# Technical Documentation: abhigyanpatwari/GitNexus

> ℹ️ **Provenance:** Multi-Tier Ingestion · [CodeWiki Reference](https://codewiki.google/github.com/abhigyanpatwari/GitNexus)

### Overview (README.md)

# GitNexus 

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  <p><strong>The context engine for Enterprise Codebases</strong></p>

  <p>
    Indexes any codebase into a knowledge graph — every dependency, call chain, cluster, and execution flow —
    then exposes it through smart MCP tools so AI agents never miss code.
  </p>

  <p>
    💬 <a href="https://discord.gg/MgJrmsqr62">Discord</a> ·
    🌐 <a href="https://gitnexus.vercel.app">Web UI</a> ·
  </p>

</div>

https://github.com/user-attachments/assets/172685ba-8e54-4ea7-9ad1-e31a3398da72

> _Like DeepWiki, but deeper._ DeepWiki helps you _understand_ code. GitNexus lets you _analyze_ it — a knowledge graph tracks every relationship, not just descriptions.

**TL;DR:** The **CLI + MCP** makes your AI agent reliable — it gives Cursor, Claude Code, Antigravity, Codex, and friends a deep architectural view of your codebase so they stop missing dependencies, breaking call chains, and shipping blind edits. Even smaller models get full architectural clarity. The **Web UI** is a quick way to chat with any repo in the browser.

## Quick Start

```bash
# 1. Index your repo (run from repo root)
npx gitnexus analyze

# 2. Connect your editors (one-time, auto-detects Claude Code, Cursor, Codex, …)
npx gitnexus setup
```

That's it. `analyze` indexes the codebase, installs agent skills, registers Claude Code hooks, and creates `AGENTS.md` / `CLAUDE.md` context files — all in one command. `setup` writes the MCP config so your AI agent can use the graph.

<details>
<summary><strong>Install problems?</strong> npm 11 crash · slow cold install · no C++ toolchain</summary>

> **On npm 11.x?** `npx` can crash during install with `Cannot destructure property 'package' of 'node.target'` (an npm/arborist bug, before GitNexus runs). Use pnpm instead — it builds the native deps explicitly:
>
> ```bash
> pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyze
> ```
>
> Or install globally (`npm install gitnexus@latest`) and run `gitnexus analyze`. See [#1939](https://github.com/abhigyanpatwari/GitNexus/issues/1939).

> **Fastest MCP startup:** install globally (`npm i gitnexus`) before running `gitnexus setup` — this writes an absolute-path MCP config that bypasses `npx` entirely. On a cold cache, an `npx`-based MCP install can exceed Claude Code's `MCP_TIMEOUT` default (~30s).

> **No C++ toolchain?** Set `GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1` before `npm install gitnexus` to skip the vendored grammar materialize/build for `tree-sitter-dart`, `tree-sitter-proto`, `tree-sitter-swift`, and `tree-sitter-kotlin` — those four languages won't be parsed, but install completes in seconds without `python3`/`make`/`g++`. Strict `=1` only — any other value falls through to the rebuild.

> **Local embeddings are opt-in.** Default `npm install` does not fetch `@huggingface/transformers` or `onnxruntime-node`. Run `gitnexus embeddings install` (or `gitnexus analyze --embeddings`, which auto-heals) to fetch the stack through your npm registry config into `~/.gitnexus/embedding-runtime`. CUDA GPU binaries still use NuGet via `--cuda` ([#2370](https://github.com/abhigyanpatwari/GitNexus/issues/2370)). The prefix needs Node with `module.registerHooks` (≥ 22.15 on 22.x, ≥ 23.5 on 23.x). A leftover 1.6.12 package-first tree is residual until a clean reinstall; `--force` only refreshes prefix overrides.

> **About `tree-sitter-kotlin`:** like Dart/Proto/Swift, Kotlin is a **vendored** grammar (under `gitnexus/vendor/tree-sitter-kotlin`). Upstream ships **source only** (no prebuilt binaries), so GitNexus cross-builds the platform prebuilds itself (via the `build-tree-sitter-prebuilds` GitHub Actions workflow) and vendors them — the same uniform pipeline used for Dart, Proto, and Swift. `node-gyp-build` selects the right `.node` at require time, so **no C/C++ toolchain is needed**. If no prebuild matches your platform-arch, only Kotlin (`.kt`/`.kts`) parsing is unavailable; the rest of `gitnexus` is unaffected.

</details>

### Deploy to Render

Deploy GitNexus in one click:

[](https://render.com/deploy?repo=https://github.com/abhigyanpatwari/GitNexus)

The Blueprint creates two services. `gitnexus-server` runs `gitnexus serve` as a private service: no public URL, reachable only over Render's private network, with a persistent disk for indexes and cloned repos. `gitnexus-web` is the public one. It serves the UI and reverse-proxies `/api/*` to the server, so the browser talks to a single origin.

At the Blueprint's defaults this runs about **$35/month**: $25 for the server's `standard` instance, $7 for the web service's `starter` instance, and $2.50 for the 10 GB disk. See [Render's pricing](https://render.com/pricing) for other plans.

The deploy generates an access token, and the UI asks for it on first use:

1. Open the `gitnexus-web` service in your [Render dashboard](https://dashboard.render.com/).
2. Copy `GITNEXUS_SERVE_AUTH_TOKEN` from its **Environment** tab.
3. Load the site and paste the token into the prompt (or the settings panel).

Every `/api/*` request carries that token as a header, and the proxy answers `401` without it. The browser keeps it in `sessionStorage`, so a new tab asks again. To rotate it, edit the environment variable and redeploy.

The proxy strips `Origin` before forwarding, so the server's CSRF guard does nothing for proxied traffic; it passes `Origin`-less requests through by design. The token is the only control on this deploy, not a second layer behind the guard. Anyone holding it can read every indexed repo. See [SECURITY.md](SECURITY.md#hosted-deploys-on-render).

Indexing is memory-bound. If `gitnexus-server` runs out of memory on a large repo, raise its `plan`, which sets available RAM: `standard` is 2 GB, `pro` is 4 GB. Raise `sizeGB` only if the disk fills with clones and indexes.

### Deploy to RepoCloud

[](https://repocloud.io/details/gitnexus/)

## Two Ways to Use GitNexus

|             | **CLI + MCP** (recommended)                                                        | **Web UI**                                                           |
| ----------- | ---------------------------------------------------------------------------------- | -------------------------------------------------------------------- |
| **What**    | Index repos locally, connect AI agents via MCP                                     | Visual graph explorer + AI chat in browser                           |
| **For**     | Daily development with Cursor, Claude Code, Antigravity, Codex, Windsurf, OpenCode | Quick exploration, demos, one-off analysis                           |
| **Scale**   | Full repos, any size                                                               | Limited by browser memory (~5k files), or unlimited via backend mode |
| **Install** | `npm install gitnexus`                                                          | No install — [gitnexus.vercel.app](https://gitnexus.vercel.app)      |
| **Storage** | LadybugDB native (fast, persistent)                                                | LadybugDB WASM (in-memory, per session)                              |
| **Parsing** | Tree-sitter native bindings                                                        | Tree-sitter WASM                                                     |
| **Privacy** | Everything local, no network                                                       | Everything in-browser, no server                                     |

> **Bridge mode:** `gitnexus serve` connects the two — the web UI auto-detects the local server and can browse all your CLI-indexed repos without re-uploading or re-indexing.

## Why a Knowledge Graph?

Tools like **Cursor**, **Claude Code**, **Codex**, **Cline**, **Roo Code**, and **Windsurf** are powerful — but they don't truly know your codebase structure. So this happens:

1. AI edits `UserService.validate()`
2. Doesn't know 47 functions depend on its return type
3. **Breaking changes ship**

Traditional Graph RAG gives the LLM raw graph edges and hopes it explores enough. GitNexus **precomputes structure at index time** — clustering, tracing, scoring — so tools return complete context in one call:

```mermaid
flowchart TB
    subgraph Traditional["Traditional Graph RAG"]
        direction TB
        U1["User: What depends on UserService?"]
        U1 --> LLM1["LLM receives raw graph"]
        LLM1 --> Q1["Query 1: Find callers"]
        Q1 --> Q2["Query 2: What files?"]
        Q2 --> Q3["Query 3: Filter tests?"]
        Q3 --> Q4["Query 4: High-risk?"]
        Q4 --> OUT1["Answer after 4+ queries"]
    end

    subgraph GN["GitNexus Smart Tools"]
        direction TB
        U2["User: What depends on UserService?"]
        U2 --> TOOL["impact UserService upstream"]
        TOOL --> PRECOMP["Pre-structured response:
        8 callers, 3 clusters, all 90%+ confidence"]
        PRECOMP --> OUT2["Complete answer, 1 query"]
    end
```

**Core innovation: Precomputed Relational Intelligence**

- **Reliability** — the LLM can't miss context; it's already in the tool response
- **Token efficiency** — no 10-query chains to understand one function
- **Model democratization** — smaller LLMs work because the tools do the heavy lifting

## What Your AI Agent Gets

### 19 MCP tools (17 per-repo + 2 group)

| Tool             | What It Does                                                           |
| ---------------- | ---------------------------------------------------------------------- |
| `list_repos`     | Discover all indexed repositories (paginated — `limit`/`offset`)       |
| `query`          | Process-grouped hybrid search (BM25 + semantic + RRF)                  |
| `context`        | 360-degree symbol view — categorized refs, process participation       |
| `impact`         | Blast radius analysis with depth grouping and confidence               |
| `trace`          | Shortest directed path between two symbols (call + class-member edges) |
| `detect_changes` | Git-diff impact — maps changed lines to affected processes             |
| `check`          | Read-only structural checks against the indexed graph                  |
| `rename`         | Multi-file coordinated rename with graph + text search                 |
| `cypher`         | Raw Cypher graph queries                                               |
| `route_map`      | API route map — which components fetch which endpoints, and handlers   |
| `tool_map`       | MCP/RPC tool definitions — where they're defined and handled           |
| `shape_check`    | Validate API response shapes against consumers' property accesses      |
| `api_impact`     | Pre-change impact report for an API route handler                      |
| `explain`        | Explain persisted taint findings (source→sink flows, `--pdg` indexes)  |
| `pdg_query`      | Query control/data dependence at statement level (`--pdg` indexes)     |
| `read_file`      | Read a checkout file (optional 0-indexed slice; `maxLines` cap)        |
| `grep`           | Regex search of the working tree for indexed files (1-based hits)      |
| `group_list`     | List configured repository groups                                      |
| `group_sync`     | Rebuild a group's Contract Registry and cross-repo links               |

> Per-repo read-only tools take an optional `repo` parameter. Omit it when only one repo is indexed, an MCP default is configured, or the GitNexus process cwd is inside a registered path without crossing into an unindexed nested Git checkout; otherwise pass it explicitly. Mutating tools require `repo` when multiple repos are indexed and no MCP default exists. Per-repo tools also take an optional `branch` for indexes pinned with `gitnexus analyze --branch`, except `read_file` and `grep`, which read the checkout and do not accept `branch`. Omitting `branch` queries the workspace index, which follows your checked-out working tree — switching branches and re-running `gitnexus analyze` updates it incrementally. `explain` and `pdg_query` need an index built with `gitnexus analyze --pdg`.

### Resources for instant context

| Resource                                | Purpose                                              |
| --------------------------------------- | ---------------------------------------------------- |
| `gitnexus://repos`                      | List all indexed repositories (read this first)      |
| `gitnexus://setup`                      | Setup and usage guidance for agents                  |
| `gitnexus://repo/{name}/context`        | Codebase stats, staleness check, and available tools |
| `gitnexus://repo/{name}/clusters`       | All functional clusters with cohesion scores         |
| `gitnexus://repo/{name}/cluster/{name}` | Cluster members and details                          |
| `gitnexus://repo/{name}/processes`      | All execution flows                                  |
| `gitnexus://repo/{name}/process/{name}` | Full process trace with steps                        |
| `gitnexus://repo/{name}/schema`         | Graph schema for Cypher queries                      |
| `gitnexus://group/{name}/contracts`     | A group's extracted contracts and cross-links        |
| `gitnexus://group/{name}/status`        | Staleness of repos in a group                        |

### 2 MCP prompts for guided workflows

| Prompt          | What It Does                                                              |
| --------------- | ------------------------------------------------------------------------- |
| `detect_impact` | Pre-commit change analysis — scope, affected processes, risk level        |
| `generate_map`  | Architecture documentation from the knowledge graph with mermaid diagrams |

### Agent skills installed to `.claude/skills/` and `.agents/skills/` (if `.agents/` exists) automatically

- **Exploring** — navigate unfamiliar code using the knowledge graph
- **Debugging** — trace bugs through call chains
- **Impact Analysis** — analyze blast radius before changes
- **Refactoring** — plan safe refactors using dependency mapping
- **Guide** — GitNexus tool/resource/schema reference for the agent
- **CLI** — run analyze/status/clean/wiki commands on request
- **PDG Query** — statement-level control/data dependence queries (`--pdg` index)
- **Taint Analysis** — source→sink data-flow findings (`--pdg` index)
- **Plan** (`/gitnexus-plan`) — implementation-ready engineering plans backed by the graph and PDG slices
- **Work** (`/gitnexus-work`) — executes a plan as impact-checked, `detect_changes`-gated atomic commits
- **Review** (`/gitnexus-review`) — graph-backed review of a PR, branch, range, or local diff, with taint pass and per-domain expert lenses
- **LFG** (`/gitnexus-lfg`) — the full pipeline: plan → user gate → work → review

**Repo-specific skills** — run `gitnexus analyze --skills` and GitNexus detects the functional areas of your codebase (via Leiden community detection) and generates each one as a direct project skill under `.claude/skills/gitnexus-area-<name>/`. Each skill describes a module's key files, entry points, execution flows, and cross-area connections, and is regenerated on each `--skills` run to stay current.

When a repo contains an `.agents/` directory, the standard and generated skills are also mirrored to `.agents/skills/` (e.g. `.agents/skills/gitnexus-cli/`, `.agents/skills/gitnexus-area-<name>/`) so agents that read repo-local `.agents/skills/` (like Codex) stay in sync.

## Editor Setup

`gitnexus setup` auto-detects your editors and writes the correct global MCP config. Run it once. To configure only selected integrations, pass `--coding-agent`/`-c` with a comma-separated list, e.g. `gitnexus setup -c cursor,codex`.

| Editor                   | MCP | Skills | Hooks (auto-augment)                                                                                              | Support      |
| ------------------------ | --- | ------ | ----------------------------------------------------------------------------------------------------------------- | ------------ |
| **Claude Code**          | Yes | Yes    | Yes (PreToolUse + PostToolUse)                                                                                    | **Full**     |
| **Cursor**               | Yes | Yes    | Yes (postToolUse, [manual install](gitnexus-cursor-integration/README.md#hook-install))                           | **Full**     |
| **Antigravity** (Google) | Yes | Yes    | Yes (AfterTool, [Gemini CLI hooks schema](https://geminicli.com/docs/hooks/reference/))[¹](#fn-antigravity-hooks) | **Full**     |
| **Codex**                | Yes | Yes    | Yes (PreToolUse + PostToolUse, [Codex hooks](https://developers.openai.com/codex/hooks))                          | **Full**     |
| **Factory** (Droid)      | Yes | Yes    | Yes (PostToolUse, [plugin](gitnexus-factory-plugin/))                                                             | **Full**     |
| **OpenCode**             | Yes | Yes    | —                                                                                                                 | MCP + Skills |
| **CodeBuddy** (Tencent)  | Yes | Yes    | —                                                                                                                 | MCP + Skills |
| **Qoder** (Alibaba)      | Yes | Yes    | —                                                                                                                 | MCP + Skills |
| **Windsurf**             | Yes | —      | —                                                                                                                 | MCP          |

> **Full** means MCP tools + agent skills + hooks that enrich searches with graph context. **Claude Code** and **Codex** go deepest: their PreToolUse hooks enrich the search before it runs, and their PostToolUse hooks also detect a stale index after commits and prompt the agent to reindex. **Cursor**, **Antigravity**, and **Factory** augment from a post-tool hook only, so they enrich the result rather than the query and do not carry the stale-index hint.

<a id="fn-antigravity-hooks"></a>

> ¹ **Antigravity hooks** follow the [Gemini CLI hooks reference](https://geminicli.com/docs/hooks/reference/) (Antigravity 2.0 is the documented successor to Gemini CLI). Augmentation runs in `AfterTool` because `BeforeTool` has no context-injection channel in the Gemini contract — the agent sees graph context appended to the tool result via `hookSpecificOutput.additionalContext`. Stale-index hints land in the same channel after a successful `git commit/merge/rebase/cherry-pick/pull`. The schema may evolve if Antigravity-specific hook docs diverge from Gemini CLI's; the implementation will track those changes.

<details>
<summary><strong>Manual MCP configuration</strong> (if you prefer not to run <code>gitnexus setup</code>)</summary>

**Claude Code** (full support — MCP + skills + hooks):

```bash
# macOS / Linux
claude mcp add gitnexus -- npx -y gitnexus@latest mcp

# Windows
claude mcp add gitnexus -- cmd /c npx -y gitnexus@latest mcp
```

**Codex** (full support — MCP + skills + hooks):

```bash
codex mcp add gitnexus -- npx -y gitnexus@latest mcp
```

Or via `~/.codex/config.toml` (system scope) / `.codex/config.toml` (project scope):

```toml
[mcp_servers.gitnexus]
command = "npx"
args = ["-y", "gitnexus@latest", "mcp"]
```

Codex hooks (PreToolUse graph enrichment + PostToolUse stale-index detection in `~/.codex/hooks.json`, [same schema as Claude Code](https://developers.openai.com/codex/hooks)) need the bundled adapter script, so they are installed by `gitnexus setup -c codex` rather than manually.

Alternatively, install everything as a [Codex plugin](https://developers.openai.com/codex/plugins/build) (MCP + skills + hooks in one step):

```bash
codex plugin marketplace add abhigyanpatwari/GitNexus
# then inside Codex: /plugins → install "GitNexus"
```

> **Codex notes:** SessionStart is intentionally not registered — Codex reads [AGENTS.md natively](https://developers.openai.com/codex/guides/agents-md), which already carries the GitNexus context block. Newly installed hooks need a one-time approval in Codex via `/hooks` before they run. Pick **one** install route (`gitnexus setup -c codex` **or** the plugin): plugin hooks load alongside `~/.codex/hooks.json`, so installing both can fire duplicate hooks per tool call.

**Factory** (Droid) — MCP + skills via `gitnexus setup -c droid`, or add the server manually to `~/.factory/mcp.json` ([user scope](https://docs.factory.ai/cli/configuration/mcp), applies to all projects):

```json
{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}
```

`gitnexus setup -c droid` also installs skills to `~/.factory/skills/`. For the PostToolUse search-augment hook, install the bundled [`gitnexus-factory-plugin/`](gitnexus-factory-plugin/) — from a marketplace that includes this repo, run `droid plugin install gitnexus@<marketplace>`, or point Droid at it via `extraKnownMarketplaces` in `.factory/settings.json`. Factory reads [`AGENTS.md` natively](https://docs.factory.ai/), which already carries the GitNexus context block.

**Cursor** (`~/.cursor/mcp.json` — global, works for all projects):

```json
{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}
```

**Antigravity** (Google) — `~/.gemini/antigravity/mcp_config.json`:

```json
{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}
```

> `gitnexus setup` also merges an `AfterTool` entry into `~/.gemini/settings.json` (under the canonical [Gemini CLI hooks schema](https://geminicli.com/docs/hooks/reference/)) and installs skills to `~/.gemini/antigravity/skills/`. Existing user hooks are preserved. The hook adapter's path is rewritten at install time, so run `gitnexus setup` rather than hand-editing.

**OpenCode** (`~/.config/opencode/config.json`):

```json
{
  "mcp": {
    "gitnexus": {
      "type": "local",
      "command": ["gitnexus", "mcp"]
    }
  }
}
```

**CodeBuddy** (Tencent) — priority chain, edit the **first non-empty file that exists**: `~/.codebuddy/.mcp.json` (recommended) → `~/.codebuddy/mcp.json` (deprecated) → `~/.codebuddy.json` (legacy). CodeBuddy reads only the first existing file, so adding servers to a higher-priority file than the one currently in use would hide the servers below it. Create `~/.codebuddy/.mcp.json` only if none exist:

```json
{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}
```

**Qoder** (Alibaba) — `~/.qoder.json`:

```json
{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}
```

</details>

<details>
<summary><strong>MCP read-only mode</strong></summary>

Set `GITNEXUS_MCP_READ_ONLY=1` before starting the MCP server to expose only the proven single-repository read surface. Raw `cypher`, rename and group tools, group routing, and group resources are omitted from discovery and rejected before backend dispatch. Tool descriptions and generated setup/context resources are scrubbed so they do not recommend unavailable routes.

The default is unchanged when the variable is unset or `0`. Any other value fails server startup rather than silently weakening the policy.

</details>

<details>
<summary><strong>MCP repository policy</strong></summary>

Set `GITNEXUS_MCP_ALLOWED_REPOS` to a comma-separated list of canonical registry names or absolute indexed paths. Entries are trimmed, resolved against the registry, and deduplicated at startup. When exactly one repository is allowed it becomes the implicit default; when several are allowed, callers must select one unless `GITNEXUS_MCP_DEFAULT_REPO` is also set.

The default repository must resolve to an allowed repository. Invalid, ambiguous, blank, or mismatched configuration fails startup before stdio or HTTP begins serving. The allowlist applies to tools, aliases, discovery, resources, templates, implicit resolution, and embedded HTTP; hidden repository details are not included in selection errors. Setting only `GITNEXUS_MCP_DEFAULT_REPO` chooses a default without restricting explicit repository selections. An allowed repository whose name is duplicated in the registry must be configured by path, and its context resource is only served for the unique name form.

</details>

<details>
<summary><strong>MCP response budgets</strong></summary>

The `query`, `context`, and `impact` tools accept an optional positive-integer `maxTokens` argument. It bounds the complete formatted MCP response, including hints and error text, using a deterministic four-UTF-8-bytes-per-token estimate. When truncation is required, the response ends with `…` and remains valid UTF-8.

Set `GITNEXUS_MCP_DEFAULT_MAX_TOKENS` to apply the same guardrail when callers do not send `maxTokens`. An explicit tool argument takes precedence. Leaving both unset preserves the existing response byte-for-byte; this is a transport guardrail, not semantic pagination or an exact model-specific tokenizer limit.

</details>

## CLI Reference

Everyday commands:

```bash
gitnexus setup                   # Configure MCP for detected editors (one-time; -c to select)
gitnexus analyze [path]          # Index a repository (or update a stale index)
gitnexus analyze [path] --watch  # Watch local files and serialize incremental refreshes
gitnexus mcp                     # Start MCP server (stdio) — serves all indexed repos
gitnexus serve                   # Start local HTTP server (multi-repo) for web UI connection
gitnexus eval-server             # Start lightweight evaluation HTTP tools (loopback by default)
gitnexus list                    # List all indexed repositories
gitnexus status                  # Show index status for current repo
gitnexus clean                   # Delete index for current repo
gitnexus wiki [path]             # Generate repository wiki from knowledge graph
gitnexus uninstall               # Preview removal of GitNexus MCP/skills/hooks (--force to apply)
```

You can also query the graph directly from the terminal — `gitnexus query`, `context`, `impact`, `trace`, `cypher`, `detect-changes`, and `check` mirror the MCP tools of the same names, and `gitnexus doctor` prints runtime platform capabilities.

`gitnexus analyze --watch` requires a Git repository. It runs one initial
analysis, then debounces scanner-admitted working-tree changes for 300 ms by
default and applies serialized incremental refreshes. Events arriving during a
refresh remain queued, and retryable failures retain the same batch with bounded
backoff. Invalid `.gitnexusrc` or ignore-file reloads pause ordinary refreshes
until the control file is fixed. Stop the watcher with Ctrl+C.

Watch mode accepts `--debounce`, `--workers`, `--worker-timeout`,
`--max-file-size`, `--max-processes`, `--max-process-branching`,
`--max-process-trace-depth`, `--max-entry-point-candidates`, `--branch`, `--pdg`, `--skip-fts`, `--name`, `--allow-duplicate-name`, and
`--verbose`. Explicit one-shot options such as `--force`, `--repair-fts`,
embedding flags, `--skills`, `--self-commit`, `--index-only`, and `--skip-git`
are rejected. Unsupported defaults from `.gitnexusrc` are ignored with a
warning rather than making an otherwise valid repository unwatchable.

POSIX requests clone-first copy-and-swap publication when the live index has no
orphan sidecars. Windows and sidecar fallback runs update in place: failures
known to occur before writes are retried, while a failure that may have mutated
the live index stops the watcher. Watch mode does not pull remotes. Running MCP
and `serve` processes reopen a newly published index automatically; MCP observes
the replacement on its next tool call, typically within five seconds, so no
restart is required.

<details>
<summary><strong>Authenticated <code>eval-server</code> binding</strong></summary>

`gitnexus eval-server` binds to `127.0.0.1` by default. Loopback bindings do not require authentication. Any non-loopback bind, including `0.0.0.0`, a LAN address, or a hostname that resolves to a LAN IPv4 address, requires `GITNEXUS_AUTH_TOKEN`. Every endpoint then requires an exact `Authorization: Bearer <token>` header.

```bash
GITNEXUS_AUTH_TOKEN='replace-me' gitnexus eval-server --host 0.0.0.0
```

The token may be set in the shell, `.env.local`, or `.env` in the working directory. Precedence is shell > `.env.local` > `.env`. Only `GITNEXUS_AUTH_TOKEN` is read from those files; their other values are not added to the process environment. Keep token files uncommitted.

</details>

<details>
<summary><strong>All <code>analyze</code> flags</strong></summary>

```
/* Detailed source-code truncated for AI context efficiency. */
```

`--skip-fts` (or `GITNEXUS_SKIP_FTS=1`) disables FTS extension loading and keyword-index construction for this analysis. Graph queries, communities, processes, and existing embeddings remain available. Status and search report "FTS disabled for this index". Remove both the flag and environment setting and run `analyze` again to restore keyword search, even at the same commit. Only the exact environment value `1` enables the opt-out; the flag takes precedence. It cannot be combined with `--repair-fts`. Disabling an existing FTS index may require one graph-store rebuild to avoid unsafe writes through native indexes.

`--spring-actuator` is explicitly opt-in and accepts either a JSON bundle keyed by `mappings`, `beans`, `conditions`, `configprops`, and/or `env`, or a directory containing endpoint-named JSON files. It confirms matching static nodes and adds conservative runtime-only routes, beans, and property keys. The configured input is excluded from source scanning; only normalized repository-relative exclusions are retained for future scans, never absolute paths. Env/configprops values, origins, condition messages, and source names are never persisted or printed. Because snapshots are external runtime state, an enabled run always rebuilds; the first later run without the option rebuilds once to remove runtime evidence. The same path can be set as `springActuator` in `.gitnexusrc`.

`--asyncapi-spec` is explicitly opt-in and accepts a directory of AsyncAPI documents or a single document; the path is resolved against the repository root, so a committed `docs/asyncapi` and an absolute cache written by something else both work. Each `operations[]` entry of an **AsyncAPI 3.x** document can contribute a `Destination` node keyed by broker and address, with `action: send` emitting `PUBLISHES_TO` and `action: receive` emitting `CONSUMES_FROM`, so a document and source code that name one address on one broker land on the same node. Edges start at the document, not at a callable — a document states that the service talks to an address, not which method does — and no address a document names is ever attached to an unresolved source site.

An operation must name a protocol, either through its own `bindings` or through the `servers[].protocol` of the servers its channel resolves to (a channel that lists no `servers` resolves to all of them); operations that name none are refused, as are operations whose two readings name different brokers, and channels that inherit a multi-protocol server set without choosing. HTTP and WebSocket documents are refused for destination minting: there the host rather than the address names the place, and an HTTP endpoint is already modelled as a `Route`. A parameterized address — a channel declaring `parameters`, or an address containing `{` — is refused rather than keyed: two services publishing `{env}.orders` share a pattern, not a queue. AsyncAPI **2.x is refused** under its own counted reason and never mapped, because its `publish`/`subscribe` are inverted relative to 3.x `send`/`receive` and a naive mapping would reverse the async graph while leaving it connected. Every refusal is counted, and a configured path that yields nothing is reported rather than passed over in silence.

Like Actuator snapshots, documents are external to git freshness — replacing one moves no commit and dirties no file — so an enabled run always rebuilds, and the first later run without the option rebuilds once to remove document-derived evidence. There is no glob-based auto-discovery, and the option is unsupported with `--watch`.

If `analyze` reports a worker parse timeout on a large or unusual repository, it keeps running and falls back safely. To give slow worker jobs more time, use `--worker-timeout 60` or set `GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS=60000`. For very large files, `GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES` controls the worker job byte budget.

**Embeddings node limit** — `gitnexus analyze --embeddings` generates semantic search vectors with a default 50,000-node safety cap to protect memory on large repositories:

```bash
gitnexus analyze --embeddings          # default 50,000 node safety cap
gitnexus analyze --embeddings 0        # disable the cap entirely
gitnexus analyze --embeddings 100000   # custom cap
```

If embeddings are skipped on a large repository, the indexed graph likely exceeds the default cap — re-run with `--embeddings 0` or a higher limit.

</details>

<details>
<summary><strong>Keep remote repositories indexed with <code>gitnexus auto-sync</code></strong></summary>

`gitnexus auto-sync` clones or pulls configured repositories, analyzes new commits, and optionally syncs their group. It runs once immediately, then repeats on the configured interval. It runs in the foreground; use your process manager if it must survive a shell session. `gitnexus watch` is reserved and prints this split; it does not start auto-sync or local file watching.

```bash
# 1. Create the config once. It never overwrites an existing file.
gitnexus auto-sync init

# 2. Edit $GITNEXUS_HOME/watch_config.yml, then start it.
gitnexus auto-sync start              # `gitnexus auto-sync` is equivalent
gitnexus auto-sync status
gitnexus auto-sync restart            # Required after config changes
gitnexus auto-sync stop
gitnexus auto-sync reset             # Clear failure state; leaves clones and indexes intact
```

`GITNEXUS_HOME` defaults to `~/.gitnexus`. A minimal configuration:

```yaml
sync_interval_minutes: 10
analyze_timeout: 5m
# Extra hosts beyond github.com, gitlab.com, and gitee.com. Exact names only.
# allowed_hosts: [gitlab.mycompany.com]
projects:
  - local_path: /absolute/path/to/clones
    branches: [main, master]
    # pdg: omit = preserve live index mode; true = keep PDG current;
    # false = init default (warns, then strips PDG on the next successful rebuild).
    # Do not paste pdg: false onto an existing watch file unless you intend to drop PDG.
    pdg: false
    overwrite_local_changes: false
    remote_urls:
      - git@github.com:owner/repo.git
```

- `sync_interval_minutes` must be at least `5`; `local_path` must be an absolute path. Clones are stored below it as `host/namespace/repo`.
- Remote URLs may use SSH SCP or HTTPS. Hosts are github.com, gitlab.com, and gitee.com unless listed in top-level `allowed_hosts` (exact DNS names, no wildcards). The CLI image includes OpenSSH; mount keys yourself. Invalid `watch_config.yml` skips auto-sync immediately. Auto-sync honors `.gitnexusrc` embeddings (HTTP embeddings env still required in the image).
- `branches` are tried in order. The legacy `branch` field is supported, but do not set both.
- Set per-project `pdg: true` to keep the full control-flow, control/data-dependence, and taint layers current. Untouched configs that omit `pdg` preserve an existing index's mode and cannot silently strip PDG data. Do not paste `pdg: false` from this example onto an existing watch file unless you intend to drop PDG; an explicit `false` opt-out logs a warning before removing existing PDG data. Auto-sync requests atomic incremental publication where supported, so readers keep using the previous graph until a successful update is ready and a failed staged analysis leaves it intact; unsupported paths retain the analyzer's existing in-place behavior.
- Analysis runs in an isolated worker; `analyze_timeout` defaults to half of `sync_interval_minutes`, but may be longer (for example, a `30m` analysis timeout with `5` minute polling) up to Node's timer limit. If a polling tick arrives while analysis is active, it is coalesced into one immediate follow-up run using the newest commit. If the parent times out and leaves that worker running, the follow-up is deferred to the next interval so a leftover lock holder is not counted as a hard analyze failure. Timeout and `auto-sync stop` request safe cancellation; a worker in native work exits after reaching a JS-visible safe point. Until then, auto-sync reports `cancelling` or `stopping` and retains ownership so another auto-sync cannot take over, for up to 5 seconds — after that the parent stops waiting and leaves the worker to exit on its own rather than killing it mid-write. This behavior is the same on macOS and Windows. `overwrite_local_changes` defaults to `false`, so a dirty local clone is skipped rather than overwritten; setting it to `true` also deletes untracked files in the clone, while keeping ignored paths.
- Add `group_name` only after creating that group with `gitnexus group create <name>`. Partial clone output is isolated and removed after 14 days.

See the [full auto-sync configuration and runtime reference](gitnexus/README.md#gitnexus-auto-sync) for concurrency, timeouts, failure thresholds, and runtime files.

</details>

<details>
<summary><strong>Repository groups</strong> (multi-repo / monorepo service tracking)</summary>

```bash
gitnexus group create <name>                           # Create a repository group
gitnexus group add <group> <groupPath> <registryName>  # Add a repo. <groupPath> is a hierarchy path
                                                       # (e.g. hr/hiring/backend); <registryName> is the
                                                       # repo's name from the registry (see `gitnexus list`)
gitnexus group remove <group> <groupPath>              # Remove a repo by its hierarchy path
gitnexus group list [name]                             # List groups, or show one group's config
gitnexus group sync <name>                             # Extract contracts and match across repos/services
gitnexus group contracts <name>                        # Inspect extracted contracts and cross-links
gitnexus group query <name> <q>                        # Search execution flows across all repos in a group
gitnexus group status <name>                           # Check staleness of repos in a group
gitnexus group impact <name> --target <symbol> --repo <groupPath>  # Cross-repo blast radius
```

</details>

<details>
<summary><strong>Project config (<code>.gitnexusrc</code>)</strong></summary>

Commit a `.gitnexusrc` JSON file at the repo root to preconfigure recurring `analyze` options per project, instead of re-passing the same flags every run. It is read from the resolved repo root (not `.gitnexus/`, which is gitignored index storage). **CLI flags always override `.gitnexusrc`.**

```jsonc
{
  // Default branch used in the generated regression-compare example (base_ref).
  // Use this so a project on `develop`/`master` doesn't get "main" rewritten
  // over its fix on every analyze. (Alias: "branch".)
  "defaultBranch": "develop",
  "skipContextFiles": true, // alias of skipAgentsMd: keep your own AGENTS.md/CLAUDE.md
  "skipSkills": true, // don't install standard skill files under .claude/skills/ and .agents/skills/
  "embeddings": true, // generate embeddings by default
  "springActuator": "./actuator", // optional local runtime snapshot directory or bundle
  "workerTimeout": 60,
}
```

A nested `analyze` block is also accepted (and overrides flat keys for the same option):

```json
{ "analyze": { "defaultBranch": "develop", "skipSkills": true } }
```

Notes:

- The default branch is resolved as: `--default-branch` > `.gitnexusrc` `defaultBranch`/`branch` > auto-detected `origin/HEAD` > `main`.
- `skipContextFiles` / `skipAiContext` are aliases for `skipAgentsMd` — they skip the `AGENTS.md` / `CLAUDE.md` block only. They do **not** imply `skipSkills`. `indexOnly` is the stronger option that skips all file injection.
- Supported keys: `defaultBranch` (`branch`), `skipAgentsMd` (`skipContextFiles`, `skipAiContext`), `skipSkills`, `indexOnly`, `stats`/`noStats`, `embeddings`, `dropEmbeddings`, `name`, `allowDuplicateName`, `maxFileSize`, `workerTimeout`, `walCheckpointThreshold`, `workers`, `maxProcesses`, `maxProcessBranching`, `maxProcessTraceDepth`, `maxEntryPointCandidates`, `springActuator`, `embeddingThreads`, `embeddingBatchSize`, `embeddingSubBatchSize`, `embeddingDevice`.
- The file is JSON only. Unknown keys and wrong JSON types fail fast with an actionable error before analysis starts. Process-detection knobs (`maxProcesses`, `maxProcessBranching`, `maxProcessTraceDepth`, `maxEntryPointCandidates`) that are not a positive integer warn and fall through to env, then the built-in default.

</details>

<details>
<summary><strong>Environment variables</strong></summary>

Most `analyze` knobs are also CLI flags (`--workers`, `--worker-timeout`, `--max-file-size`, `--verbose`). Use the env-var form when you'd otherwise repeat the same flag every run, or when invoking GitNexus from a long-running host (MCP server, eval-server, CI shell) that already manages its own environment. CLI flags take precedence over `.gitnexusrc`, which takes precedence over env vars, which take precedence over built-in defaults.

| Variable                                        | Default                            | Effect                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Tune when…                                                                                                                                                                            |
| ----------------------------------------------- | ---------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `GITNEXUS_TEST_REPORT` | unset | Write a JSON execution receipt from `scripts/run-cross-platform.ts`; accepts a basename ending in `.json`. | CI platform shards use distinct filenames so the completeness check can require every report. |
| `GITNEXUS_WORKER_POOL_SIZE`                     | `cores - 1`, capped at 16          | Parse worker pool size (must be ≥ 1). Equivalent to `--workers <n>`. The worker pool is the sole parse path — there is no sequential parser, so `0` is rejected with an actionable error (the pool self-heals via quarantine + respawn).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 | Constrained containers (cgroup CPU limits) or CI runners with explicit quotas. To narrow down a worker crash set `1` for a single-worker pool — not `0`.                              |
| `GITNEXUS_PARSE_CHUNK_CONCURRENCY`              | `2`                                | Number of chunks whose file contents may be read into memory in parallel while the pool dispatches the current chunk. Worker dispatch itself stays serial.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | Repos large enough to chunk (multi-MB total source) where disk I/O is a measurable fraction of analyze wall-clock.                                                                    |
| `GITNEXUS_VERBOSE`                              | unset                              | When `1`, enables verbose ingestion logs (skipped-file warnings, per-chunk throughput, parse-cache stats). Equivalent to `--verbose`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | Debugging an analyze that "completed" but seems to have missed files; tuning `--workers` / chunk concurrency against observable throughput.                                           |
| `GITNEXUS_EMBEDDING_RETRY_TIMEOUTS`             | unset                              | When truthy (`1`/`true`/`yes`), per-attempt HTTP embedding timeouts (`TimeoutError` on fetch or body read) go through the bounded `GITNEXUS_EMBEDDING_MAX_ATTEMPTS` retry loop instead of failing the job. Any other value leaves it off, so cloud/default timeouts remain terminal.                                                                                                                                                                                                                                                                                                                                                      | Local accelerators that drop a device lock when the client disconnects and succeed on the next request (observed with FastFlowLM on Ryzen AI).                                        |
| `GITNEXUS_EMBEDDING_SIDECAR_TIMEOUT_MS`         | `180000` (3 minutes)               | Per-request IPC timeout for local embedding sidecar embed batches. On overrun the parent SIGKILLs the sidecar child and rejects the batch. Init still uses the HF download budget (`HF_DOWNLOAD_TIMEOUT_MS` × attempts), not this knob.                                                                                                                                                                                                                                                                                                                                  | Large embed batches or slow local ONNX inference cause sidecar request timeouts during `analyze --embeddings`, `embeddings sync`, serve, or MCP.                                      |
| `GITNEXUS_VECTOR_MAX_DISTANCE` | `0.6` for CLI/MCP `query`; `0.5` for standalone semantic search | Maximum cosine distance for vector hits, applied to both indexed search and exact-scan fallback. Hits must have `distance < cutoff`. Unset/blank uses the default; non-numeric, non-finite, zero, or negative values warn and use the default; finite values above `2` warn and clamp to `2`. | Paraphrased queries have weak semantic recall with your embedding model. See [Vector cutoff tuning](#vector-cutoff-tuning). |
| `GITNEXUS_ANALYZER_IDENTITY_IN_PROCESS_GUARDS`  | unset                              | When truthy (`1`/`true`/`yes`), forces in-process cache-guard validation once a batch has ≥128 requests. In-process mode also auto-selects when `packageRoot`/`buildRoot` fail `W_OK` with `EACCES`/`EROFS`. Otherwise those large batches use a Node subprocess probe. Batches under 128 always stay in-process.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | Trusted or read-only installs where two identity subprocess spawns per analyze dominate wall time; leave unset to keep the default isolation path on writable trees. |
| `GITNEXUS_RESOLVE_DEF_GRAPH_ID_MEMO`            | on (unset)                         | Memoizes `resolveDefGraphId` per `nodeLookup` instance (WeakMap). Enabled by default. Set to `0`/`false`/`off`/`no` to disable and recompute on every call (debug / bisect memo bugs).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Suspecting stale graph-id resolution after a lookup rebuild, or comparing memo vs uncached cost on a large index. |
| `GITNEXUS_AUTH_TOKEN`                           | unset                              | Bearer token required when `eval-server` binds beyond loopback. May also be read from `.env.local` or `.env`; shell values take precedence.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | Exposing the evaluation HTTP tools to a container, VM, or LAN.                                                                                                                        |
| `GITNEXUS_MCP_AUTH_TOKEN`                       | unset                              | Bearer token for the dedicated `gitnexus mcp --http` server, for a **directly reachable** `gitnexus serve` `/api/mcp` route, and for the `docker-server` / web proxy in front of one. A non-loopback dedicated MCP bind requires it; `serve` enables protocol-layer MCP auth when it is set. Behind a proxy, set the **same** value on both services: the proxy spends the edge `GITNEXUS_SERVE_AUTH_TOKEN`, then replaces `Authorization` with this token on `/api/mcp` only.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | Dedicated MCP, a `serve` the client can reach directly, or a proxied deploy (Render Blueprint) where the backend runs protocol-layer MCP auth — configure it on the proxy too.        |
| `GITNEXUS_PROFILE_DEFERRED`                     | unset                              | When `1`, emits `[deferred-profile]` timing/progress logs for the post-chunk deferred resolution band (imports → heritage → buildHeritageMap → legacy call resolution). Implied by `GITNEXUS_VERBOSE`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Diagnosing analyze stalls in "Resolving calls (all chunks)" on large Java/Kotlin repos (issue #1741) without the full verbose ingestion noise.                                        |
| `GITNEXUS_PROFILE_DEFERRED_SLOW_MS`             | `3000` (verbose) / `5000`          | Per-file threshold in ms above which `processCallsFromExtracted` emits a `slow file …` log line. Parsed via `Number()`: accepts integers (`5000`), scientific notation (`2.5e3`), decimals (`.5`), and hex (`0x10`). Non-finite or non-positive values fall back to the default.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Hunting a few outlier files dominating the deferred call-resolution stage; lower to surface more, raise to focus only on the worst.                                                   |
| `PROF_LBUG_LOAD`                                | unset                              | When `1`, emits one `[lbug-load prof]` summary line per `loadGraphToLbug` call breaking the graph-DB persistence wall into stages (`csv-emit` / `copy-nodes` / `copy-rels` / `fallback` / `total`) plus node & edge counts. Zero-cost when unset.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | Attributing large-repo analyze wall time across CSV generation vs. LadybugDB `COPY` (issue #2203) — the analyze "emit" timing is the scope-resolution bucket, not this DB-write path. |
| `GITNEXUS_MAX_FILE_SIZE`                        | `512` (KB)                         | Walker skip threshold in KB. Hard cap is `32768` (tree-sitter buffer ceiling). Equivalent to `--max-file-size <kb>`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | Indexing repos with intentionally-large source files (generated parsers, vendored bundles) that should still be parsed.                                                               |
| `GITNEXUS_MAX_PROCESSES`                        | dynamic (`max(20, round(symbols/10))`) | Analyze-time process-detection process cap. Equivalent to `--max-processes <n>` / `.gitnexusrc` `maxProcesses`. Explicit values replace the dynamic formula (not a multiplier). `0` is invalid, not unlimited. Changing this re-detects flows on the next analyze without `--force`. Distinct from query-time `IMPACT_MAX_CHUNKS`. | `[processes] … whole flows are MISSING` names `--max-processes` after entry points were never traced or flows were dropped. Tracing does not start the next entry once collected traces already reach `maxProcesses * 2`; a started entry can still emit every trace that entry produces. |
| `GITNEXUS_MAX_PROCESS_BRANCHING`                | `4`                                | Analyze-time per-node branching cap during flow tracing. Equivalent to `--max-process-branching <n>`. Shape-only: raising it shortens fewer traces; it does not restore whole missing flows. | A flow is present but `calleesDropped` is high at debug. |
| `GITNEXUS_MAX_PROCESS_TRACE_DEPTH`              | `10`                               | Analyze-time DFS depth cap during flow tracing. Equivalent to `--max-process-trace-depth <n>`. Shape-only. | A reported flow is shorter than the code path (`tracesDepthCapped` at debug). |
| `GITNEXUS_MAX_ENTRY_POINT_CANDIDATES`           | `200`                              | Ranked entry-point candidate pool. Equivalent to `--max-entry-point-candidates <n>`. Raising `--max-processes` alone does not clear `entryPointCandidatesDropped`. Doubling the current cap is the usual first raise; setting it to the full remaining candidate count can exhaust CPU and memory. | The `[processes]` warning reports candidate entry points that never ranked in. |
| `GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS`          | `30000`                            | Worker idle timeout in milliseconds before retry/fallback. Equivalent to `--worker-timeout <seconds>` × 1000.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Slow-parsing files (large minified JS, deeply-nested TS types) that legitimately need more than 30s.                                                                                  |
| `GITNEXUS_WORKER_READY_TIMEOUT_MS`              | `5000`                             | Startup budget in milliseconds for a parse worker to load its grammar bindings and report `{type:'ready'}`. Slots that miss it are treated as startup crashes.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | Slow or heavily loaded hosts where a full pool cold-starting concurrently needs more than 5s, and analyze aborts with "did not report ready within 5000ms".                           |
| `GITNEXUS_FTS_STEMMER`                          | `porter`                           | Stemmer used when rebuilding BM25/FTS indexes. Use `none` for CJK-heavy repositories, or a language stemmer such as `german`, `french`, or `spanish` for matching repository comments. Re-run `gitnexus analyze --repair-fts` after changing it.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Keyword search quality is poor for non-English comments or identifiers under English stemming.                                                                                        |
| `GITNEXUS_STORAGE_PATH`                         | unset (`<repo>/.gitnexus/`)        | Complete external index directory. This preserves the existing configuration semantics and takes precedence over `GITNEXUS_STORAGE_ROOT` when both are set.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | You already keep one repository index outside its checkout or need one explicit index location.                                                                                       |
| `GITNEXUS_STORAGE_ROOT`                         | unset                              | Absolute root directory for external indexes. GitNexus creates an isolated `<repo-basename>-<canonical-path-hash>/` slot beneath it for each repository, then registers the resolved slot so `status`, MCP, and `serve` can reopen it later.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | You want to manage multiple repository indexes centrally or keep generated data outside source checkouts.                                                                             |
| `GITNEXUS_SHARED_STORE`                         | unset (on)                         | Set to `off` (or `0`, `false`, `no`) to turn off shared index stores for both linked git worktrees and sibling clones; every checkout then indexes into its own `.gitnexus/`. Sharing is also off whenever `GITNEXUS_STORAGE_PATH` or `GITNEXUS_STORAGE_ROOT` is set.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Disk or memory is not a concern, or you want each worktree's index fully independent.                                                                                                 |
| `GITNEXUS_CONTENT_RETENTION`                    | `full`                             | Source-text retention profile: `full` keeps file and symbol text, `symbol` keeps symbol snippets without full file content, and `none` keeps the structural graph without source body text.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | You need to reduce persisted source text while preserving graph structure.                                                                                                            |
| `GITNEXUS_SKIP_FTS` | unset | When exactly `1`, skips FTS extension loading and keyword index creation during analyze. Equivalent to `--skip-fts`; a later analyze without either option restores FTS. | Graph-only consumers with their own retrieval, or short-lived indexes that do not need keyword search. |
| `GITNEXUS_WAL_CHECKPOINT_THRESHOLD`             | `67108864` (64 MiB)                | LadybugDB WAL auto-checkpoint threshold in bytes. Equivalent to `--wal-checkpoint-threshold <bytes>`. `-1` keeps LadybugDB's stock threshold (~16 MiB). Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | You need a larger or smaller WAL auto-checkpoint threshold for your analyze workload.                                                                                                 |
| `GITNEXUS_LBUG_BUFFER_POOL_SIZE`                | min(2 GiB, 80% RAM)                | LadybugDB buffer-pool ceiling in bytes for every GitNexus database (analyze, MCP server, serve, group bridges). `0` restores LadybugDB's native unbounded default of 80% of system RAM; invalid values warn and fall back to the default (#2557). During `analyze` the pool is right-sized to the graph, scaled on non-4 KiB-page hosts by the page-size granule ratio up to min(2 GiB × pageSize/4 KiB, 80% RAM) (#2631); this env var overrides all of that as an absolute value.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | A long-lived `gitnexus mcp` or a big incremental `analyze` uses too much memory, or a huge repo's working set genuinely needs a pool larger than 2 GiB.                               |
| `GITNEXUS_LBUG_MAX_DB_SIZE`                     | `17179869184` (16 GiB)             | Maximum size in bytes of a single LadybugDB database file — an mmap/disk-address-space ceiling, not a memory limit (it does not constrain the buffer pool). Invalid values silently fall back to the default.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | Indexing a genuinely huge monorepo whose on-disk graph index approaches 16 GiB.                                                                                                       |
| `GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES`           | `8388608` (8 MB)                   | Per-job byte budget the pool will send to a worker in one `postMessage`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 | Very large individual files; mostly diagnostic — bumping past 8 MB risks structured-clone memory pressure.                                                                            |
| `GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT`         | `3`                                | Max replacement spawns per worker slot before the slot is dropped from the active rotation. Bounds respawn loops on a chronically-crashing slot.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Hosts where a flaky worker should retry more (raise) or fail-fast (lower) before the slot is dropped.                                                                                 |
| `GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS`     | `5 × subBatchTimeoutMs`            | Total retry wall-time budget per job before quarantining. Combined with `timeoutBackoffFactor`, prevents exponentially-growing retries from stalling for hours.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Slow files that legitimately need long total retry windows; lower to fail-fast on stalls.                                                                                             |
| `GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD` | `max(3, poolSize)`                 | Per-slot consecutive deaths before the pool's circuit breaker trips. After tripping, every subsequent dispatch rejects until a fresh pool is created.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | Hosts where a SIGSEGV-prone native grammar should trip the breaker sooner; CI runners that should fail loudly.                                                                        |
| `GITNEXUS_WORKER_SHUTDOWN_DRAIN_MS`             | `30000`                            | Max wait at pool shutdown for a retired worker still inside native code. The worker is terminated at its next JS-safe point instead of mid-native-call (which aborts the whole process with `Napi::Error`, #2432); on expiry it is left running, unref'd, and terminated when it surfaces.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | Shutdown latency matters more than draining a wedged worker (lower), or a legitimately-slow native grammar needs longer to surface (raise).                                           |
| `GITNEXUS_CPP_CAPTURE_BUDGET_MS`                | `20000`                            | Per-file wall-clock budget for C++ capture extraction. On breach the file keeps the captures accumulated so far and logs a warning — the worker returns to JS instead of stalling in native-heavy loops (#2432). `0` expires immediately.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | Pathological generated C++ that still exceeds the budget after the indexed lookups; raise for completeness, lower to fail-fast.                                                       |
| `GITNEXUS_CHUNK_BYTE_BUDGET`                    | `2097152` (2 MB)                   | Per-bucket byte budget for parse-cache packing. Files are grouped by `(language, hash(path) mod 128)`; packs inside a bucket are cut at this limit. Smaller = finer-grained invalidation and more dispatch. Default is always 2 MiB and no longer scales with worker count.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | Tuning incremental-analyze cache invalidation on monorepos without changing `--workers`.                                                                                              |
| `GITNEXUS_NO_GITIGNORE`                         | unset                              | When set, skips `.gitignore` parsing. `.gitnexusignore` is still honored.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | Indexing a repo whose `.gitignore` excludes files you actually want indexed (e.g., generated code committed for cross-repo lookup).                                                   |
| `GITNEXUS_SKIP_OPTIONAL_GRAMMARS`               | unset                              | When `=1` strictly, skips the vendored grammar materialize for `tree-sitter-dart`, `tree-sitter-proto`, `tree-sitter-swift`, and `tree-sitter-kotlin` at install time (and the Dart/Proto source builds). Those four won't be parsed; the install still succeeds.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | Installing on a host without a C++ toolchain or where the vendored prebuilds don't match; willing to skip Dart/Proto/Swift/Kotlin parsing.                                            |
| `GITNEXUS_MCP_READ_ONLY`                        | unset                              | Set to `1` to expose only proven single-repository read tools and resources; `0` disables the policy and any other value fails startup.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | The MCP server runs in an environment where graph mutation, raw Cypher, and cross-repository group routing must be unavailable.                                                       |
| `GITNEXUS_MCP_ALLOWED_REPOS`                    | unset                              | Comma-separated allowlist of canonical indexed repository names or absolute paths. Invalid, ambiguous, or blank entries fail startup.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | One MCP process must expose only a bounded subset of the repositories in the global registry.                                                                                         |
| `GITNEXUS_MCP_DEFAULT_REPO`                     | unset                              | Canonical indexed repository name or absolute path used when a tool or resource omits its repository. Must belong to the allowlist when one is set.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | Several repositories are available but unqualified MCP calls should resolve deterministically.                                                                                        |
| `GITNEXUS_MCP_DEFAULT_MAX_TOKENS`               | unset                              | Default positive-integer response budget for MCP `query`, `context`, and `impact`, estimated at four UTF-8 bytes per token. Explicit `maxTokens` wins.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Long MCP responses consume too much model context and callers cannot reliably add a per-request budget.                                                                               |
| `GITNEXUS_PUBLIC_ORIGIN`                        | unset                              | The single browser origin `serve` is reached through, added to the CORS allowlist and to the write-route origin guard. A wildcard bind (`0.0.0.0`) has no host identity, so without this the server's own UI is refused. **Setting it currently refuses to start:** `serve` has no authentication, requests carrying no `Origin` header already reach `POST /api/analyze` and `DELETE /api/repo`, and this is the setting that would admit browser writes on top of that. Matching rules for when the gate lifts: the hostname must match exactly, and so must the scheme. A value with no scheme (`app.example.com`) means `https`, since a bare host comes from platform service discovery and those terminate TLS; spell out `http://app.example.com` for plain HTTP. An explicit port must match; with no port, any port on that hostname is accepted. Anything that is not one reachable host (a list, `*`, a bare port number, a `:0` port, a trailing dot) warns at startup and allows nothing.                   | `gitnexus serve` runs behind a reverse proxy or on a wildcard bind, and the UI's index/delete requests return `origin_not_allowed`.                                                   |
| `GITNEXUS_TRUST_PROXY`                          | `loopback, linklocal, uniquelocal` | Express `trust proxy` value — which upstream hops may set `X-Forwarded-*`, and so what the per-IP rate limiter reads as the client IP. Set it to the exact number of proxies you control. Every hop past that is one more entry of the chain the caller gets to write. `false`/`no`/`off` (and a `0` hop count) trust no hop; a proxy list Express can compile (`loopback`, `10.0.0.0/8, 127.0.0.1`) names them instead. `true`/`yes`/`on` is **rejected**: it reads the client-controlled leftmost `X-Forwarded-For` entry, so a spoofed chain earns a fresh rate-limit key per request, and express-rate-limit rejects it too (`ERR_ERL_PERMISSIVE_TRUST_PROXY`). Counts above `16` are rejected as well, as a sanity ceiling rather than a safety boundary. Any invalid value warns and falls back to the default. Bind non-loopback with this unset and `serve` warns: a load balancer outside the private ranges is untrusted, so every request keys to the balancer and the per-IP limit becomes one shared limit. | `serve` sits behind a load balancer outside the private ranges (AWS ALB, Cloudflare, CGNAT), where every request otherwise collapses to the proxy hop and rate limiting goes global.  |

### Vector cutoff tuning

`GITNEXUS_VECTOR_MAX_DISTANCE` controls which vector candidates enter hybrid search. Cosine distance is lower for more similar vectors; the appropriate cutoff depends on the embedding model and repository. A higher cutoff can recover useful semantic matches, but can also admit less relevant hits and change the fused ranking. The default is `0.6` for CLI and MCP `query`, and `0.5` for the standalone semantic-search function.

For an index that already has embeddings, compare the default with `0.8` and `1.0` on representative queries, including paraphrases, exact symbol names, and queries that should have no relevant result:

```bash
GITNEXUS_VECTOR_MAX_DISTANCE=0.8 gitnexus query "how are expired sessions removed" --limit 10
```

Check both whether the expected symbols appear and where they rank. In [#3457](https://github.com/abhigyanpatwari/GitNexus/issues/3457), the reporter's `voyage-code-4` sample found 20 of 32 paraphrased targets at `0.6`, 25 at `0.8`, and 28 at `1.0`. Those values are a tuning starting point for that model, not universal recommendations: one paraphrased target fell from first to twelfth at `1.0`. The sample covered eight repositories, recorded no raw distances, used agent-written queries after reading the code, and did not send Voyage's `input_type`.

Set the variable in the process that runs the search. For MCP, add it to the server's launch environment and restart the server; for `gitnexus serve`, set it in that process's environment and restart it. Setting it only during `analyze`, or exporting it in another shell, does not configure an existing server. Changing the cutoff requires no reindex.

The cutoff only filters available vector candidates. It cannot add missing embeddings or repair a mismatch between the indexing and query-time embedding configuration; see the [embeddings runbook](RUNBOOK.md#embeddings). A cutoff of `2` is very permissive, but still rejects distance exactly `2` and retains the search candidate limits.

</details>

<details>
<summary><strong><code>gitnexus uninstall</code></strong></summary>

`gitnexus uninstall` reverses `gitnexus setup` — it removes the GitNexus MCP entries, hooks, and skill directories it added to each detected editor. Skill directories are identified **by bundled gitnexus skill name** (e.g. `gitnexus-cli/`), so if you customized files inside an installed skill directory, back them up first. It is a dry-run preview by default and prints the exact paths it would remove; pass `--force` to apply. Per-repo indexes (`gitnexus clean --all`) and the global npm package (`npm uninstall -g gitnexus`) are left for you to remove.

</details>

<details>
<summary><strong>Publishing to understand-quickly</strong> (opt-in)</summary>

[`looptech-ai/understand-quickly`](https://github.com/looptech-ai/understand-quickly) is a public registry of code-knowledge graphs that lists `gitnexus@1` as a first-class format. After registering your repo once (`npx @understand-quickly/cli add` or the [wizard](https://looptech-ai.github.io/understand-quickly/add.html)), `gitnexus publish` fires a single `repository_dispatch` event so the registry resyncs your entry on demand instead of waiting for the nightly job.

It is opt-in and a no-op without `UNDERSTAND_QUICKLY_TOKEN` — a fine-grained GitHub PAT with `Repository dispatches: write` on the registry repo. Nothing else happens; no graph file is uploaded. See the [protocol spec](https://github.com/looptech-ai/understand-quickly/blob/main/docs/integrations/protocol.md) for the full contract.

</details>

## How It Works

GitNexus builds a complete knowledge graph of your codebase through a multi-phase indexing pipeline:

1. **Structure** — walks the file tree and maps folder/file relationships
2. **Parsing** — extracts functions, classes, methods, and interfaces using Tree-sitter ASTs
3. **Resolution** — resolves imports, function calls, heritage, constructor inference, and `self`/`this` receiver types across files with language-aware logic
4. **Clustering** — groups related symbols into functional communities
5. **Processes** — traces execution flows from entry points through call chains
6. **Search** — builds hybrid search indexes for fast retrieval

### Supported Languages

| Language   | Imports | Named Bindings | Exports | Heritage | Type Annotations | Constructor Inference | Config | Frameworks | Entry Points |
| ---------- | ------- | -------------- | ------- | -------- | ---------------- | --------------------- | ------ | ---------- | ------------ |
| TypeScript | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| JavaScript | ✓       | ✓              | ✓       | ✓        | —                | ✓                     | ✓      | ✓          | ✓            |
| Python     | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| Java       | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
| Kotlin     | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
| C#         | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| Go         | ✓       | —              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| Rust       | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| PHP        | ✓       | ✓              | ✓       | —        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| Ruby       | ✓       | —              | ✓       | ✓        | —                | ✓                     | —      | ✓          | ✓            |
| Swift      | —       | —              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| C          | —       | —              | ✓       | —        | ✓                | ✓                     | —      | ✓          | ✓            |
| C++        | —       | —              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
| Objective-C | ✓      | —              | ✓       | ✓        | ✓                | —                     | —      | —          | —            |
| Dart       | ✓       | —              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
| Zig        | ✓       | —              | ✓       | —        | ✓                | ✓                     | ✓      | —          | ✓            |

**Imports** — cross-file import resolution · **Named Bindings** — `import { X as Y }` / re-export tracking · **Exports** — public/exported symbol detection · **Heritage** — class inheritance, interfaces, mixins · **Type Annotations** — explicit type extraction for receiver resolution · **Constructor Inference** — infer receiver type from constructor calls (`self`/`this` resolution included for all languages) · **Config** — language toolchain config parsing (tsconfig, go.mod, etc.) · **Frameworks** — AST-based framework pattern detection · **Entry Points** — entry point scoring heuristics

**Control flow (CFG, opt-in `--pdg`)** — per-function control-flow graphs (`BasicBlock` nodes + `CFG` edges) feeding the PDG/taint substrate, currently **TypeScript & JavaScript** (#2081 M1); other languages planned. Off by default.

### Multi-Repo Architecture

GitNexus uses a **global registry** so one MCP server can serve multiple indexed repos. No per-project MCP config needed — set it up once and it works everywhere.

Each `gitnexus analyze` stores the index in `.gitnexus/` inside the repo by default (portable, gitignored). `GITNEXUS_STORAGE_PATH` selects one complete external index directory and preserves the established configuration behavior. To manage multiple repositories under one external directory, set `GITNEXUS_STORAGE_ROOT`; GitNexus derives an isolated `<repo-basename>-<canonical-path-hash>/` slot beneath it for each repository. If both variables are set, `GITNEXUS_STORAGE_PATH` takes precedence. GitNexus registers the resolved slot in `~/.gitnexus/registry.json`, allowing later `status`, MCP, and `serve` commands to reopen the index without repeating the environment variable. LadybugDB connections are opened lazily on first query and evicted after 5 minutes of inactivity (max 5 concurrent). Read-only tools can omit `repo` when only one repo is indexed, an MCP default is configured, or the GitNexus process cwd is inside a registered path without crossing into an unindexed nested Git checkout. Outside those paths—and for mutating tools with multiple indexed repos and no MCP default—pass `repo` explicitly.

**Worktrees share one index store.** When a repository has linked worktrees (`git worktree add`), the main checkout and every worktree index into one store at `~/.gitnexus/stores/<repo>/` instead of each keeping a full `.gitnexus/`. Checkouts at the same commit with no local changes read one shared, read-only graph: one copy on disk and one open database in MCP. A checkout with uncommitted changes gets its own graph, copied from the nearest shared graph and updated incrementally rather than rebuilt. Parse caches are shared too. Each worktree keeps a small `.gitnexus/store.json` pointer, and an index it had before sharing is left in place; `gitnexus status` reports it and `gitnexus clean --local-index --force` removes it. `gitnexus clean` in one worktree removes only that worktree's slot and any shared graph no other checkout uses; `gitnexus clean --gc` also drops slots whose worktree was deleted. Independent clones of one repository share too: when another registered clone has the same `origin` URL, `gitnexus analyze` in a clone joins that clone's store (or starts one the other clone joins on its next analyze). A lone clone keeps its own `.gitnexus/`. `gitnexus analyze --share-with <name-or-path>` joins a specific checkout's store after checking the `origin` URLs match, and `--no-share` moves a clone back to its own `.gitnexus/` and keeps it out until `--share-with`. On filesystems with copy-on-write clones (APFS, btrfs, XFS) a checkout's private graph shares its unchanged pages with the shared graph on disk; elsewhere it is a full copy, and `gitnexus status` says which. Queries cannot combine two graphs, because LadybugDB reads one database per query, so a checkout with edits always has a complete graph of its own. Set `GITNEXUS_SHARED_STORE=off` (or `0`, `false`, `no`) to turn sharing off for worktrees and clones alike.

<details>
<summary><strong>Architecture diagram</strong></summary>

```mermaid
flowchart TD
    subgraph CLI [CLI Commands]
        Setup["gitnexus setup"]
        Analyze["gitnexus analyze"]
        Clean["gitnexus clean"]
        List["gitnexus list"]
    end

    subgraph Registry ["~/.gitnexus/"]
        RegFile["registry.json"]
    end

    subgraph Repos [Project Repos]
        RepoA[".gitnexus/ in repo A"]
        RepoB[".gitnexus/ in repo B"]
    end

    subgraph MCP [MCP Server]
        Server["server.ts"]
        Backend["LocalBackend"]
        Pool["Connection Pool"]
        ConnA["LadybugDB conn A"]
        ConnB["LadybugDB conn B"]
    end

    Setup -->|"writes global MCP config"| CursorConfig["~/.cursor/mcp.json"]
    Analyze -->|"registers repo"| RegFile
    Analyze -->|"stores index"| RepoA
    Clean -->|"unregisters repo"| RegFile
    List -->|"reads"| RegFile
    Server -->|"reads registry"| RegFile
    Server --> Backend
    Backend --> Pool
    Pool -->|"lazy open"| ConnA
    Pool -->|"lazy open"| ConnB
    ConnA -->|"queries"| RepoA
    ConnB -->|"queries"| RepoB
```

</details>

## Tool Examples

### Impact Analysis

```
impact({target: "UserService", direction: "upstream", minConfidence: 0.8})

TARGET: Class UserService (src/services/user.ts)

UPSTREAM (what depends on this):
  Depth 1 (WILL BREAK):
    handleLogin [CALLS 90%] -> src/api/auth.ts:45
    handleRegister [CALLS 90%] -> src/api/auth.ts:78
    UserController [CALLS 85%] -> src/controllers/user.ts:12
  Depth 2 (LIKELY AFFECTED):
    authRouter [IMPORTS] -> src/routes/auth.ts
```

Options: `maxDepth`, `minConfidence`, `relationTypes` (`CALLS`, `IMPORTS`, `EXTENDS`, `IMPLEMENTS`), `includeTests`, `limit` (max symbols per depth, default 100), `offset` (pagination start per depth), `summaryOnly` (counts and risk only, omits symbol list)

**Disambiguation** — when several symbols share the target name, `impact` returns a ranked `ambiguous` candidate list instead of guessing. Narrow it with `target_uid` (exact, zero-ambiguity), `file_path`, or `kind` (`Function`, `Class`, `Method`, …). From the CLI these are `--uid`, `--file`, and `--kind`, matching `gitnexus context`:

```bash
gitnexus impact get_embeddings                       # → ambiguous: lists ranked candidates
gitnexus impact get_embeddings --file src/embed.py   # → resolves to the one in that file
gitnexus impact get_embeddings --uid "Function:src/embed.py:get_embeddings"  # exact
```

<details>
<summary><strong>More examples:</strong> search · context · detect_changes · rename · Cypher</summary>

### Process-Grouped Search

```
query({search_query: "authentication middleware"})

processes:
  - summary: "LoginFlow"
    priority: 0.042
    symbol_count: 4
    process_type: cross_community
    step_count: 7

process_symbols:
  - name: validateUser
    type: Function
    filePath: src/auth/validate.ts
    process_id: proc_login
    step_index: 2

definitions:
  - name: AuthConfig
    type: Interface
    filePath: src/types/auth.ts
```

### Context (360-degree Symbol View)

```
context({name: "validateUser"})

symbol:
  uid: "Function:validateUser"
  kind: Function
  filePath: src/auth/validate.ts
  startLine: 15

incoming:
  calls: [handleLogin, handleRegister, UserController]
  imports: [authRouter]

outgoing:
  calls: [checkPassword, createSession]

processes:
  - name: LoginFlow (step 2/7)
  - name: RegistrationFlow (step 3/5)
```

### Detect Changes (Pre-Commit)

```
detect_changes({scope: "all"})

summary:
  changed_count: 12
  affected_count: 3
  changed_files: 4
  risk_level: medium

changed_symbols: [validateUser, AuthService, ...]
affected_processes: [LoginFlow, RegistrationFlow, ...]
```

### Rename (Multi-File)

```
rename({symbol_name: "validateUser", new_name: "verifyUser", dry_run: true})

status: success
files_affected: 5
total_edits: 8
graph_edits: 6     (high confidence)
text_search_edits: 2  (review carefully)
changes: [...]
```

### Cypher Queries

```cypher
-- Find what calls auth functions with high confidence
MATCH (c:Community {heuristicLabel: 'Authentication'})<-[:CodeRelation {type: 'MEMBER_OF'}]-(fn)
MATCH (caller)-[r:CodeRelation {type: 'CALLS'}]->(fn)
WHERE r.confidence > 0.8
RETURN caller.name, fn.name, r.confidence
ORDER BY r.confidence DESC
```

</details>

## Wiki Generation

Generate LLM-powered documentation from your knowledge graph:

```bash
# Requires an LLM API key (OPENAI_API_KEY, etc.)
gitnexus wiki

# Use a custom model or provider (default model: minimax/minimax-m2.5)
gitnexus wiki --model gpt-4o
gitnexus wiki --base-url https://api.anthropic.com/v1
gitnexus wiki --provider grok   # local Grok Build CLI (uses `grok login`, no API key)

# Force full regeneration
gitnexus wiki --force

# Increase the timeout or retries for large codebases or slow LLM providers
gitnexus wiki --timeout <seconds>  # LLM request timeout in seconds (default: disabled)
gitnexus wiki --retries <n>        # Max LLM retry attempts per request (default: 3)

# Allow a specific LAN/self-hosted HTTP LLM host (HTTPS is preferred for remote endpoints)
gitnexus wiki --base-url http://llama-box.local:8080/v1 --allow-insecure-connection llama-box.local
# Or set a comma-separated host allowlist:
GITNEXUS_ALLOW_INSECURE_CONNECTION=llama-box.local,192.168.1.23

# Change the output language
gitnexus wiki --lang <lang>  # e.g. english, chinese, spanish, japanese
```

For safety, `http://` LLM base URLs are allowed by default only for loopback hosts (`localhost`, `127.0.0.1`, `::1`). `--allow-insecure-connection` and `GITNEXUS_ALLOW_INSECURE_CONNECTION` accept exact hostnames or IP addresses only; do not include schemes, ports, paths, credentials, or wildcards.

The wiki generator reads the indexed graph structure, groups files into modules via LLM, generates per-module documentation pages, and creates an overview page — all with cross-references to the knowledge graph.

## Web UI (browser-based)

A client-side graph explorer and AI chat — your code never leaves your machine.

**Try it now:** [gitnexus.vercel.app](https://gitnexus.vercel.app) — run `npx gitnexus@latest serve` locally and the page auto-connects to your local backend.

<img width="2550" height="1343" alt="gitnexus_img" src="https://github.com/user-attachments/assets/cc5d637d-e0e5-48e6-93ff-5bcfdb929285" />

The web UI uses the same indexing pipeline as the CLI but runs entirely in WebAssembly (Tree-sitter WASM, LadybugDB WASM, in-browser embeddings). It's great for quick exploration but limited by browser memory for larger repos.

**Local Backend Mode:** run `gitnexus serve` and open the web UI — it auto-detects the server and shows all your indexed repos, with full AI chat support. No re-upload, no re-index. The agent's tools (Cypher queries, search, code navigation) route through the backend HTTP API automatically.

<details>
<summary><strong>Run the frontend locally</strong></summary>

```bash
git clone https://github.com/abhigyanpatwari/gitnexus.git
cd gitnexus/gitnexus-web && npm install
# Compile sibling gitnexus-shared with this package's TypeScript 7 (do not npm ci shared).
cd ../gitnexus-shared && node ../gitnexus-web/node_modules/typescript/lib/tsc.js
cd ../gitnexus-web && npm run dev
# Then in another terminal, start the backend the frontend connects to:
npx gitnexus@latest serve
```

</details>

## Docker

```bash
docker compose up -d
```

This starts the server on `http://localhost:4747` and the web UI on `http://localhost:4173`. The UI auto-detects the server because the browser runs on the host and reaches the container via the mapped port.

The official setup ships **two signed images**, published identically to **GitHub Container Registry** (GHCR) and **Docker Hub** — same build, same digest, same Cosign signature:

| Purpose                                                                | GHCR (default in `docker-compose.yaml`)       | Docker Hub mirror              |
| ---------------------------------------------------------------------- | --------------------------------------------- | ------------------------------ |
| CLI / `gitnexus serve` backend (HTTP API on port `4747`, MCP, indexer) | `ghcr.io/abhigyanpatwari/gitnexus:latest`     | `akonlabs/gitnexus:latest`     |
| Static web UI (port `4173`)                                            | `ghcr.io/abhigyanpatwari/gitnexus-web:latest` | `akonlabs/gitnexus-web:latest` |

A named volume (`gitnexus-data`) persists the global registry, indexes, and cloned repos at `/data/gitnexus` inside the server container. To make repos on your host machine indexable, set `WORKSPACE_DIR` before bringing the stack up:

```bash
WORKSPACE_DIR=$HOME/code docker compose up -d
# Inside the server container the directory is mounted read-only at /workspace.
docker compose exec gitnexus-server gitnexus index /workspace/my-repo
```

> **Heads-up — image rename.** Earlier releases published the web UI under `ghcr.io/abhigyanpatwari/gitnexus`. That slug now hosts the CLI/server image and the UI moved to `ghcr.io/abhigyanpatwari/gitnexus-web`. Previous tags remain pullable, but new versions are only published under the new slugs — update your `docker run` / compose files (or just adopt the bundled compose).

<details>
<summary><strong>Direct <code>docker run</code> & env file</strong></summary>

```bash
# Server
docker run --rm -d \
  --name gitnexus-server \
  -p 4747:4747 \
  -v gitnexus-data:/data/gitnexus \
  ghcr.io/abhigyanpatwari/gitnexus:latest

# Web UI
docker run --rm -d \
  --name gitnexus-web \
  -p 4173:4173 \
  ghcr.io/abhigyanpatwari/gitnexus-web:latest
```

Optional env file (override image tags, container names, ports, workspace dir):

```bash
cp .env.example .env
docker compose --env-file .env up -d
```

Files:

- [Dockerfile.web](Dockerfile.web) — builds `gitnexus-shared` and `gitnexus-web`, then serves the production frontend.
- [Dockerfile.cli](Dockerfile.cli) — builds the CLI/server (with its native deps) and runs `gitnexus serve --host 0.0.0.0`. Local embeddings are **not** in the image (`onnxruntime-node` is opt-in; runtime npm is stripped). Bind-mount a prefix or set `GITNEXUS_EMBEDDING_URL`.
- [docker-compose.yaml](docker-compose.yaml) — starts both signed images side by side.
- [.env.example](.env.example) — overrides for image names, container names, ports, and the workspace mount.

</details>

<details>
<summary><strong>Versioning & supply-chain protection</strong> (Cosign signatures, provenance, Kubernetes admission policy)</summary>

The Docker images are version-locked to the npm package:

- Stable images are **only published from `vX.Y.Z` git tags** (via `docker.yml` triggered directly by the tag push), and the workflow refuses to build unless the tag exactly matches `gitnexus/package.json`'s version. So `ghcr.io/abhigyanpatwari/gitnexus:1.6.2` (and its Docker Hub mirror `akonlabs/gitnexus:1.6.2`) is byte-for-byte the same release as `npm install gitnexus@1.6.2` — no drift, no floating builds from `main`. Both registries receive the same digest from a single build step, so you can pull from either and the signature verifies identically.
- Release-candidate images (e.g. `:1.7.0-rc.1`) are published alongside each RC npm release. They are built by `publish.yml` calling `docker.yml` as a reusable workflow after the RC tag is created and pushed.
- `:latest` is auto-promoted only from non-prerelease tags by the Docker metadata action, so it always points at a real, npm-published version.

Both images are signed with [Cosign keyless signing][cosign-keyless] using the workflow's GitHub OIDC identity, and shipped with build provenance and SBOM attestations. **This is your protection against supply-chain attacks**: even if an attacker republishes a same-named image elsewhere (or somehow pushes to a typo-squatted registry), they cannot forge a Cosign signature tied to `abhigyanpatwari/GitNexus`'s `docker.yml`. Always verify before pulling into sensitive environments.

**Stable releases** — signed from the `v*` tag ref:

```bash
cosign verify ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
  --certificate-identity-regexp '^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
  --certificate-oidc-issuer https://token.actions.githubusercontent.com

# Same signature verifies the Docker Hub mirror (identical digest):
cosign verify docker.io/akonlabs/gitnexus:1.6.2 \
  --certificate-identity-regexp '^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
  --certificate-oidc-issuer https://token.actions.githubusercontent.com
```

The regex pins the certificate identity to this repo's `docker.yml` workflow **run from a `v*` tag** — rejecting unsigned images, images signed by other workflows, and images signed from unprotected refs. It is identical for both registries because both sets of tags were signed at the same digest in one workflow run.

**Release candidates** — signed from `refs/heads/main` (the caller's ref when `publish.yml` invokes `docker.yml` as a reusable workflow):

```bash
cosign verify ghcr.io/abhigyanpatwari/gitnexus:1.7.0-rc.1 \
  --certificate-identity 'https://github.com/abhigyanpatwari/GitNexus/.github/workflows/docker.yml@refs/heads/main' \
  --certificate-oidc-issuer https://token.actions.githubusercontent.com
```

You can also inspect the build provenance and SBOM:

```bash
cosign download attestation ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
  --predicate-type https://slsa.dev/provenance/v1
```

**Kubernetes: enforce signatures at admission.** Ship the bundled [`ClusterImagePolicy`](deploy/kubernetes/cluster-image-policy.yaml) so the [Sigstore policy-controller][policy-controller] rejects any GitNexus pod whose image is not signed by this repo's `docker.yml` running from a `vX.Y.Z` tag — the same identity the `cosign verify` snippet above pins.

```bash
# 1. Install the controller (one-time, cluster-wide)
helm repo add sigstore https://sigstore.github.io/helm-charts && helm repo update
helm install policy-controller -n cosign-system --create-namespace \
  sigstore/policy-controller

# 2. Opt your namespace in
kubectl label namespace <your-ns> policy.sigstore.dev/include=true

# 3. Apply the policy
kubectl apply -f deploy/kubernetes/cluster-image-policy.yaml
```

After this, attempting to deploy an unsigned image — or one signed by anything other than `abhigyanpatwari/GitNexus`'s `docker.yml` at a `v*` tag — fails the admission webhook before a pod is ever created. This turns the verifiable signature into an enforced policy, which is the supply-chain control most clusters actually need.

[cosign-keyless]: https://docs.sigstore.dev/cosign/signing/overview/
[policy-controller]: https://docs.sigstore.dev/policy-controller/overview/

</details>

## Enterprise

GitNexus is available as an **enterprise offering** — fully managed **SaaS** or **self-hosted** deployment. Commercial use of the OSS version is also available with proper licensing.

Enterprise includes:

- **PR Review** — automated blast radius analysis on pull requests
- **Auto-updating Code Wiki** — always up-to-date documentation (Code Wiki is also available in OSS)
- **Auto-reindexing** — knowledge graph stays fresh automatically
- **Multi-repo support** — unified graph across repositories
- **OCaml support** — additional language coverage
- **Priority feature/language support** — request new languages or features

**Upcoming:** auto regression forensics · end-to-end test generation

👉 Learn more at [akonlabs.com](https://akonlabs.com) — for commercial licensing or enterprise inquiries, ping us on [Discord](https://discord.gg/AAsRVT6fGb) or email founders@akonlabs.com

## Community Integrations

Built by the community — not officially maintained, but worth checking out.

| Project                                                                       | Author                                                 | Description                                                             |
| ----------------------------------------------------------------------------- | ------------------------------------------------------ | ----------------------------------------------------------------------- |
| [pi-gitnexus](https://github.com/tintinweb/pi-gitnexus)                       | [@tintinweb](https://github.com/tintinweb)             | GitNexus plugin for [pi](https://pi.dev) — `pi install npm:pi-gitnexus` |
| [gitnexus-stable-ops](https://github.com/ShunsukeHayashi/gitnexus-stable-ops) | [@ShunsukeHayashi](https://github.com/ShunsukeHayashi) | Stable ops & deployment workflows (Miyabi ecosystem)                    |
| [KiloCode MCP workflow](Documentation/kilo-code-mcp.md)                       | [@oktanishq](https://github.com/oktanishq)             | Guide to connect GitNexus MCP to Kilo Code and verify tools.            |

> Have a project built on GitNexus? Open a PR to add it here!

## Roadmap

**Actively building:**

- [ ] **LLM Cluster Enrichment** — semantic cluster names via LLM API
- [ ] **AST Decorator Detection** — parse @Controller, @Get, etc.
- [ ] **Incremental Indexing** — only re-index changed files

**Recently completed:**

- [x] Constructor-Inferred Type Resolution, `self`/`this` Receiver Mapping
- [x] Wiki Generation, Multi-File Rename, Git-Diff Impact Analysis
- [x] Process-Grouped Search, 360-Degree Context, Claude Code Hooks
- [x] Multi-Repo MCP, Zero-Config Setup, 14 Language Support
- [x] Community Detection, Process Detection, Confidence Scoring
- [x] Hybrid Search, Vector Index

## Development

- [ARCHITECTURE.md](ARCHITECTURE.md) — packages, index → graph → MCP flow, where to change code
- [RUNBOOK.md](RUNBOOK.md) — analyze, embeddings, stale index, MCP recovery, CI snippets
- [GUARDRAILS.md](GUARDRAILS.md) — safety rules and operational "Signs" for contributors and agents
- [CONTRIBUTING.md](CONTRIBUTING.md) — license, setup, commits, and pull requests
- [TESTING.md](TESTING.md) — test commands for `gitnexus` and `gitnexus-web`

## Tech Stack

| Layer               | CLI                                   | Web                                     |
| ------------------- | ------------------------------------- | --------------------------------------- |
| **Runtime**         | Node.js (native)                      | Browser (WASM)                          |
| **Parsing**         | Tree-sitter native bindings           | Tree-sitter WASM                        |
| **Database**        | LadybugDB native                      | LadybugDB WASM                          |
| **Embeddings**      | HuggingFace transformers.js (GPU/CPU) | transformers.js (WebGPU/WASM)           |
| **Search**          | BM25 + semantic + RRF                 | BM25 + semantic + RRF                   |
| **Agent Interface** | MCP (stdio)                           | LangChain ReAct agent                   |
| **Visualization**   | —                                     | Sigma.js + Graphology (WebGL)           |
| **Frontend**        | —                                     | React 18, TypeScript, Vite, Tailwind v4 |
| **Clustering**      | Graphology                            | Graphology                              |
| **Concurrency**     | Worker threads + async                | Web Workers + Comlink                   |

## Security & Privacy

- **CLI**: everything runs locally on your machine. No network calls. Indexes are stored in `.gitnexus/` by default (gitignored), in the complete external directory selected by `GITNEXUS_STORAGE_PATH`, or in repository-specific slots beneath `GITNEXUS_STORAGE_ROOT`. Global registry at `~/.gitnexus/` stores only paths and metadata.
- **Web**: everything runs in your browser. No code uploaded to any server. API keys stored in localStorage only.
- Open source — audit the code yourself.

## Star History

[](https://www.star-history.com/#abhigyanpatwari/GitNexus&type=date&legend=top-left)

## Acknowledgments

- [Tree-sitter](https://tree-sitter.github.io/) — AST parsing
- [LadybugDB](https://ladybugdb.com/) — embedded graph database with vector support (formerly KuzuDB)
- [Sigma.js](https://www.sigmajs.org/) — WebGL graph rendering
- [transformers.js](https://huggingface.co/docs/transformers.js) — browser ML
- [Graphology](https://graphology.github.io/) — graph data structures
- [MCP](https://modelcontextprotocol.io/) — Model Context Protocol

---

### Documentation Kilo Code Mcp (`Documentation/kilo-code-mcp.md`)

# Connect GitNexus to Kilo Code via MCP

This guide shows how to connect GitNexus to the Kilo Code VS Code extension using Kilo’s MCP support, based on a setup that has been tested successfully.

## Prerequisites

GitNexus should already be installed globally and working on the target repository, and the repository should be indexed successfully with `gitnexus analyze` before testing inside Kilo.

## Tested Versions

| Component | Version |
| --- | --- |
| VS Code | 1.125.1 (user setup) |
| Node.js | 24.15.0 |
| Kilo Code | 7.3.50 |
| OS | Windows 11 25H2 / Windows_NT x64 10.0.26200 |
| GitNexus | 1.6.7 |

## Where Kilo Stores MCP Config

Kilo Code stores MCP server configuration in its main config file. For the VS Code extension, config can be stored at either the global or project level.

| Scope | Config path |
| --- | --- |
| Global | `~/.config/kilo/kilo.jsonc` |
| Project | `kilo.jsonc` or `.kilo/kilo.jsonc` in the project root |

Check latest path : https://kilo.ai/docs/automate/mcp/using-in-kilo-code

## Add GitNexus as an MCP Server

Kilo supports local MCP servers through STDIO, and GitNexus should be added as a local server under the `mcp` key in `kilo.jsonc`. Use this configuration:

```jsonc
{
  "mcp": {
    "gitnexus": {
      "type": "local",
      "command": ["npx", "-y", "gitnexus@latest", "mcp"],
      "enabled": true,
      "timeout": 10000
    }
  }
}
```

## Check It Through the Kilo UI

1. restart kilo code extension or vs code
2. open kilo code settings
3. select mcp server section

#### From there, Kilo allows adding, editing, enabling, disabling, and deleting MCP servers, and it writes changes directly to the appropriate config file.





## Test the Connection

After configuration, Kilo automatically detects the tools exposed by the MCP server and can use them from chat once the server is available.

A practical test flow is:

1. Open the indexed repository in VS Code.
2. Confirm `gitnexus analyze`completed successfully.
3. Open Kilo chat and ask: `Use GitNexus and explain What does index.php do?`.
4. Approve the MCP tool call if prompted.

#### Full Support will be added Soon 😎

## Troubleshooting

1. If the server shows `failed`, check the CLI output and confirm the command and paths are correct.
2. If no tools appear, confirm the MCP server is enabled and GitNexus is exposing the expected tools.
3. If Kilo does not automatically select GitNexus, note the exact settings you changed and mark them as an observed workaround.

---

### Languages Jupyter Notebook (`docs/languages/jupyter-notebook.md`)

# Jupyter notebook (.ipynb) indexing

Status: implemented (Python code cells)

GitNexus indexes Jupyter notebooks by extracting Python code cells and parsing them with the existing Python language provider. Notebooks are not executed.

## Goal

After `analyze`, functions, classes, and imports defined in Python code cells are queryable like ordinary `.py` files.

## Compatibility

- `.ipynb` is detected as Python (`gitnexus-shared` `EXTENSION_MAP` and `pythonProvider.extensions`).
- Extraction lives in `gitnexus/src/core/ingestion/ipynb-extractor.ts`. Shared ingestion modules do not name nbformat AST types.
- Notebooks are **not** Python import targets. A notebook may import `.py` modules; `import some_notebook` does not resolve to an `.ipynb`.
- Files over the walker size cap (default 512KB, `GITNEXUS_MAX_FILE_SIZE`) are skipped like any other oversized file. Output-heavy notebooks may need a higher cap. Outputs are not stripped in this slice.
- Group-layer FastAPI/Flask/Django scanners that require a `.py` suffix still ignore notebooks.

## Kernel and magics

- Skip the file when `kernelspec.language` or `language_info.name` is present and is not a Python-family name (`python`, `python2`, `python3`, `ipython`, `python 3`, `ipython3`). `python` and `python3` together still index.
- If `kernelspec.language` is missing, `kernelspec.name` is used only when it is an obvious language id (`python3`, `ir`, `julia-1.8`). Conda env names are ignored.
- If `language_info.name` is missing, `language_info.file_extension` (`.py` vs `.r` / `.jl`) is used the same way.
- If those fields are absent, code cells are treated as Python unless a cell's own `language`, `metadata.language`, or `metadata.vscode.languageId` says otherwise.
- A cell whose first non-empty line is a foreign cell magic (`%%bash`, `%%html`, `%%sql`, `%%R`) is skipped. Python-body cell magics (`%%time`, `%%timeit`, `%%capture`, `%%prun`, `%%debug`, `%%px`, `%%python`) stay, with the magic line commented.
- `%run`, `%load`, and `%loadpy` of a local `.py` path become `import module` on that same line so the notebook links to the file. URLs, `..` paths, and `.ipynb` targets stay comments. The notebook is not executed.
- Sage, SageMath, MicroPython, Pyodide, PyPy, and PySpark kernels are indexed as Python. SQL, R, and Julia cells are not.
- A cell with an unclosed string or bracket is commented out so it cannot hide later cells. Those cells are concatenated in order; one syntax error no longer drops the rest of the notebook.
- Line magics (`%`), shell (`!`), and IPython help (`train?`, `?train`) are commented in place so JSON line mapping stays affine.
- nbformat v4 `cells` / `source` is the normal path. nbformat v3 `worksheets[].cells` and code-cell `input` are accepted. A leading UTF-8 BOM is accepted. Markdown and raw cells are not code.

## Line numbers

Graph `startLine` / `endLine` are 0-based coordinates in the on-disk `.ipynb` JSON. FTS/MCP symbol snippets reconstruct cell Python; they do not slice raw JSON.

Concatenating cells in document order is notebook semantics. An earlier cell with a syntax error may cause later definitions to be missed; that is a documented limitation, not a per-cell fallback parse.

## Tests

- `gitnexus/test/unit/ipynb-extractor.test.ts`
- `gitnexus/test/unit/ingestion-utils.test.ts` (`.ipynb` detection)
- `gitnexus/test/integration/resolvers/ipynb-python-pipeline.test.ts`

No Jupyter, nbconvert, or nbformat runtime dependency.

---

### Languages Local Import Scoping (`docs/languages/local-import-scoping.md`)

# Local import scoping

GitNexus resolves statically known local imports through their lexical owner and
actual declaration identity. A nearer name that is unresolved, unavailable, or
noncallable blocks an unrelated outer or workspace fallback. An absent name can
continue through the existing lookup rules. This is static analysis: it does not
execute loaders or infer arbitrary runtime initialization order.

## Shared contract

Language rules stay in providers. The shared
[name-claim lookup](../../gitnexus-shared/src/scope-resolution/name-claims.ts)
distinguishes `absent`, `blocked`, and `resolved` before filtering by target kind.
Its [regressions](../../gitnexus/test/unit/scope-resolution/lexical-name-claims.test.ts)
cover noncallable barriers, unresolved imports, type/value lookup, declaration
positions, and inferred aliases that retain their initializer's lookup position.
Calls, constructors, receiver/type inference, inheritance, namespace lookup, and
fallback consumers use these ownership facts rather than independently choosing a
same-named symbol.

The [shared records](../../gitnexus-shared/src/scope-resolution/types.ts) carry
ownership, activation positions, directive destinations, and lookup purpose as
serializable data. They retain declaration identity and ambiguity; they contain
no AST nodes or callbacks. `declaredAtScope` describes ownership, while
`runsOnlyWhenCalled` describes deferred execution. A function-local Rust `use` or
C `#include` is not deferred merely because of its position; Python and Ruby
loading can be. The
[function-local import chain tests](../../gitnexus/test/unit/scope-resolution/function-local-import-chain.test.ts)
pin that distinction.

## Providers with expanded lexical support

These seven entries are part of the
[18-provider registry](../../gitnexus/src/core/ingestion/languages/index.ts).
The evidence links cover exact targets and negative cases, not just edge counts.

| Provider | Supported behavior | Source and regression evidence |
| --- | --- | --- |
| Python | Function-local named, aliased, and namespace imports; compiler-local ownership; ordered class lookup; `global`/`nonlocal` destinations. | [Lexical facts](../../gitnexus/src/core/ingestion/languages/python/lexical-bindings.ts), [local imports](../../gitnexus/test/unit/scope-resolution/python/python-local-imports.test.ts), [namespace semantics](../../gitnexus/test/integration/resolvers/python-namespace-semantics.test.ts) |
| TypeScript | Literal genuine `require`, immediately awaited `import`, and import-equals; namespace, named, and renamed bindings; type/value separation. | [Loader collector](../../gitnexus/src/core/ingestion/languages/typescript/local-loaders.ts), [loader tests](../../gitnexus/test/unit/scope-resolution/typescript/local-loader-imports.test.ts), [type ownership](../../gitnexus/test/unit/scope-resolution/typescript/lexical-type-ownership.test.ts) |
| JavaScript | The same supported runtime loaders and lexical barriers, using JavaScript captures for JS/JSX. | [Captures](../../gitnexus/src/core/ingestion/languages/javascript/captures.ts), [JS/JSX loader cases](../../gitnexus/test/unit/scope-resolution/typescript/local-loader-imports.test.ts) |
| Vue | Local loader facts in extracted scripts, with original declaration graph positions preserved. Explicit JS/JSX uses its own semantic grammar inside the worker; TS reuses the cached tree. | [Script delegation](../../gitnexus/src/core/ingestion/languages/vue/captures.ts), [direct/pre-extracted parity](../../gitnexus/test/unit/scope-resolution/typescript/local-loader-imports.test.ts), [real workers](../../gitnexus/test/integration/local-import-worker-parity.test.ts) |
| Rust | Lexical `use`, producer identity for imported factories/types, and Cargo-aware crate/module identity. Unresolved explicit imports block unrelated fallback. | [Lexical facts](../../gitnexus/src/core/ingestion/languages/rust/lexical-bindings.ts), [import targets](../../gitnexus/src/core/ingestion/languages/rust/import-target.ts), [local scope](../../gitnexus/test/integration/resolvers/rust-import-scope.test.ts), [Cargo boundaries](../../gitnexus/test/integration/resolvers/rust-cargo-target-fallback.test.ts) |
| C++ | Position-sensitive local `using` declarations/directives, separate from includes; propagated header claims retain unresolved named `using` barriers. | [Captures](../../gitnexus/src/core/ingestion/languages/cpp/captures.ts), [local using](../../gitnexus/test/integration/resolvers/cpp-local-using.test.ts), [header using](../../gitnexus/test/integration/resolvers/cpp-local-using-headers.test.ts) |
| Zig | Literal `@import` namespace/member bindings, block activation, container hoisting, stable deep aliases, and inline `@import` receivers. | [Captures](../../gitnexus/src/core/ingestion/languages/zig/captures.ts), [local imports](../../gitnexus/test/integration/resolvers/zig-local-imports.test.ts), [static gating](../../gitnexus/test/integration/resolvers/zig-static-gating.test.ts) |

### Python boundaries

Compiler-local binders include parameters, assignment patterns, loop/with/except
targets, match captures, augmented assignment, deletion, and comprehension/walrus
bindings. Comprehension targets do not leak, and the first iterable is evaluated
outside the comprehension environment. Class bodies use ordered locals; methods
skip class locals for bare-name lookup while explicit instance receivers remain
available. Annotation-only declarations distinguish compiler ownership from a
runtime store. These cases are characterized in the
[Python local-import tests](../../gitnexus/test/unit/scope-resolution/python/python-local-imports.test.ts).

Mixed import/value rebinding and conflicting import identities conservatively
abstain throughout the environment, including simple sequential rebinding; this
is not a control-flow evaluator. A definite `def`/`class` declaration can still
supply its own target after activation. The
[provider policy](../../gitnexus/src/core/ingestion/languages/python/lexical-bindings.ts)
and [rebinding regressions](../../gitnexus/test/integration/resolvers/python-namespace-semantics.test.ts)
define this boundary. There is no full annotation evaluator, `exec` evaluation,
or general closure scheduling model. A deferred `global`/`nonlocal` installer is
not assumed to have executed for unrelated callers.

Conditional imports with one compatible identity remain available for structural
reference resolution, including `TYPE_CHECKING` annotations and `try` imports.
Their runtime execution is not guaranteed by a resolved graph edge.

Default expressions look up names in the enclosing environment. FastAPI's
synthetic dependency graph caller is recorded separately as `callerScope`; it
does not move lexical lookup into the handler body. Both
[direct extraction](../../gitnexus/test/unit/scope-resolution/python/python-local-imports.test.ts)
and [worker transport](../../gitnexus/test/integration/local-import-worker-parity.test.ts)
check this distinction.

### JavaScript-family boundaries

Loader recognition checks AST shape and binding identity, including parameters,
catch/destructuring bindings, temporal-dead-zone ownership, and writes to the
loader or imported handle. CommonJS forwarding uses that same identity check.
Reassigning one destructured import leaves unchanged sibling re-exports intact.
Writes to ordinary locals retain their declared type and callable-value facts.
Unawaited dynamic imports remain Promise/file-dependency facts rather than module
namespace aliases. Computed specifiers, indirect loader/Promise chains, and
unsupported destructuring remain unresolved; see the
[loader regressions](../../gitnexus/test/unit/scope-resolution/typescript/local-loader-imports.test.ts).

Vue's explicit JS/JSX script requires an additional bounded semantic parse because
the worker's structural tree uses TypeScript. That parse runs inside the real
worker. The [parity test](../../gitnexus/test/integration/local-import-worker-parity.test.ts)
witnesses returned worker facts; a main-thread fallback does not satisfy it.

### Rust, C++, and Zig boundaries

Rust uses Cargo editions, target roots, and module identities, including files
with multiple valid identities. Reusable per-analysis indexes bound repeated
lookup work; this is not a claim of a global indexing speedup. See
[Cargo metadata](../../gitnexus/src/core/ingestion/languages/rust/cargo-targets.ts)
and its [tests](../../gitnexus/test/unit/scope-resolution/rust-cargo-targets.test.ts).
Exact same-name inline `pub use` forwarding is supported. A forwarding alias that
changes symbol spelling through a file-only target conservatively remains
unresolved; ambiguous same-file homonyms and re-export cycles cannot select an
unrelated declaration. These limits are explicit in the
[Cargo fallback regressions](../../gitnexus/test/integration/resolvers/rust-cargo-target-fallback.test.ts).
Inferred receiver types retain their receiving declaration range. When same-block
shadowing replaces a retained type fact, earlier uses cannot consume the later
declaration's type and may remain unresolved; this is not full SSA inference. See
the [factory ownership regressions](../../gitnexus/test/unit/scope-resolution/rust/rust-range-binding-order.test.ts).

C++ includes keep their compilation-unit behavior alongside lexical `using`.
The header tests cover literal includes, declaration positions, unresolved named
using claims, and overload identity. They do not establish a full preprocessor,
namespace-alias evaluator, or arbitrary transitive `using namespace` chain support.
Zig nonliteral imports remain unresolved; its block-local names do not escape or
activate before their declarations.

## Retained provider behavior

The other eleven providers retain their existing import/loading models. This
work does not reinterpret every dependency construct as a local value import.

| Provider | Retained model and boundary | Evidence |
| --- | --- | --- |
| Ruby | Wildcard loading; method-local loading is deferred. The extractor recognizes string arguments to `require`, `require_relative`, and `load`. The linked behavioral tests establish `require`/`require_relative` and deferral, not arbitrary `load` execution. | [Extractor](../../gitnexus/src/core/ingestion/languages/ruby/captures.ts), [loading](../../gitnexus/test/integration/resolvers/ruby-scope.test.ts), [deferral](../../gitnexus/test/unit/scope-resolution/function-local-import-chain.test.ts) |
| PHP | Namespace `use` imports are distinct from closure capture and trait `use`. The scope provider does not propagate names through `include`/`require`. | [Query](../../gitnexus/src/core/ingestion/languages/php/query.ts), [ownership](../../gitnexus/src/core/ingestion/languages/php/simple-hooks.ts), [resolver coverage](../../gitnexus/test/integration/resolvers/php.test.ts) |
| C | Header includes remain preprocessor/compilation-unit dependencies, including includes written inside functions; no full preprocessing is added. | [Include interpretation](../../gitnexus/src/core/ingestion/languages/c/interpret.ts), [include tests](../../gitnexus/test/unit/scope-resolution/c/c-imports.test.ts), [deferral boundary](../../gitnexus/test/unit/scope-resolution/function-local-import-chain.test.ts) |
| Objective-C | Headers, modules, and compilation-unit siblings retain the dedicated provider rules. | [Provider guide](objective-c-provider.md), [resolver](../../gitnexus/src/core/ingestion/languages/objective-c/scope-resolver.ts), [workspace tests](../../gitnexus/test/unit/scope-resolution/objective-c/objc-workspace.test.ts) |
| COBOL | `COPY` stays on the dedicated copybook path with module ownership. | [Interpretation](../../gitnexus/src/core/ingestion/languages/cobol/interpret.ts), [COPY target parity](../../gitnexus/test/unit/scope-resolution/cobol-import-target-parity.test.ts) |
| Go | File imports and package sibling visibility retain separate provider rules. | [Import ownership](../../gitnexus/src/core/ingestion/languages/go/simple-hooks.ts), [imports](../../gitnexus/test/unit/scope-resolution/go/go-imports.test.ts), [package siblings](../../gitnexus/test/unit/scope-resolution/go/go-package-siblings.test.ts) |
| Java | Imports belong to the compilation unit. | [Ownership](../../gitnexus/src/core/ingestion/languages/java/simple-hooks.ts), [named/wildcard import resolution](../../gitnexus/test/integration/resolvers/java.test.ts) |
| Kotlin | File import headers retain their existing alias/package resolution. | [Header decomposition](../../gitnexus/src/core/ingestion/languages/kotlin/import-decomposer.ts), [resolver tests](../../gitnexus/test/integration/resolvers/kotlin.test.ts) |
| C# | Namespace/file `using` directives remain imports; resource `using` statements are not import directives. | [Directive query](../../gitnexus/src/core/ingestion/languages/csharp/query.ts), [import tests](../../gitnexus/test/unit/scope-resolution/csharp/csharp-imports.test.ts) |
| Swift | Imports and target/module visibility retain provider ownership. | [Ownership](../../gitnexus/src/core/ingestion/languages/swift/simple-hooks.ts), [import decomposition](../../gitnexus/test/unit/scope-resolution/swift/import-decomposer.test.ts), [target siblings](../../gitnexus/test/unit/scope-resolution/swift/target-siblings.test.ts) |
| Dart | Library imports retain existing package identity and visibility rules. | [Ownership](../../gitnexus/src/core/ingestion/languages/dart/simple-hooks.ts), [library/package regressions](../../gitnexus/test/integration/resolvers/dart.test.ts) |

## Taint provenance

Taint source, sink, and sanitizer matching uses the same lexical provenance.
A genuine external import may match its raw module name even when that package
has no indexed source. A sibling import, local shadow, or type-only import cannot
authorize that match. General copied-handle tracking is outside this support.
The [taint regressions](../../gitnexus/test/unit/taint/lexical-imports.test.ts)
cover extraction, emission, and function summaries, including abstention when
exact call-site positions are missing.

## Cache migration and verification evidence

[Parse-cache schema 136](../../gitnexus/src/storage/parse-cache.ts) replaces 133,
134, and 135. It invalidates overly broad Python/TS/JS binding barriers,
incorrect parameter-annotation lookup ownership, and embedded Vue grammar and
source positions. The same version gate applies to the
[durable ParsedFile store](../../gitnexus/src/storage/parsedfile-store.ts).
Incompatible records are rejected and rebuilt on the next analysis; unchanged
records can then be reused. The
[schema regression](../../gitnexus/test/unit/incremental-parse-cache.test.ts)
explicitly rejects valid schema-133, schema-134, and schema-135 records in both stores.
PDG-mode chunk keys also advance to `pdg:6`, so embedded-script CFGs with
incorrect call anchors are rebuilt before the resolved-callee join.

The [real-worker parity suite](../../gitnexus/test/integration/local-import-worker-parity.test.ts)
witnesses worker boot, dispatch, and returned ParsedFiles, then compares complete
provider facts with direct extraction, including `callerScope` and C++ side-channel
data. Optional grammar availability is explicit in the test gate.

The [persistence suite](../../gitnexus/test/integration/resolvers/local-import-persistence.test.ts)
loads both stores afresh from disk. Its parse-cache chunks contain no embedded
ParsedFiles, so warm equality requires durable-store reuse. It checks identical
`CALLS`/`IMPORTS` identities with zero extraction and zero worker dispatch on an
unchanged warm run. Editing a local import target or shadowing `require` removes
the stale target, and a second warm run preserves the edited graph.

Both suites are in the [cross-platform manifest](../../gitnexus/scripts/cross-platform-tests.ts);
the [shard regression](../../gitnexus/test/unit/cross-platform-shard.test.ts)
ensures each is selected exactly once across the four Windows/macOS shards.
[CI](../../.github/workflows/ci-tests.yml) owns native execution on those systems;
Ubuntu's full suite discovers the tests normally. These are focused evidence
boundaries, not a statement that the final full suite or every platform has passed.

## Relationship to main and issue #3499

The integrated main baseline `50aa4be3` already includes #3502's nested Python
declaration ownership fix for the original #3499 case and #3504's aliased package
re-export fix. Their [Python integration coverage](../../gitnexus/test/integration/resolvers/python.test.ts)
and [module namespace coverage](../../gitnexus/test/unit/scope-resolution/python/python-module-namespace-construction.test.ts)
remain relevant. This branch extends that base with the lexical claims, provider
semantics, and persistence evidence described above. Issue coverage is **Related
#3499**; this document does not assert that all dynamic Python behavior is solved
or make an issue-status claim.

---

### Languages Objective C Provider (`docs/languages/objective-c-provider.md`)

# Objective-C Language Provider

Status: implemented

The deterministic provider is covered by focused unit and integration tests. The parser-loader ABI
smoke runs in the published multi-OS test matrix, and the native prebuild workflow owns
Objective-C together with all six vendored grammar targets. This status describes the implemented
MVP; it does not promise full Objective-C runtime dispatch.

## Goal

Add deterministic, symbol-level Objective-C analysis to GitNexus. The first release must support high-confidence code navigation and direct static dependency analysis for `.m`, `.mm`, and Objective-C `.h` files. It must not imply that Objective-C runtime dispatch is fully resolved.

The provider belongs in the existing language-provider and scope-resolution extension points. Shared ingestion code must remain language-agnostic.

## Compatibility contract

- Existing language detection and parsing must remain unchanged.
- A `.h` file must be classified from its content or surrounding context; it cannot be unconditionally claimed by Objective-C because C and C++ also use that extension.
- If Objective-C grammar loading fails, the error must clearly name the missing provider/grammar and cannot corrupt a previously valid index.
- Provider and grammar versions must be stored in index metadata. A version change that can alter node identity or edges requires a full rebuild.
- No LLM participates in parsing, name resolution, or edge creation. Analysis is Tree-sitter plus deterministic static resolution.

## MVP model

The provider must extract and connect:

- Classes, superclasses, protocols, categories, class extensions, properties, ivars, C functions, imports, declarations, and implementations.
- Instance and class methods, preserving their complete multi-part selector.
- Inheritance, protocol conformance, import, declaration/implementation, host-class/category, and statically resolved call relationships.

Stable identity must include enough ownership to distinguish same-named methods. Recommended forms are:

```text
objc:class:<ClassName>
objc:protocol:<ProtocolName>
objc:category:<HostClass>:<CategoryName>
objc:method:<Owner>:-:<selector>
objc:method:<Owner>:+:<selector>
objc:function:<qualified-or-file-scoped-name>
```

For example, `-loadData:completion:` and `+loadData:completion:` are different symbols. A category method remains linked to both its category and host class; querying the host class must expose distributed implementations.

## Resolution policy

Resolution must be conservative. A missing or dynamic target is evidence of uncertainty, not proof that no target exists.

| Receiver case                                                                                             | Required result                                                                                                        |
| --------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------- |
| Explicit class name, `self`, or `super`                                                                   | Resolve when the owner is statically known.                                                                            |
| Local, parameter, property, or ivar with known static type                                                | Resolve to matching owner and selector.                                                                                |
| Protocol-typed receiver                                                                                   | Link the protocol method and identify possible implementations as candidates.                                          |
| Multiple host-class/category implementations of one selector                                              | Record all static candidates as evidence; do not emit a certain call edge because runtime image-load order is unknown. |
| `id`, `Class`, macros, reflection, `performSelector:`, `NSInvocation`, runtime injection, or unknown type | Store selector/location with `resolution=unresolved`; do not emit a certain call edge.                                 |

The provider should first collect file-local declarations, imports, and types, then resolve across the repository. It must use structured Tree-sitter captures or AST traversal, not regular expressions over source text. Multi-part selectors, block arguments, nullability annotations, generics, macros, and multiline declarations make a regex-only extractor unsafe.

## Imports and incremental correctness

- Resolve quoted project imports against the current directory, configured include roots, and indexed headers. Model framework imports as external-module evidence without downloading SDK source.
- Merge `@interface`, `@implementation`, categories, and extensions across files.
- A changed header, protocol, class declaration, or category invalidates importing and affected implementation/call-resolution state. Incremental output after such a change must match a full rebuild.
- Index metadata must record provider version, grammar version, include/exclude configuration, and parsing options used for resolution.

## Implementation sequence

1. Add and package a pinned Objective-C Tree-sitter grammar; verify macOS arm64 and the production Linux runner can load it.
2. Add language detection for `.m`, `.mm`, and content-classified `.h` files.
3. Implement AST extraction and stable IDs for declarations and definitions.
4. Implement repository-level merge, imports, inheritance, protocol, and category relationships.
5. Add conservative message-send resolution and explicit unresolved evidence.
6. Integrate invalidation, metadata comparison, MCP/CLI output, and fixtures.

## Fixtures and acceptance

Create a minimal Objective-C fixture containing a class, protocol, category, extension, superclass, properties, ivars, C function, imports, multi-part selector, block parameter, `self`, `super`, protocol receiver, and `id` receiver. Use `symodulebridge` as a real integration fixture after the minimal suite is stable.

The acceptance bar is:

- `query "SYModuleCaller"` yields class/method semantic nodes, not only file nodes.
- `context "SYModuleCaller" --file <path>` yields declaration, implementation, imports, and known references.
- Known statically typed message sends create call edges; dynamic sends are marked unresolved.
- Same selector on multiple classes, a category override, and `+` versus `-` methods remain distinct.
- A `.m`, `.h`, protocol, or category edit produces results equivalent to a clean rebuild.
- Generated documentation, dependency directories, and build output are excluded through explicit indexing configuration.

## Non-goals

The MVP does not promise exact runtime type inference for `id` or `instancetype`, reflection, swizzling, arbitrary category replacement, dynamic selector construction, or complete impact analysis across every runtime dispatch path. Tool results must surface confidence and unresolved evidence rather than presenting guesses as certain graph facts.

## Current implementation coverage

Implemented capabilities:

- Vendored `tree-sitter-objc` grammar, registered through the existing Tree-sitter loader.
- `.m` and `.mm` language mapping plus content-based `.h` classification so plain C/C++ headers are not unconditionally claimed.
- LanguageProvider extraction for classes, protocols, categories, extensions, methods, properties, ivars, C functions, imports, unresolved message evidence, stable Objective-C qualified names, and provider/grammar metadata.
- Length-preserving preprocessing of bare, file-scope all-caps macro markers before Tree-sitter parsing. This recovers declarations after wrappers such as `RCT_EXTERN_C_BEGIN` / `RCT_EXTERN_C_END` without expanding macros or adding framework-specific rules.
- ScopeResolver edges for imports, inheritance, protocol conformance, category host membership, implementation evidence, and conservative static message sends.
- Persisted query/context support for Objective-C class and method nodes, including implementation evidence via `DECLARES`.
- Regression tests for grammar loading, `.h` classification, stable identities, conservative calls, metadata feature mismatch, persisted query/context behavior, and incremental-vs-force parity for Objective-C fixture edits.

Known limits of this MVP:

- The first version does not perform full Objective-C runtime dispatch, swizzling, dynamic selector construction, macro expansion, or `id` flow inference. Bare file-scope marker macros are elided only to preserve parser recovery; their expansion semantics are not interpreted.
- Protocol receiver handling records the protocol method and candidate implementation evidence, but candidate implementations are not emitted as certain call edges.
- When a host class and one or more named categories define the same selector, the provider records candidate evidence rather than choosing a runtime winner or emitting multiple certain call edges.
- Objective-C++ `.mm` files are parsed with the Objective-C grammar path for this MVP; deep C++ semantic extraction inside Objective-C++ bodies remains outside this provider.

---

### Plans 2026 08 04 Gitnexus Plan Python Dotted Namespace Receiver (`docs/plans/2026-08-04-gitnexus-plan-python-dotted-namespace-receiver.md`)

# GitNexus Engineering Plan

> Task: Emit the missing `CALLS` edge for Python's unaliased multi-segment namespace import (`import pkg.db` + `pkg.db.session_scope()`), issue #2826.
> Evidence verified at commit b2cd1c2ad637657125248c0dd2046de71ceea965; GitNexus index 13 commits behind HEAD, refresh skipped: every cited path is byte-identical between the index commit (1ef6447e) and the pinned commit — verified by blob-id comparison, so no graph claim here rests on drifted content. PDG layer absent from this index (`MATCH ()-[r:CodeRelation {type:'CDG'}]->() RETURN count(r)` → 0); `--pdg` upgrade skipped, source reads substitute at higher evidence strength.
> Evidence provenance schema 2; global dirty digest 0912a3ee3219cb75c82aefbf9f010e8dbe313150d6553768fd55d22af87a135c; cited-path manifest 13 sorted entries; exact generated plan path excluded.

## 1. Objective

`import pkg.db` followed by `pkg.db.session_scope()` must emit a `CALLS` edge from the caller to `session_scope`, matching the three sibling import spellings that already resolve (`from pkg.db import session_scope`, `import pkg.db as pdb`, `from pkg import db`). Two same-package imports in one file (`import pkg.a` + `import pkg.b`) must not cross-resolve, and no shared file under `gitnexus/src/core/ingestion/` may name a language (AGENTS.md §42).

## 2. Current Behaviour

The failure is a **key/lookup mismatch inside one map**, not a missing resolution path.

For `import pkg.db`, `splitImportStmt` emits one match with `@import.source` = the whole `dotted_name` text `"pkg.db"` `[verified]` (`gitnexus/src/core/ingestion/languages/python/import-decomposer.ts:46-54`). `interpretPythonImport`'s `'plain'` arm then splits it `[verified]` (`gitnexus/src/core/ingestion/languages/python/interpret.ts:33-42`):

```ts
    case 'plain': {
      // `import numpy`
      if (sourceCap === undefined) return null;
      return {
        kind: 'namespace',
        localName: sourceCap.text.split('.')[0]!, // `import a.b.c` exposes `a`
        importedName: sourceCap.text,
        targetRaw: sourceCap.text,
      };
    }
```

`finalizeImportEdges` carries both halves onto the edge: `localName` verbatim, and `targetExportedName = parsed.importedName` for `kind === 'namespace'` `[verified]` (`gitnexus-shared/src/scope-resolution/finalize-algorithm.ts:398-406, 434-447`). So the finalized `ImportEdge` is `{ localName: 'pkg', targetExportedName: 'pkg.db', targetFile: 'pkg/db.py', kind: 'namespace' }`.

`collectNamespaceTargets` keys **only on `localName`** `[verified]` (`gitnexus/src/core/ingestion/scope-resolution/scope/namespace-targets.ts:44-57`), producing `{'pkg' → ['pkg/db.py']}`.

At the call site, Python's query binds the attribute's `object` field with a wildcard — `object: (_) @reference.receiver` `[verified]` (`gitnexus/src/core/ingestion/languages/python/query.ts:267-270`) — so for `pkg.db.session_scope()` the receiver node is the inner `attribute`, and `extractExplicitReceiver` takes its raw text `[verified]` (`gitnexus/src/core/ingestion/scope-extractor.ts:1235-1239`): `receiverName === 'pkg.db'`.

`emitReceiverBoundCalls` then walks its cases `[verified]` (`gitnexus/src/core/ingestion/scope-resolution/passes/receiver-bound-calls.ts:404-421, 546-655, 831-848`):

- **Case 0 (compound receiver)** fires because `receiverName.includes('.')` (line 563-567). It asks `resolveCompoundReceiverClass` for a **class**; `pkg.db` names a module, so it returns `undefined`, sets `compoundReceiverUnresolved = true`, and — critically — does **not** `handledSites.add`, so control falls through (lines 577, 622-655).
- **Case 1 (namespace receiver)** runs `namespaceTargets.get('pkg.db')` (line 832). The map holds `'pkg'`. Miss.
- **Case 1.5** needs `provider.resolveQualifiedReceiverMember`, implemented only by the C++ provider `[verified]` (`gitnexus/src/core/ingestion/languages/cpp/scope-resolver.ts:399-406`; `context` on that symbol shows one outgoing call to `resolveCppQualifiedNamespaceMember` and no other implementer). Python leaves it undefined, so the case is skipped.

No later case types a module receiver, so the site drops. Reproduced on both `origin/main` and PR #2810's head; PR #2810 changes Python receiver *typing* (`languages/python/receiver-binding.ts`) and does not touch this path `[verified]` by running the repro against both trees.

The three sibling spellings resolve because each binds a **single-segment** local name: `pdb` (alias arm), `session_scope` (named binding, not a receiver at all), and `db` (reclassified to `kind: 'namespace'` by #2770's `isNamespaceImport` hook, keying the map on `'db'`).

## 3. Relevant Architecture

`collectNamespaceTargets` is the shared, language-neutral bridge between finalized import edges and receiver resolution. Its contract note already states that `ImportEdge.kind === 'namespace'` is authoritative and that providers may reclassify into it — that reclassification hook (`isNamespaceImport`) is #2770's extension point `[verified]` (`gitnexus-shared/src/scope-resolution/finalize-algorithm.ts:99-107`).

Its output feeds three consumers, all per-file (`fileCompoundOpts`, `receiver-bound-calls.ts:405-406`):

1. `emitReceiverBoundCalls` Case 1 — namespace-receiver member calls (`receiver-bound-calls.ts:832`);
2. `resolveConstructionExpressionClass` — namespace-qualified construction `pkg.db.Model()` (`compound-receiver.ts:245-260`);
3. `resolveCompoundReceiverClass`'s namespace-qualified-constructor disambiguation `options.namespaceTargets?.has(objExpr)` (`compound-receiver.ts:759-766`).

AGENTS.md line 42 is the binding constraint: *"Shared code in `gitnexus/src/core/ingestion/` must not name languages — plug language behavior in via `LanguageProvider` / `ScopeResolver` hooks."* `[verified]`

## 4. GitNexus Findings

- `context({name: 'collectNamespaceTargets', repo: 'GitNexus'})` — `epistemic: "exact"`; incoming calls are exactly two: `emitReceiverBoundCalls` (`.../passes/receiver-bound-calls.ts`) and a test-local `build` in `test/unit/scope-resolution/python/python-module-namespace-construction.test.ts`. `[graph]` These are the d=1 dependents; the two `compound-receiver.ts` consumers reach the map by parameter rather than by call, so they do not appear here and were found by source grep `[verified]`.
- `context({name: 'resolveQualifiedReceiverMember', repo: 'GitNexus'})` — resolves to a single definition at `languages/cpp/scope-resolver.ts:399`, `outgoing.calls: [resolveCppQualifiedNamespaceMember]`, no incoming. `[graph]` Confirms the Case-1.5 hook is C++-only, matching the issue reporter's read of the published bundle.
- `cypher({statement: "MATCH ()-[r:CodeRelation {type: 'CDG'}]->() RETURN count(r)"})` — `| cdg_rows | 0 |`. `[graph]` The index carries no PDG layer; §5 is therefore empty by fact, not by omission.
- Related tests located by directory listing `[verified]`: `test/fixtures/lang-resolution/` already holds `python-module-import`, `python-bare-import`, `python-plain-import-alias`, `python-multi-segment-ancestor-import`, `python-function-local-namespace-import`, `python-class-body-namespace-import`, and #2770's `python-from-module-alias`. `test/integration/resolvers/python.test.ts` is the convention-matching home for the new assertions (#2770 added its coverage there, +38 lines).

## 5. Statement-Level PDG Findings

Empty by fact: the current index has zero `CDG` rows, so no statement-level slice exists to build. A `--pdg` re-index was deliberately not run — it is the largest fixed cost available to this session, the analyzer holds no writer lock against a live MCP server (#2658), and every constraint the slice would supply (which case gates the namespace lookup, whether Case 0's failure falls through) was read directly from source at higher evidence strength in §2.

## 6. Proposed Changes

### 6.1 `collectNamespaceTargets` — also key on the dotted access path

- **File:** `gitnexus/src/core/ingestion/scope-resolution/scope/namespace-targets.ts`
- **Symbol:** `collectNamespaceTargets` (source-verified)
- **Responsibility:** map every receiver spelling that names an imported module to that module's file(s).
- **Change:** inside the existing edge loop, after recording `edge.localName`, also record `edge.targetExportedName` **when it contains a dot and its first dot-separated segment equals `edge.localName`**. Same array-dedupe as the existing key.
- **Why this is language-neutral (AGENTS.md §42):** the condition names no language. It encodes one structural fact — *a namespace binding whose exported module name is a dotted path rooted at the local name is also reachable under that whole path.* Verified against every other namespace-emitting provider at the pinned commit `[verified]`:
  - TypeScript `import * as X from './y'` → `localName 'X'`, `importedName './y'`; first segment `''` ≠ `'X'` → no key (`languages/typescript/interpret.ts:77-81, 118-122`).
  - C# `using System.Collections.Generic` → `localName 'Generic'` (last segment), `importedName 'System.Collections.Generic'`; first segment `'System'` ≠ `'Generic'` → no key (`languages/csharp/interpret.ts:33-37, 62-66`).
  - Go / Rust / Ruby → `localName === importedName`, no dot → no key (`languages/{go,rust,ruby}/interpret.ts`).
  - Python `import pkg.db` → `'pkg' === 'pkg.db'.split('.')[0]` → key `'pkg.db'` added. This is the only provider the predicate admits today.
- **Constraint:** additive only. The existing `localName` key must keep its current value and ordering so no currently-resolving site changes target.
- **Two-package safety:** `import pkg.a` + `import pkg.b` in one file yields `{'pkg' → ['pkg/a.py','pkg/b.py'], 'pkg.a' → ['pkg/a.py'], 'pkg.b' → ['pkg/b.py']}`. Receiver `pkg.a` hits exactly one file; the ambiguous `'pkg'` bucket is only reachable by a receiver literally spelled `pkg`, which is unchanged from today. `[inferred]` — pinned by a test in §8.

### 6.2 `isNamespaceNameShadowed` — test the root segment, not the dotted path

- **File:** `gitnexus/src/core/ingestion/scope-resolution/passes/compound-receiver.ts`
- **Symbol:** `isNamespaceNameShadowed` (source-verified, lines 152-183) and its one call site at line 250.
- **Defect this fix activates:** the guard walks the scope chain looking for a binding, type binding, lexical name, or owned def **named exactly `namespaceName`**. With 6.1 in place, `namespaceName` can be `'pkg.db'`, but Python binds only `pkg` — so a local `pkg = something` that genuinely shadows the import would fail to suppress the namespace interpretation, and the "verified namespace is authoritative" branch (line 249-259) would return a wrong class instead of declining.
- **Change:** shadow-test the first dot-separated segment of `namespaceName` (identical behaviour for the single-segment names it sees today, since root === whole name).
- **Not scope creep:** 6.1 is what first routes a dotted name into this guard; shipping 6.1 without it introduces the false positive.

### 6.3 No change required in `receiver-bound-calls.ts`

Case 1's lookup already uses the full dotted `receiverName` and Case 0's failure already falls through to it (`receiver-bound-calls.ts:577, 622-655, 832`) `[verified]`. Recorded here so the executor does not "fix" a path that is already correct.

## 7. Implementation Sequence

1. **Add the failing fixture and assertions first.** Create `gitnexus/test/fixtures/lang-resolution/python-dotted-namespace-import/` (files in §8) and a `describe` block in `gitnexus/test/integration/resolvers/python.test.ts` following the file's existing `writeFixtureRepo` + `mkdtempSync` convention. Confirm the dotted row fails and all three control rows pass. Delete the scratch `gitnexus/test/integration/resolvers/repro-2826-python-dotted-import.test.ts` in this step — its content is superseded by the fixture-backed tests.
2. **Implement 6.1** in `namespace-targets.ts`, and update its header contract note to state that a namespace edge may be keyed both by its local name and by a dotted access path rooted at that name. Re-run the step-1 tests: the dotted row must flip to passing with the controls still green.
3. **Implement 6.2** in `compound-receiver.ts` with the shadowing test from §8 (a local `pkg = Decoy()` must suppress, not misresolve).
4. **Run the regression surface**: full resolver + scope-resolution integration suites, both packages' `tsc --noEmit`.
5. **Regenerate recorded baselines once, last.** Run each `--check` gate; regenerate only the baselines that actually moved (`bench/receiver-resolution/baseline.json` is the expected one — this change adds resolved edges). Per plan-template §7, this is deliberately the final step so intermediate commits do not churn and re-drift the artifacts.

## 8. Test Strategy

**New fixture** `gitnexus/test/fixtures/lang-resolution/python-dotted-namespace-import/`:

| file | contents |
| --- | --- |
| `pkg/__init__.py` | empty |
| `pkg/db.py` | `def session_scope(): ...` |
| `pkg/cache.py` | `def session_scope(): ...` — the decoy that makes cross-resolution detectable |
| `caller_dotted.py` | `import pkg.db` + `def uses_dotted(): return pkg.db.session_scope()` |
| `caller_from.py`, `caller_alias.py`, `caller_frommod.py` | the three sibling controls from the issue |
| `caller_two_pkgs.py` | `import pkg.db` **and** `import pkg.cache`, one function calling each |
| `caller_deep.py` | `import pkg.sub.deep` + `pkg.sub.deep.f()` (3-segment) |
| `caller_shadowed.py` | module-level `import pkg.db`, then a function with a local `pkg = Decoy()` before `pkg.db.session_scope()` |

**Scenarios** (input → action → expected):

1. `caller_dotted.py` → run pipeline → `CALLS` edge `uses_dotted` → `pkg/db.py:session_scope`, `reason: 'import-resolved'`. **This is the issue's acceptance row.**
2. The three sibling callers → same run → all three still resolve to `pkg/db.py:session_scope`. Regression control: a run where the controls also broke would prove nothing about row 1.
3. `caller_two_pkgs.py` → `pkg.db.session_scope()` resolves **only** to `pkg/db.py` and `pkg.cache.session_scope()` **only** to `pkg/cache.py`; assert the absence of the crossed pair explicitly, not just the presence of the right one.
4. `caller_deep.py` → 3-segment receiver resolves — proves the predicate is not hard-coded to two segments.
5. `caller_shadowed.py` → **no** edge from the shadowed function to `pkg/db.py` (6.2's guard). Fails loudly if 6.2 regresses.
6. Cross-language non-regression: the existing TypeScript / C# / Go namespace-import resolver tests must stay green unchanged — that is the executable proof the new key is not minted for them.

**Tests to update:** `gitnexus/test/integration/resolvers/python.test.ts` (add the describe block). `gitnexus/test/unit/scope-resolution/python/python-module-namespace-construction.test.ts` is a direct `collectNamespaceTargets` caller — re-run it; extend it only if its expectations enumerate map keys exhaustively.

**Verification commands** (each verified to exist in `gitnexus/package.json` / `.github/workflows/ci-tests.yml` at the pinned commit):

```bash
# from gitnexus/ — pretest:integration runs scripts/build.js, so the parse worker exists
GITNEXUS_WORKER_READY_TIMEOUT_MS=60000 npm run test:integration -- test/integration/resolvers/python.test.ts
GITNEXUS_WORKER_READY_TIMEOUT_MS=60000 npm run test:integration -- test/integration/resolvers
npm run test:unit -- test/unit/scope-resolution
npx tsc --noEmit                     # and the same in ../gitnexus-shared
node --import tsx bench/receiver-resolution/measure.mjs --check
node --import tsx bench/python-scope/measure.mjs --check
node --import tsx bench/python-scope/import-target-fingerprint.mjs --check
node --import tsx bench/scope-capture/measure.mjs --check
```

`GITNEXUS_WORKER_READY_TIMEOUT_MS=60000` is required on this host: the default 5000 ms worker-ready deadline fails as a crash-loop here (observed while reproducing the issue), which is environmental, not a code fault.

## 9. Risk and Impact Analysis

Accounting for every direct (d=1) dependent of the changed map:

| d=1 dependent | risk | mitigation |
| --- | --- | --- |
| `emitReceiverBoundCalls` Case 1 (`receiver-bound-calls.ts:832`) | New keys make previously-dropped sites resolve. A wrong target would be a *new* false edge. | The predicate admits only Python's `import a.b` shape; each new key maps to exactly one file per import statement. §8 scenario 3 pins non-crossing. |
| `resolveConstructionExpressionClass` (`compound-receiver.ts:245-260`) | `pkg.db.Model()` now takes the "verified namespace is authoritative" branch, which deliberately does **not** fall through on a miss or ambiguity — so a wrong key would convert a working heuristic resolution into a silent decline. | The branch requires `namespaceFiles.length > 0`, i.e. the import genuinely resolved. Ambiguity still returns `undefined` (`namespaceMatches.length === 1` guard). Shadowing is fixed by 6.2. |
| `resolveCompoundReceiverClass` namespace-constructor disambiguation (`compound-receiver.ts:759-766`) | `namespaceTargets.has(objExpr)` now true for dotted namespaces, routing `pkg.db.Model(x).run()` into the construction interpretation. | Correct by intent — that branch exists precisely to make a namespace-qualified bare constructor safe. Behaviour change, so §8 should include a construction row if the fixture's cost is low. |
| `test/unit/scope-resolution/python/python-module-namespace-construction.test.ts:build` | May assert exact map contents. | Re-run in step 4; extend rather than weaken if it enumerates keys. |
| C++ provider | Case 1 is skipped entirely for C++ (`provider.resolveQualifiedReceiverMember !== undefined`), but the two `compound-receiver.ts` consumers are **not** provider-gated. | C++ `#include` does not produce a `kind: 'namespace'` edge with a dotted `targetExportedName` rooted at its local name; the predicate declines. Covered by the existing C++ suites plus `bench/cpp-qualified-ns/measure.mjs --check`. |

**Recorded-artifact risk:** `bench/receiver-resolution/measure.mjs --check` gates both a shape matrix and a drop-count arm; new resolved edges are expected to move the count arm and the gate fails on drift. Regenerating in step 5 only (per §7) keeps intermediate commits clean. `bench/python-scope/*` and `bench/scope-capture/*` fingerprint captures and import-target resolution — neither is touched by this change, so a movement there is a signal to stop and investigate, not to regenerate.

**Performance:** one extra `Map.set` per multi-segment namespace import per file; the loop is already O(module import edges). No new traversal.

**No schema/version impact:** this changes what the resolver produces, not how it is stored. Existing indexes need a re-analyze to show the new edges — matching the note PR #2810 carried for the same reason.

## 10. Files Expected to Change

| File | Symbols | Reason |
| ---- | ------- | ------ |
| `gitnexus/src/core/ingestion/scope-resolution/scope/namespace-targets.ts` | `collectNamespaceTargets` | Add the dotted-access-path key (§6.1) and update the contract note |
| `gitnexus/src/core/ingestion/scope-resolution/passes/compound-receiver.ts` | `isNamespaceNameShadowed` | Shadow-test the root segment (§6.2) |
| `gitnexus/test/integration/resolvers/python.test.ts` | new `describe` block | Issue acceptance row + controls + regression rows |
| `gitnexus/test/fixtures/lang-resolution/python-dotted-namespace-import/**` | — | New fixture (§8) |
| `gitnexus/test/integration/resolvers/repro-2826-python-dotted-import.test.ts` | — | Delete; superseded by the fixture-backed tests |
| `gitnexus/bench/receiver-resolution/baseline.json` | — | Regenerate once, final step, only if `--check` moves |

## 11. Reusable Implementation Context

```
/* Detailed source-code truncated for AI context efficiency. */
```

## 12. Assumptions and Open Questions

**Assumptions** (each re-checkable cheaply by the executor):

1. Every non-Python namespace-emitting provider fails the `dotted && first segment === localName` predicate. Verified at `b2cd1c2ad` for TypeScript, C#, Go, Rust and Ruby by reading each `interpret.ts`; JavaScript, Java and PHP emit no `kind: 'namespace'` import there. **Re-check:** grep `kind: 'namespace'` across `gitnexus/src/core/ingestion/languages/*/interpret.ts`.
2. `python.test.ts` runs unconditionally — no `REGISTRY_PRIMARY_PYTHON` gate remains at the pinned commit (zero grep hits). An older parity-leg convention no longer applies.
3. The index's 13-commit lag is harmless here because every cited path is byte-identical at the index commit and the pinned commit.

**Open questions / explicitly deferred:**

- **The bogus first-segment key.** For `import pkg.db`, the map still holds `'pkg' → ['pkg/db.py']`, so `pkg.helper()` would resolve into `pkg/db.py` if that file happens to define `helper` — a pre-existing false positive this plan does **not** fix. Removing it is a separate behaviour change with its own regression surface (`python-multi-segment-ancestor-import`, `python-bare-import`). Worth pinning the current behaviour in a test so it is visible rather than silent.
- **`import a.b.c` also binds `a.b`.** Python makes intermediate packages reachable; the proposed predicate keys only the exact imported path, so `a.b.f()` under `import a.b.c` alone stays unresolved. Narrower follow-up.
- **C# has the mirror-image gap.** `using System.Collections.Generic` + `System.Collections.Generic.List` fails the predicate because C# sets `localName` to the *last* segment. Deliberately out of scope; deserves its own issue.
- **Construction coverage.** §8 does not currently include a `pkg.db.Model()` row. Add one if the fixture cost is trivial — that path (`compound-receiver.ts:245-260`) changes behaviour and is otherwise untested by this plan.

## 13. Definition of Done

1. `CALLS` edge `uses_dotted` → `pkg/db.py:session_scope` (`reason: 'import-resolved'`) is emitted, asserted by a fixture-backed test in `python.test.ts`.
2. All three sibling control rows still resolve in the same run.
3. `import pkg.a` + `import pkg.b` in one file resolve only to their own modules; the crossed pair is asserted **absent**.
4. A 3-segment receiver resolves; a package root shadowed by a local binding does **not**.
5. The scratch `repro-2826-python-dotted-import.test.ts` is deleted.
6. No file under `gitnexus/src/core/ingestion/` names a language.
7. `npm run test:integration -- test/integration/resolvers` and `npm run test:unit -- test/unit/scope-resolution` pass; `tsc --noEmit` clean in both packages.
8. Every bench `--check` in §8 passes, with `bench/receiver-resolution/baseline.json` regenerated exactly once in the final commit if and only if it moved — and any movement in `python-scope`/`scope-capture` investigated rather than regenerated.

---

### Plans 2026 08 28 Gitnexus Plan Impact File Risk (`docs/plans/2026-08-28-gitnexus-plan-impact-file-risk.md`)

# GitNexus Engineering Plan

> Task: Fix #3075 — File `impact` risk is not comparable to Function/Method risk.
> Evidence verified at commit `6bff33d14cbfe1e7b4f04bca51507e9f64ef579c` (`feat/kotlin-const-resolver`); GitNexus index 129 commits behind, refresh skipped: full-repo `--index-only --pdg` rebuild is impractical this session. Scorer and schema claims are `[verified]` from source; live inversion numbers are `[graph]` on the stale index.

## 1. Objective

Make File vs symbol `impact.risk` honest for consumers: either they can tell the scales differ, or they can compare on a shared two-axis score. Do **not** DEFINES-bridge processes/modules onto File targets (issue reporter sampled 8/10 one-importer files jumping to HIGH/CRITICAL). Do **not** retune Function HIGH/CRITICAL thresholds (agent warn-before-edit).

Acceptance:

- A File with a wider blast radius than a Function in the same file no longer looks “safer” when a consumer only reads `risk`, **or** the result states that `risk` is not comparable across kinds and offers `riskSharedAxes` for comparison.
- File targets still cannot trip HIGH/CRITICAL via `processes_affected` / `modules_affected` unless those axes become real in the index (they are not today).
- Existing Function/Method labels under the current four-axis ladder stay the same for the same inputs.
- MCP `riskNote` remains UNKNOWN-only (`tools.ts` contract).

## 2. Current Behaviour

Callgraph `impact` ends in `LocalBackend._runImpactBFS` (`gitnexus/src/mcp/local/local-backend.ts`). After BFS it enriches impacted ids with `STEP_IN_PROCESS` and `MEMBER_OF`, then scores:

```7720:7738:gitnexus/src/mcp/local/local-backend.ts
    } else if (
      directCount >= 30 ||
      processCount >= 5 ||
      moduleCount >= 5 ||
      impacted.length >= 200
    ) {
      risk = 'CRITICAL';
    } else if (
      directCount >= 15 ||
      processCount >= 3 ||
      moduleCount >= 3 ||
      impacted.length >= 100
    ) {
      risk = 'HIGH';
    } else if (directCount >= 5 || impacted.length >= 30) {
      risk = 'MEDIUM';
    } else {
      risk = 'LOW';
    }
```

Empty upstream → `UNKNOWN` + `riskNote`. Downstream empty stays LOW. `skipEnrichment` (ambiguous probes) already scores on direct+total only. PDG mode forces `risk: UNKNOWN` (`composeUnifiedPdgImpactResult`) — out of scope.

File BFS walk is mostly File←IMPORTS File. Enrichment queries those File ids. Processes are CALLS traces (`process-processor.ts`); communities admit only Function/Class/Method/Interface (`isCommunitySymbol` in `community-processor.ts:412-416`). File is not in that set. `enrichCandidateLabels` UNION also **omits File**, so File `target.type` is often `""`; detect File via `id` prefix `File:`.

Web Graph RAG (`gitnexus-web/src/core/llm/tools.ts` ~1331–1346) duplicates the same ladder.

## 3. Relevant Architecture

| Layer | Role |
|---|---|
| Index | File never sources `STEP_IN_PROCESS` / `MEMBER_OF` by construction |
| MCP `_runImpactBFS` | Blast radius + four-axis `risk` |
| Ambiguous probes | `skipEnrichment` → 2-axis `risk` already |
| `mergeRisk` | Group overlay; monotone in crossings; does not know target kind |
| CLI `formatImpactResult` | Prints counts; **does not print `risk`** on the resolved callgraph path; JSON `impactCommand` still ships `risk` |
| `ai-context.ts` / `tools.ts` | Agent contract: warn on HIGH/CRITICAL; `riskNote` UNKNOWN-only |
| Web LLM `impact` | Same formula, prose `RISK:` line |

Modules: Local (MCP), Cli (format/docs), Group (`mergeRisk`), gitnexus-web LLM tools. Shared package `gitnexus-shared` is already a dependency of both CLI and web.

## 4. GitNexus Findings

- Primary: `_runImpactBFS` — d=1 `[graph]` `impact(target:_runImpactBFS, maxDepth:1, includeTests:true)`: `_impactImpl`, `impactByUid`. Production chain `[verified]`: `impact` → `_impactImpl` → `_runImpactBFS`; `impactByUid` skips per-symbol process lists but **not** aggregation (`skipPerSymbolEnrichment` only).
- `LocalBackend.impact` d=1 `[graph]` `context`: `callTool`.
- Duplicate scorer `[verified]` grep: `gitnexus-web/src/core/llm/tools.ts`.
- `mergeRisk` `[verified]` callers in `src/`: only `runGroupImpact` (`cross-impact.ts:907`). Graph d=1 listed a test File (`impact-pdg-shape.test.ts`) and missed `runGroupImpact` — trust source.
- Schema `[verified]`: `isCommunitySymbol` excludes File; `schema.ts` documents MEMBER_OF as Function/Class/Method/Interface only.
- Live inversion `[graph]` stale index, `impact summaryOnly` on GitNexus:

| target | kind | impacted | direct | processes | modules | risk |
|---|---|---|---|---|---|---|
| `lbug-config.ts` | File | 54 | 12 | 0 | 0 | MEDIUM |
| `openLbugConnection` | Function | 16 | 9 | 3 | 2 | HIGH |
| `local-backend.ts` | File | 12 | 10 | 0 | 0 | MEDIUM |
| `refreshRepos` | Method | 50 | 5 | 4 | 7 | CRITICAL |

- Clusters/processes resources `[graph]`: Local/Cli/Group sit in the impact path; process traces are function-stepped, not File-stepped.
- Related tests `[verified]`: `test/unit/impact-pagination.test.ts` (CRITICAL from `direct=400`); `test/integration/impact-zero-caller-risk.test.ts` (`withTestLbugDB` seed — pattern to extend); `test/unit/eval-formatters.test.ts` (`formatImpactResult`); group `mergeRisk` tests.

## 5. Statement-Level PDG Findings

PDG unavailable (`pdg_query` on `_runImpactBFS`: “no PDG layer”). Recommend `node .gitnexus/run.cjs analyze --index-only --pdg` before any future statement-slice work. Control flow of the scorer is a straight if/else after enrichment; no hidden guards. `skipEnrichment` is the only branch that structurally zeros process/module counts besides File ids.

## 6. Proposed Changes

### 6.1 Extract `scoreImpactRisk` — `gitnexus-shared/src/impact-risk.ts` (new)

- **Responsibility:** Pure function: `{ direction, directCount, processCount, moduleCount, impactedCount, unusedAxes }` → `{ risk, riskSharedAxes, riskScale }`.
- **Behaviour:** Existing UNKNOWN/CRITICAL/HIGH/MEDIUM/LOW thresholds unchanged when `unusedAxes` is empty. `riskSharedAxes` always scores as if `processCount=0` and `moduleCount=0` (UNKNOWN rule still applies). `riskScale.comparableAcrossKinds` is false iff `unusedAxes` is non-empty. `riskScale.unusedAxes` lists `{ axis, reason }`.
- **Constraints:** Zero deps. Export from `gitnexus-shared/src/index.ts`. Do not put MCP types here.
- **File detection:** caller passes unused axes; helper does not parse UIDs.

### 6.2 Wire MCP — `_runImpactBFS` in `local-backend.ts`

- After computing `processCount`/`moduleCount`, set `unusedAxes`:
  - target `id` starts with `File:` **or** `symType === 'File'` → processes + modules, reason `file-nodes-have-no-process-or-community-membership`;
  - `skipEnrichment` → same axes, reason `enrichment-skipped` (ambiguous probes).
- Replace inline ladder with `scoreImpactRisk`.
- Spread `riskScale` and `riskSharedAxes` on the result next to `risk`. Do **not** set `riskNote` for File.
- Ambiguous candidate summaries: forward the new fields (probes already skip enrichment).
- `target.type` for File: if still `""`, prefer `'File'` when `id` starts with `File:` (display-only; helps CLI).

### 6.3 Web duplicate — `gitnexus-web/src/core/llm/tools.ts`

- Import `scoreImpactRisk` from `gitnexus-shared`. Print `RISK:` from `risk`; if `!comparableAcrossKinds`, one extra line: not comparable to Function risk; shared-axes label is `riskSharedAxes`.

### 6.4 Agent/MCP contract copy

- `gitnexus/src/mcp/tools.ts` impact description: document `riskScale` / `riskSharedAxes`; keep `riskNote` UNKNOWN-only; say File `risk` is not comparable to symbol `risk`.
- `gitnexus/src/cli/ai-context.ts`: HIGH/CRITICAL warning still applies; add: do not rank a File `MEDIUM` below a contained Function `HIGH` without `riskSharedAxes`.
- `formatImpactResult`: on resolved callgraph results with `risk`, print `Risk: {risk}` and, when incomparable, `Shared-axes risk: {riskSharedAxes} (File/process axes unused)`.

### 6.5 Explicitly not changing

- DEFINES-bridge, community/process indexers, `mergeRisk` formula, PDG `UNKNOWN`, `detectChanges` `risk_level`, Function thresholds.

## 7. Implementation Sequence

1. Add `gitnexus-shared` helper + unit table (issue-shaped inputs + UNKNOWN + skipEnrichment). Shared package tests if present; otherwise `gitnexus/test/unit/impact-risk.test.ts` importing the helper.
2. Switch `_runImpactBFS` + candidate probe payload. Tree still coherent: old `risk` values identical for Function fixtures.
3. Integration seed in `impact-zero-caller-risk.test.ts` **or** new `impact-file-risk-scale.test.ts`: File with ≥5 File IMPORTS (MEDIUM on direct) vs Function with 3 process-member callers (HIGH); assert File `riskScale.comparableAcrossKinds === false`, Function true, File `riskSharedAxes === risk`, Function `riskSharedAxes` is LOW/MEDIUM while `risk` is HIGH.
4. CLI formatter + `eval-formatters.test.ts`.
5. `tools.ts` + `ai-context.ts` wording.
6. Web import + a unit assertion on the printed RISK block if a test already covers that tool.
7. `npx tsc --noEmit` in `gitnexus/` and `gitnexus-web/`; `cd gitnexus && npm run test:unit -- test/unit/impact-risk.test.ts test/unit/eval-formatters.test.ts`; integration file from step 3.

## 8. Test Strategy

| File | Scenarios |
|---|---|
| `gitnexus/test/unit/impact-risk.test.ts` (new) | Issue table: File(25,13,0,0)→MEDIUM; Function(15,2,4,2)→HIGH; shared-axes File MEDIUM vs Function LOW; empty upstream UNKNOWN; downstream empty LOW; skipEnrichment unused axes; CRITICAL via direct≥30 still works with unused process axes |
| `gitnexus/test/integration/impact-file-risk-scale.test.ts` (new) | `withTestLbugDB` seed: `File:src/crypto.ts` ← 13 File IMPORTS, no File STEP_IN_PROCESS; `getEncryptionKey` with 2 CALLS from functions that have STEP_IN_PROCESS to 4 distinct Process nodes — reproduce inversion; assert new fields |
| `gitnexus/test/integration/impact-zero-caller-risk.test.ts` | Unchanged UNKNOWN/`riskNote`; candidates may grow `riskScale` — assert still present only when UNKNOWN for `riskNote` |
| `gitnexus/test/unit/impact-pagination.test.ts` | Hub CRITICAL unchanged |
| `gitnexus/test/unit/eval-formatters.test.ts` | Resolved result prints Risk + shared-axes line for File-shaped `riskScale` |
| Web | Only if an existing Graph RAG impact test snapshots `RISK:` |

Commands (exist in `gitnexus/package.json`): `npm run test:unit`, `npm test` (full vitest), `npx tsc --noEmit`. Web: `npm test`, `npx tsc -b --noEmit`. Integration needs `pretest:integration` / `npm run test:integration` (runs `scripts/build.js`).

## 9. Risk and Impact Analysis

Direct dependents of `_runImpactBFS` `[graph]`: `_impactImpl`, `impactByUid`. `_impactImpl` is the only d=1 of `impact` besides the method’s own class. Any JSON consumer of `impact` (MCP, CLI `output(result)`, group local leg) sees additive fields — compatible if they ignore unknowns.

- **HIGH workflow:** Function HIGH/CRITICAL unchanged. File still cannot reach HIGH via processes; a File with `direct≥15` or `total≥100` still can. Agents that compare File MEDIUM vs Function HIGH must start using `riskSharedAxes` or `riskScale`.
- **Ambiguous `maxRisk`:** probes skip enrichment, so File vs Function candidates are already 2-axis there — inversion is weaker on that path.
- **Group `mergeRisk`:** still compares incomparable File local `risk` to crossing count. Do not retune this PR; if a group File target is common, follow-up.
- **Web:** browser bundle picks up `gitnexus-shared` export — confirm `gitnexus-shared` build/exports include the new file.
- **Performance:** none (pure arithmetic after existing enrichment).
- **Ladybug empty labels:** File detection must not rely on `symType` alone.

## 10. Files Expected to Change

| File | Symbols | Reason |
|---|---|---|
| `gitnexus-shared/src/impact-risk.ts` | `scoreImpactRisk` | New shared scorer |
| `gitnexus-shared/src/index.ts` | exports | Public helper |
| `gitnexus/src/mcp/local/local-backend.ts` | `_runImpactBFS`, ambiguous candidate map | Wire scorer + File unused axes |
| `gitnexus/src/mcp/tools.ts` | `impact` description | Contract |
| `gitnexus/src/cli/ai-context.ts` | generated Always Do | Agent warning |
| `gitnexus/src/cli/eval-server.ts` | `formatImpactResult` | Print scale |
| `gitnexus-web/src/core/llm/tools.ts` | web `impact` | Same formula |
| `gitnexus/test/unit/impact-risk.test.ts` | — | Table tests |
| `gitnexus/test/integration/impact-file-risk-scale.test.ts` | — | Seeded inversion |
| `gitnexus/test/unit/eval-formatters.test.ts` | `formatImpactResult` | Formatter |

## 11. Reusable Implementation Context

```
/* Detailed source-code truncated for AI context efficiency. */
```

## 12. Assumptions and Open Questions

**Assumptions**

- Indexer will not start attaching File→Process/Community in this change (`isCommunitySymbol` stays). `[verified]` source; `[assumed]` future indexers.
- Ignoring unknown JSON keys is safe for MCP clients; any `toEqual` goldens in-repo must be updated. `[assumed]` — grep during implement.
- Stale-index inversion (`lbug-config.ts` vs `openLbugConnection`) is illustrative; the integration seed is the regression lock. `[graph]` vs `[verified]` seed.

**Open questions**

- Group `mergeRisk` + File local risk: copy `riskScale` onto `GroupImpactResult`? Default **no** unless a test breaks.
- Class/Interface STEP_IN_PROCESS sparsity: out of scope (#3075 is File).
- Printing `risk` on CLI formatted output is new (JSON already has it). Keep the extra lines short.

**Deferred**

- Recalibrated File-only HIGH thresholds.
- Indexing File community membership.
- DEFINES-bridge after a threshold RFC.
- Related #2975 (docs vs scorer wording) except as touched by `tools.ts`.

## 13. Definition of Done

- [ ] `scoreImpactRisk` is the only callgraph ladder in MCP and web.
- [ ] File (and skipEnrichment) results include `riskScale.comparableAcrossKinds === false` and `riskSharedAxes`.
- [ ] Function four-axis HIGH/CRITICAL cases in unit tests still pass with the same labels.
- [ ] Integration seed proves wider File blast + lower `risk` than a contained Function, and `riskSharedAxes` orders them without pretending processes existed on the File.
- [ ] `riskNote` still absent unless `risk === 'UNKNOWN'`.
- [ ] `tools.ts` + `ai-context.ts` state that File `risk` is not comparable to symbol `risk`.
- [ ] `cd gitnexus && npx tsc --noEmit` and the named unit/integration commands pass; web typecheck passes.

---

--- METRICS ---
- Files Extracted: 7
- Estimated Token Budget: ~49202 tokens
- Canonical Reference: https://codewiki.google/github.com/abhigyanpatwari/GitNexus
