GitNexus/gitnexus/skills/gitnexus-cli.md

name	description
gitnexus-cli	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.

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, not just the current one

wiki — Generate documentation from the graph

node .gitnexus/run.cjs wiki

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.

Flag	Effect
--force	Force full regeneration, also required to re-generate an existing wiki in a different language
--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.
--model <model>	LLM model (default: MiniMax-M3)
--base-url <url>	LLM API base URL
--api-key <key>	LLM API key
--concurrency <n>	Parallel LLM calls (default: 3)
--timeout <seconds>	LLM request timeout in seconds (default: disabled)
--retries <n>	Max LLM retry attempts per request (default: 3)
--lang <lang>	Output language for generated documentation (e.g. english, chinese, spanish, japanese)
--gist	Publish wiki as a public GitHub Gist

list — Show all indexed repos

node .gitnexus/run.cjs list

Lists all repositories registered in ~/.gitnexus/registry.json. The MCP list_repos tool provides the same information.

After Indexing

1. Read gitnexus://repo/{name}/context to verify the index loaded
2. Use the other GitNexus skills (exploring, debugging, impact-analysis, refactoring) for your task

Troubleshooting

• "Not inside a git repository": Run from a directory inside a git repo
• 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
• Embeddings slow: Omit --embeddings (it's off by default) or set OPENAI_API_KEY for faster API-based embedding