gitnexus-cli

name	gitnexus-cli
description	Use for read-only GitNexus index maintenance: check index status, list indexed repos, register or (re)build the index. Examples: "Is the GitNexus index current?", "List indexed repos", "Register this repo"

GitNexus CLI Commands

All commands work via npx — no global install required.

Read-only / analysis only. GitNexus must never write tracked files. These commands manage the index (.gitnexus/, gitignored) and the global registry (~/.gitnexus/) only. analyze is the one command that can touch CLAUDE.md / AGENTS.md — always pass --skip-agents-md, run it only when genuinely needed, and revert any tracked file it changes. Wiki/doc generation is not used under this policy. See the Read-Only Analysis Policy in agent_docs/gitnexus.md (mirrored in AGENTS.md).

Commands

analyze — (re)build the index — index-only, not routine

npx gitnexus analyze --skip-agents-md

Run from the project root. This parses all source files, builds the knowledge graph, and writes it to .gitnexus/ (gitignored). Always pass --skip-agents-md — without it, analyze ALSO rewrites the optimizer-managed CLAUDE.md / AGENTS.md context sections. Run analyze only when the index is genuinely missing/stale AND the current task needs it; it is not a routine step.

Flag	Effect
--skip-agents-md	Preserve AGENTS.md/CLAUDE.md sections — mandatory on every analyze
--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 (default: preserve them)

Mandatory revert guard: even with --skip-agents-md, after any analyze run git status and git checkout -- <paths> for any tracked file it touched (.claude/**, CLAUDE.md, AGENTS.md, docs/wiki/**). Only analyze writes tracked files — status, index, and list never do. The index itself (.gitnexus/) stays gitignored and uncommitted — never in a commit or PR.

When to run: only when gitnexus://repo/{name}/context (or status) reports the index missing/stale and the task needs a fresh index. There is no auto-analyze hook — GitNexus is analysis-only; index freshness is on-demand, never enforced on every commit/merge.

index — Register repo in global registry

npx gitnexus index .

Registers the current repo in ~/.gitnexus/registry.json so MCP tools can find it. Use this when gitnexus_query returns empty results despite a local .gitnexus/ directory existing — the local index is fine but the global registry doesn't know about it.

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 — disabled under the read-only policy

npx gitnexus wiki generates documentation files (e.g. under docs/wiki/**) from the graph — that is a write operation, so it is out of scope here. Do not run it as part of any task. If the user explicitly asks for generated docs, treat that as a separate, explicitly-requested task — never an automatic GitNexus side-effect.

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

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
• MCP tools return empty for known repo: run npx gitnexus index . to register
• Index is stale after re-analyzing: Restart the MCP host (e.g. Claude Code) to reload the MCP server
• Embeddings slow: Omit --embeddings (off by default) or set OPENAI_API_KEY for faster API-based embedding