feat(plugin): add marketplace, fix manifest, and add CLI commands skill

Add .claude-plugin/marketplace.json at repo root so users can permanently
install via `/plugin marketplace add nicosxt/gitnexus`. Remove invalid
hooks/mcpServers fields from plugin.json (auto-discovered at default
locations). Add cli skill covering all agent-relevant CLI commands
(analyze, status, clean, wiki, list) with correct flags. Update guide
skill and CLAUDE.md generator routing tables.

.claude-plugin/marketplace.json

@@ -0,0 +1,19 @@
+{
+  "name": "gitnexus-marketplace",
+  "owner": {
+    "name": "GitNexus",
+    "email": "nico@gitnexus.dev"
+  },
+  "metadata": {
+    "description": "Code intelligence powered by a knowledge graph — execution flows, blast radius, and semantic search",
+    "homepage": "https://github.com/nicosxt/gitnexus"
+  },
+  "plugins": [
+    {
+      "name": "gitnexus",
+      "version": "1.2.8",
+      "source": "./gitnexus-claude-plugin",
+      "description": "Code intelligence powered by a knowledge graph. Provides execution flow tracing, blast radius analysis, and augmented search across your codebase."
+    }
+  ]
+}

gitnexus-claude-plugin/.claude-plugin/plugin.json

@@ -7,7 +7,5 @@
   },
   "homepage": "https://github.com/nicosxt/gitnexus",
   "repository": "https://github.com/nicosxt/gitnexus",
-  "keywords": ["code-intelligence", "knowledge-graph", "mcp", "static-analysis"],
-  "hooks": "./hooks",
-  "mcpServers": "./.mcp.json"
+  "keywords": ["code-intelligence", "knowledge-graph", "mcp", "static-analysis"]
 }

gitnexus-claude-plugin/skills/cli/SKILL.md

@@ -0,0 +1,82 @@
+---
+name: gitnexus-cli
+description: GitNexus CLI commands — index, status, clean, and wiki generation
+---
+
+# 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.
+
+### 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

gitnexus-claude-plugin/skills/cli/mcp.json

@@ -0,0 +1,8 @@
+{
+  "mcpServers": {
+    "gitnexus": {
+      "command": "npx",
+      "args": ["-y", "gitnexus@latest", "mcp"]
+    }
+  }
+}

gitnexus-claude-plugin/skills/guide/SKILL.md

@@ -26,6 +26,7 @@ For any task involving code understanding, debugging, impact analysis, or refact
 | Trace bugs / "Why is X failing?" | `debugging` |
 | Rename / extract / split / refactor | `refactoring` |
 | Tools, resources, schema reference | `guide` (this file) |
+| Index, status, clean, wiki CLI commands | `cli` |
 
 ## Tools Reference
 

gitnexus/skills/cli.md

@@ -0,0 +1,82 @@
+---
+name: gitnexus-cli
+description: GitNexus CLI commands — index, status, clean, and wiki generation
+---
+
+# 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.
+
+### 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

gitnexus/skills/guide.md

@@ -26,6 +26,7 @@ For any task involving code understanding, debugging, impact analysis, or refact
 | Trace bugs / "Why is X failing?" | `debugging` |
 | Rename / extract / split / refactor | `refactoring` |
 | Tools, resources, schema reference | `guide` (this file) |
+| Index, status, clean, wiki CLI commands | `cli` |
 
 ## Tools Reference
 

gitnexus/src/cli/ai-context.ts

@@ -59,6 +59,7 @@ This project is indexed by GitNexus as **${projectName}** (${stats.nodes || 0} s
 | Trace bugs / "Why is X failing?" | \`.claude/skills/gitnexus/debugging/SKILL.md\` |
 | Rename / extract / split / refactor | \`.claude/skills/gitnexus/refactoring/SKILL.md\` |
 | Tools, resources, schema reference | \`.claude/skills/gitnexus/guide/SKILL.md\` |
+| Index, status, clean, wiki CLI commands | \`.claude/skills/gitnexus/cli/SKILL.md\` |
 
 ${GITNEXUS_END_MARKER}`;
 }
@@ -144,6 +145,10 @@ async function installSkills(repoPath: string): Promise<string[]> {
       name: 'guide',
       description: 'GitNexus quickstart — tools, resources, schema, and workflow reference',
     },
+    {
+      name: 'cli',
+      description: 'GitNexus CLI commands — index, status, clean, and wiki generation',
+    },
   ];
 
   for (const skill of skills) {

gitnexus/src/cli/setup.ts

@@ -217,7 +217,7 @@ async function setupOpenCode(result: SetupResult): Promise<void> {
 
 // ─── Skill Installation ───────────────────────────────────────────
 
-const SKILL_NAMES = ['exploring', 'debugging', 'impact-analysis', 'refactoring', 'guide'];
+const SKILL_NAMES = ['exploring', 'debugging', 'impact-analysis', 'refactoring', 'guide', 'cli'];
 
 /**
  * Install GitNexus skills to a target directory.