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+---
+name: gitnexus-cli
+description: "Use when the user needs to run GitNexus CLI commands like analyze/index a repo, check status, clean the index, generate a wiki, or list indexed repos. Examples: \"Index this repo\", \"Reanalyze the codebase\", \"Generate a wiki\""
+---
+
+# GitNexus CLI Commands
+
+All commands work via `npx` — no global install required.
+
+## Commands
+
+### analyze — Build or refresh the index
+
+```bash
+npx gitnexus analyze
+```
+
+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. In Claude Code, a PostToolUse hook runs `analyze` automatically after `git commit` and `git merge`, preserving embeddings if previously generated.
+
+### status — Check index freshness
+
+```bash
+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
+
+```bash
+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
+
+```bash
+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 <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
+
+```bash
+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
+- **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