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* feat(storage): add configurable index storage and content retention tiers Rebase #3060 onto current origin/main. Keep GITNEXUS_STORAGE_PATH, GITNEXUS_STORAGE_ROOT, and GITNEXUS_CONTENT_RETENTION, and fold in main's FTS skip, embed-session, and help-text updates. Co-authored-by: Cursor <cursoragent@cursor.com> * Address PR review feedback (#3060) Keep legacy registry rows on the local storage fallback, resolve symlinks before the destructive-path guard, and align hook lookup with CLI branch slugs, branch-slot metadata, and longest-path match. Co-authored-by: Cursor <cursoragent@cursor.com> * Address PR review feedback (#3060) Only list swept upload directories after a successful removal so callers cannot treat a permission or transient rm failure as gone. Co-authored-by: Cursor <cursoragent@cursor.com> * Address PR review feedback (#3060) Document that getStoragePath may consult registered storage while this module still does not mutate the global registry. Co-authored-by: Cursor <cursoragent@cursor.com> * fix(storage): close review findings for external indexes and retention Re-inspect ownership under the analyze lock, fail-closed when the registry file is missing, and keep skip-git hook discovery plus retention fields on HTTP/MCP list surfaces. /api/file stays 410 unless contentRetention is full. Co-authored-by: Cursor <cursoragent@cursor.com> * chore(autofix): apply prettier + eslint fixes via /autofix command * Address PR review feedback (#3060) Treat lock-only index dirs as empty, honor HTTP --force storage policy, and prefer registered plus branch-aware slots in hooks and augment. Co-authored-by: Cursor <cursoragent@cursor.com> * Address PR review feedback (#3060) Keep hook fallbacks inside the current worktree, compare foreign-local slots canonically, and make storage fixtures survive ownership validation. Co-authored-by: Cursor <cursoragent@cursor.com> * Fix macOS hook test expecting realpath'd registry paths. resolveHookRepo returns the written registry path, not a filesystem realpath, so the assertion must match that. * Address gitnexus-check warnings on hook install docs and slot tests. The Cursor troubleshooting list omitted registry-query.cjs, and the writable-slot test only checked that isDirectory exists instead of that the path is a directory. * Align the HTTP catalog source-scan with skippable resolveRepo validation. resolveRepo lists fresh repos with validate: options.validateStorage !== false so DELETE can skip prune; the test still required a literal validate: true. * Harden storage path sinks so CodeQL path-injection and ReDoS alerts clear. Contain every filesystem probe inside the resolved storage slot with the inline path.relative idiom, reject filesystem-root slots, and trim slot basenames in linear time. * Settle bridge stamps before writing so CI size/mtime matches stay stable. LadybugDB can still flush into bridge.lbug after close+rename; persist whole-millisecond mtimes and wait for consecutive stats to agree so a freshly written pair matches. * Type the settled bridge stat as fs.Stats so tsc does not see bigint. Awaited<ReturnType<typeof fsp.stat>> collapsed the bigint overload and broke prepare/typecheck on CI. * Keep the bridge mtime stamp exact so same-size swaps still fail the pair check. Co-authored-by: Cursor <cursoragent@cursor.com> * Wrap the bridge stamp predicate so prettier --check stays green. Co-authored-by: Cursor <cursoragent@cursor.com> * Require a quiet interval before stamping a settled bridge file. Co-authored-by: Cursor <cursoragent@cursor.com> * Reuse shared storage and settle helpers instead of local copies. Co-authored-by: Cursor <cursoragent@cursor.com> --------- Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com> Co-authored-by: Cursor <cursoragent@cursor.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
110 lines
8.1 KiB
Markdown
110 lines
8.1 KiB
Markdown
---
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name: gitnexus-cli
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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\""
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---
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# GitNexus CLI Commands
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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.
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> **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).
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## Commands
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### analyze — Build or refresh the index
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```bash
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node .gitnexus/run.cjs analyze
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```
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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.
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| Flag | Effect |
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| -------------- | ---------------------------------------------------------------- |
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| `--watch` | Keep a Git repository index current with serialized refreshes |
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| `--debounce <ms>` | Watch quiet period before refresh (default: 300 ms) |
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| `--force` | Force full re-index even if up to date |
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| `--embeddings` | Enable embedding generation for semantic search (off by default) |
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| `--drop-embeddings` | Drop existing embeddings on rebuild. By default, an `analyze` without `--embeddings` preserves them. |
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| `--pdg` | Build the program-dependence layers used by `explain` and `pdg_query` (taint, CDG, and REACHING_DEF). |
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| `--spring-actuator <path>` | Import opt-in Spring Boot Actuator mappings, beans, conditions, configprops, and env snapshots. Forces a full rebuild; unsupported with `--watch`. |
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| `--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`. |
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**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.
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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.
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## Index storage and retention
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Default location is `<repo>/.gitnexus/`. Override with environment variables (also documented in README):
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| Env | Effect |
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| --- | ------ |
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| `GITNEXUS_STORAGE_PATH` | One complete external index directory. Wins if both storage vars are set. |
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| `GITNEXUS_STORAGE_ROOT` | Absolute root; GitNexus creates an isolated `<repo-basename>-<12-hex>/` slot per repository. |
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| `GITNEXUS_CONTENT_RETENTION` | `full` (default) keeps file text; `symbol` keeps snippets; `none` keeps the graph only. |
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`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`.
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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.
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### status — Check index freshness
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```bash
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node .gitnexus/run.cjs status
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```
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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.
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### clean — Delete the index
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```bash
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node .gitnexus/run.cjs clean
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```
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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.
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| Flag | Effect |
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| --------- | ------------------------------------------------- |
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| `--force` | Skip confirmation prompt |
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| `--all` | Clean all indexed repos, not just the current one |
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### wiki — Generate documentation from the graph
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```bash
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node .gitnexus/run.cjs wiki
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```
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Generates repository documentation from the knowledge graph using an LLM. HTTP providers require an API key (saved to `~/.gitnexus/config.json` on first use). Local CLI providers (`--provider cursor|claude|codex|opencode|grok`) use your existing CLI login.
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| Flag | Effect |
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| ------------------- | ----------------------------------------- |
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| `--force` | Force full regeneration, also required to re-generate an existing wiki in a different language |
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| `--provider <name>` | LLM provider: minimax, openai, openrouter, azure, custom, cursor, claude, codex, opencode, or grok (default: minimax). Local CLIs (`cursor`, `claude`, `codex`, `opencode`, `grok`) use your existing CLI login and skip `--api-key`. |
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| `--model <model>` | LLM model (default: MiniMax-M3) |
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| `--base-url <url>` | LLM API base URL |
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| `--api-key <key>` | LLM API key |
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| `--concurrency <n>` | Parallel LLM calls (default: 3) |
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| `--timeout <seconds>` | LLM request timeout in seconds (default: disabled) |
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| `--retries <n>` | Max LLM retry attempts per request (default: 3) |
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| `--lang <lang>` | Output language for generated documentation (e.g. english, chinese, spanish, japanese) |
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| `--gist` | Publish wiki as a public GitHub Gist |
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### list — Show all indexed repos
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```bash
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node .gitnexus/run.cjs list
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```
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Lists all repositories registered in `~/.gitnexus/registry.json`. The MCP `list_repos` tool provides the same information.
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## After Indexing
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1. **Read `gitnexus://repo/{name}/context`** to verify the index loaded
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2. Use the other GitNexus skills (`exploring`, `debugging`, `impact-analysis`, `refactoring`) for your task
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## Troubleshooting
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- **"Not inside a git repository"**: Run from a directory inside a git repo
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- **Index is stale after re-analyzing**: Wait for the next MCP tool call to reopen the published index; this normally takes no more than five seconds
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- **Embeddings slow**: Omit `--embeddings` (it's off by default) or set `OPENAI_API_KEY` for faster API-based embedding
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