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
--force
Force full re-index even if up to date
--embeddings
Enable embedding generation for semantic search (off by default)
When to run:
First time in a project, after major code changes, or when
gitnexus://repo/{name}/context
reports the index is stale.
status — Check index freshness
npx 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
npx 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
npx 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
LLM model (default: minimax/minimax-m2.5)
--base-url
LLM API base URL
--api-key
LLM API key
--concurrency
Parallel LLM calls (default: 3)
--gist
Publish wiki as a public GitHub Gist
list — Show all indexed repos
npx gitnexus list
Lists all repositories registered in
~/.gitnexus/registry.json
. The MCP
list_repos
tool provides the same information.
After Indexing
Read
gitnexus://repo/{name}/context
to verify the index loaded
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