/gitnexus-cli

name: gitnexus-cli
description: "Use when the user needs to run GitNexus CLI commands like analyze/index a repo, check status, clean the index, generate a wiki, or list indexed repos. Examples: \"Index this repo\", \"Reanalyze the codebase\", \"Generate a wiki\""

GitNexus CLI Commands

Commands below use `node .gitnexus/run.cjs <command>` — the project-local runner `gitnexus analyze` drops next to the index. It auto-selects an available runner at call time (global `gitnexus`, else `pnpm dlx`, else `bunx`, else `npx`), so no package-manager assumption and no global install is required — including on a bun-only machine, which has no npm, npx or pnpm at all.

> **Not analyzed yet, or `node .gitnexus/run.cjs` reports `Cannot find module`** (the gitignored runner is absent — e.g. a fresh clone or `git clean`)? (Re)generate it with `npx gitnexus analyze` from the project root, or `bunx gitnexus@latest analyze` on a bun-only machine. On **npm 11.x**, if `npx` crashes during install (`node.target is null`), install once with `npm i -g gitnexus` (then `gitnexus analyze`), or use `bunx gitnexus@latest analyze`, or `pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyze`. See [#1939](https://github.com/abhigyanpatwari/GitNexus/issues/1939).

Commands

analyze — Build or refresh the index

node .gitnexus/run.cjs analyze

Run from the project root. This parses all source files, builds the knowledge graph, writes it to `.gitnexus/`, and generates CLAUDE.md / AGENTS.md context files.

| Flag | Effect | | -------------- | ---------------------------------------------------------------- | | `--watch` | Keep a Git repository index current with serialized refreshes | | `--debounce <ms>` | Watch quiet period before refresh (default: 300 ms) | | `--force` | Force full re-index even if up to date | | `--embeddings` | Enable embedding generation for semantic search (off by default) | | `--drop-embeddings` | Drop existing embeddings on rebuild. By default, an `analyze` without `--embeddings` preserves them. | | `--pdg` | Build the program-dependence layers used by `explain` and `pdg_query` (taint, CDG, and REACHING_DEF). | | `--spring-actuator <path>` | Import opt-in Spring Boot Actuator mappings, beans, conditions, configprops, and env snapshots. Forces a full rebuild; unsupported with `--watch`. | | `--asyncapi-spec <path>` | Read opt-in AsyncAPI 3.x documents (directory or single file) and mint `Destination` nodes from their operations. 2.x is refused, not mapped. Unsupported with `--watch`. |

**When to run:** First time in a project, after major code changes, or when `gitnexus://repo/{name}/context` reports the index is stale. In Claude Code, a PostToolUse hook detects staleness after `git commit` and `git merge` and notifies the agent to run `analyze` — the hook does not run analyze itself, to avoid blocking the agent for up to 120s and risking KuzuDB corruption on timeout.

For Spring runtime enrichment, pass a JSON bundle, one endpoint JSON file, or a directory containing endpoint files. Route evidence is authoritative only when `runtimeConfirmed === true`; `runtimeSource` records provenance and may also accompany `handler-conflict`. Env/configprops values are never persisted.

Index storage and retention

Default location is `<repo>/.gitnexus/`. Override with environment variables (also documented in README):

| Env | Effect | | --- | ------ | | `GITNEXUS_STORAGE_PATH` | One complete external index directory. Wins if both storage vars are set. | | `GITNEXUS_STORAGE_ROOT` | Absolute root; GitNexus creates an isolated `<repo-basename>-<12-hex>/` slot per repository. | | `GITNEXUS_CONTENT_RETENTION` | `full` (default) keeps file text; `symbol` keeps snippets; `none` keeps the graph only. |

`list_repos`, `gitnexus://repo/{name}/context`, and HTTP `GET /api/repos` / `GET /api/repo` expose `storagePath`, `contentRetention`, and `sourceAvailable`. HTTP `/api/file` and `/api/grep` return 410 unless retention is `full`. MCP `include_content` may still return symbol spans when retention is `symbol`.

Use `node .gitnexus/run.cjs analyze --watch` for a long-lived local Git repository. It performs an initial analysis, queues scanner-admitted file changes, and retries intact failed batches with bounded backoff. Watch refreshes update only the graph: they skip AGENTS.md / CLAUDE.md injection and standard skill installation, so run a one-shot `analyze` when those generated files need updating. Watch rejects one-shot or context-output flags including `--force`, embedding flags, `--skills`, `--default-branch`, `--skip-agents-md`, `--skip-skills`, `--no-stats`, `--self-commit`, `--index-only`, and `--skip-git`. It never pulls remotes. Scheduled remote clone/pull is a different command: `gitnexus auto-sync`. Bare `gitnexus watch` is reserved and does not start either job. Running MCP and `serve` processes periodically check for a published replacement and reopen it without a restart. MCP checks are throttled to once every five seconds, so a tool call before the next check can briefly use the previous index.

status — Check index freshness

node .gitnexus/run.cjs status

Shows whether the current repo has a GitNexus index, when it was last updated, and symbol/relationship counts. Use this to check if re-indexing is needed.

clean — Delete the index

node .gitnexus/run.cjs clean

Deletes the `.gitnexus/` directory and unregisters the repo from the global registry. Use before re-indexing if the index is corrupt or after removing GitNexus from a project.

| Flag | Effect | | --------- | ------------------------------------------------- | | `--force` | Skip confirmation prompt | | `--all` | Clean all indexed repos, n