GitNexus CLI Commands

Genesis uses the reviewed global GitNexus pin. Do not use npx: its floating package resolution can write an index format the reviewed binary cannot read.

Commands

analyze — Build or refresh the index

scripts/lib/code_intel_index.sh "$PWD" gitnexus fast

Run from the project root. The managed entrypoint provides single-flight and resource caps while GitNexus refreshes .gitnexus/. It deliberately skips linked worktrees; use Serena for live worktree truth.

The managed entrypoint accepts Genesis's fast, moderate, or full mode as its final argument. It deliberately does not forward arbitrary GitNexus flags.

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 index corruption on timeout.

status — Check index freshness

.claude/mcp/run-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

.claude/mcp/run-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

.claude/mcp/run-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-M3)
--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

.claude/mcp/run-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