GitNexus CLI Commands

In this repo, run GitNexus through direnv exec . gitnexus ... from the repo root. The checked-in AGENTS guidance depends on the repo-local .envrc plus ignored .envrc.local embedding settings; do not use npx here.

Commands

analyze — Build or refresh the index

direnv exec . gitnexus analyze --embeddings --skip-agents-md

Run from the project root after the LM Studio embedding server is running. In a linked worktree, copy the ignored root .envrc.local into the worktree and run direnv allow first. This parses source files, builds the knowledge graph, writes ignored output to .gitnexus/, and leaves the checked-in AGENTS map as the repository source of truth.

Flag	Effect
--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.

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.

status — Check index freshness

direnv exec . gitnexus 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

direnv exec . gitnexus 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

direnv exec . gitnexus wiki

Generates repository documentation from the knowledge graph using an LLM. Requires an API key (saved to ~/.gitnexus/config.json on first use).

Flag	Effect
--force	Force full regeneration
--model <model>	LLM model (default: minimax/minimax-m2.5)
--base-url <url>	LLM API base URL
--api-key <key>	LLM API key
--concurrency <n>	Parallel LLM calls (default: 3)
--gist	Publish wiki as a public GitHub Gist

list — Show all indexed repos

direnv exec . gitnexus 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: Restart Claude Code to reload the MCP server
• Embeddings slow: Omit --embeddings (it's off by default) or set OPENAI_API_KEY for faster API-based embedding