/workbench.test.ts (14/14), npm run build, npm run architecture:check, git diff --check, and full npm test (341/341) passed. Chrome DevTools Protocol smoke against http://127.0.0.1:61381/projects/verification/frames/reference-audit confirmed the transcript plan card is visible, the Plan pane renders 5 steps, View plan and Your files composer actions switch panes, and there were zero page exceptions. Screenshots: /tmp/feynman-workbench-plan-card-visible.png, /tmp/feynman-workbench-plan-pane-visible.png, /tmp/feynman-workbench-plus-view-plan-visible.png, and crop /tmp/feynman-workbench-plan-card-crop.png.
- Next: Add a generated plan mutation path equivalent to Claude Science's generate_plan/update_step_status, then connect Pi tool events and Feynman artifact writes into a frame-level execution log.

2026-06-30 19:19 PDT — open-science-workbench-rpc-chat Copy Section

- Objective: Correct the workbench chat from stable one-shot Pi turns to a real inside-the-app session bridge like Claude Science's persistent research frame.
- Researched: Drove the installed Claude Science app locally through the Example project, Files view, Customize modal, composer plus menu, session options, model menu, and plan/artifact split view. Rechecked the Claude Science SQLite schema/tool counts and unpacked bundle chunk names, then re-read Pi RPC/SDK/session docs and source for exact --session-id, JSONL framing, prompt, state, entries, tree, model, thinking, and event behavior.
- Changed: Replaced the workbench streaming runtime with a long-lived per-session Pi RPC client using strict LF-only JSONL parsing, exact stable --session-id reuse, prompt response correlation, live message/tool event forwarding, server-close cleanup, and a smaller RPC prompt that avoids replaying prior transcript turns into Pi history. Added a protocol regression test and updated the open-science parity plan.
- Verified: npm run typecheck, focused tests/workbench.test.ts (14/14), npm run build, and npm run architecture:check passed. Browser smoke against http://127.0.0.1:63637/projects/verification/frames/reference-audit sent a real prompt through the UI and got assistant reply feynman-rpc-smoke; the Pi strip and Agent tab showed the same active feynman-workbench-reference-audit JSONL session with 2 messages, model, cwd, thinking level, and timeline. Screenshots: /tmp/feynman-workbench-rpc-smoke.png and /tmp/feynman-workbench-rpc-agent-pane.png.
- Next: Add Claude Science-style generated plan/status cards and artifact lineage/execution-log surfaces from Pi events and Feynman artifact writes.

2026-06-30 19:18 PDT — open-science-workbench-agent-pane Copy Section

- Objective: Move the Feynman workbench closer to Claude Science's chat-inside-a-research-frame control plane by grounding the UI in real Pi session data.
- Researched: Inspected the installed Claude Science bundle/runtime/SQLite org database and Pi Coding Agent docs for sessions, JSON event mode, SDK, RPC, extensions, and session format. Claude Science's seed has projects/frames/messages/artifacts around real science workflows; Pi exposes persistent JSONL session trees, event streams, entries, tools, branch state, and commands for embedded UIs.
- Changed: Added an Agent tab to the workbench right pane, and extended Pi session parsing to expose the current-branch timeline plus per-tool summaries from the real Pi JSONL session file. Added outputs/.plans/open-science-workbench.md as the durable parity checklist.
- Verified: npm run typecheck, focused tests/workbench.test.ts (13/13), npm run build, npm run architecture:check, full npm test (340/340), and git diff --check passed. Browser smoke against http://127.0.0.1:56964/projects/verification/frames/reference-audit confirmed the Agent tab opens and renders the Pi session status, metrics, runtime, tools, and timeline states without layout overlap; screenshot saved at /tmp/feynman-workbench-agent-pane.png.
- Next: Replace spawn-per-turn print mode with a long-lived Pi SDK/RPC runtime per workbench session, then add execution-log and plan-approval surfaces.

2026-06-30 18:39 PDT — open-science-workbench-pi-session-provenance Copy Section