By name: codeindex-cli description: "Use only when the user explicitly asks to run CodeIndex CLI commands like analyze/index a repo, check status, clean the index, generate a wiki, or list indexed repos. Do not use this for normal code navigation, stale-index warnings, or missing MCP tools. Examples: "Index this repo", "Reanalyze the codebase", "Generate a wiki""
CodeIndex CLI Commands
Use these commands only for explicit index/setup/maintenance requests. For normal agent work, use the MCP tools (query, context, impact) and verify stale results against source files.
Commands
analyze — Build or refresh the index
codeindex analyze
Run from the project root. This parses all source files, builds the knowledge graph, writes it to ~/.codeindex/<ProjectName>/ (global cache — NEVER inside the working copy), and generates CLAUDE.md / AGENTS.md context files in the project root.
| 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 or when the user explicitly asks to
rebuild the index. Do not run this automatically just because
codeindex://repo/{name}/context reports stale data.
For Klai in Conductor, do not run ad hoc analyze/update commands from a
feature worktree. That warning can be caused by a worktree overlay or by the
registered checkout not being on main. Run scripts/codeindex-health.sh first;
only if it reports the shared base index is stale, run
scripts/codeindex-health.sh --repair.
update — Refresh an existing index
codeindex update
Use this only when the user explicitly asks to refresh a stale index. For Klai
Conductor worktrees, prefer scripts/codeindex-health.sh --repair for the
shared main index.
status — Check index freshness
codeindex status
Shows whether the current repo has a CodeIndex index, when it was last updated, and symbol/relationship counts. Use this to check if re-indexing is needed.
clean — Delete the index
codeindex clean
Deletes the repo's entry under ~/.codeindex/<ProjectName>/ and unregisters it from the global registry. Use before re-indexing if the index is corrupt or after removing CodeIndex from a project. Never deletes anything inside the working copy.
If you find a stray
.codeindex/directory inside a project root it is leftover from an older CodeIndex version. Safe to delete — the current version never writes there.
| Flag | Effect |
|---|---|
--force |
Skip confirmation prompt |
--all |
Clean all indexed repos, not just the current one |
wiki — Generate documentation from the graph
codeindex wiki
Generates repository documentation from the knowledge graph using an LLM. Requires an API key (saved to ~/.codeindex/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
codeindex list
Lists all repositories registered in ~/.codeindex/registry.json. The MCP list_repos tool provides the same information.
After Indexing
- Read
codeindex://repo/{name}/contextto verify the index loaded - Use the other CodeIndex 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 during a code task: In Conductor, run
scripts/codeindex-health.sh; if the shared main index is healthy, treat CodeIndex results as advisory and verify branch-local code with source files - Embeddings slow: Omit
--embeddings(it's off by default) or setOPENAI_API_KEYfor faster API-based embedding