# MCP Server Setup Guide

The Molecule AI MCP server lets any MCP-compatible AI agent (Claude Code, Cursor, etc.) manage workspaces, agents, secrets, memory, schedules, channels, and more through the platform API.

## Quick Start

### 1. Install

The MCP server is published as `@molecule-ai/mcp-server` on npm.

```bash
npx @molecule-ai/mcp-server
```

### 2. Configure in `.mcp.json`

Add to your project's `.mcp.json`:

```json
{
  "mcpServers": {
    "molecule": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@molecule-ai/mcp-server"],
      "env": {
        "MOLECULE_URL": "http://localhost:8080"
      }
    }
  }
}
```

For production/SaaS deployments, set `MOLECULE_URL` to your tenant URL:
```json
"MOLECULE_URL": "https://hongming-wang.moleculesai.app"
```

### 3. Verify

Once configured, your MCP client should show 87 Molecule AI tools. Test with:
```
list_workspaces
```

## Environment Variables

| Variable | Default | Description |
|----------|---------|-------------|
| `MOLECULE_URL` | `http://localhost:8080` | Platform API URL |

## Tool Reference

### Workspace Management

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_workspaces` | `/workspaces` | GET | List all workspaces |
| `get_workspace` | `/workspaces/:id` | GET | Get workspace details |
| `create_workspace` | `/workspaces` | POST | Create a new workspace |
| `update_workspace` | `/workspaces/:id` | PATCH | Update workspace fields |
| `delete_workspace` | `/workspaces/:id` | DELETE | Delete a workspace |
| `restart_workspace` | `/workspaces/:id/restart` | POST | Restart workspace container |
| `pause_workspace` | `/workspaces/:id/pause` | POST | Pause workspace |
| `resume_workspace` | `/workspaces/:id/resume` | POST | Resume paused workspace |
| `discover_workspace` | `/registry/discover/:id` | GET | Get workspace URL + agent card |

### Agent Management

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `assign_agent` | `/workspaces/:id/agent` | POST | Assign agent to workspace |
| `remove_agent` | `/workspaces/:id/agent` | DELETE | Remove agent |
| `replace_agent` | `/workspaces/:id/agent` | PATCH | Replace agent config |
| `move_agent` | `/workspaces/:id/agent/move` | POST | Move agent to different workspace |

### Communication

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `chat_with_agent` | `/workspaces/:id/a2a` | POST | Send A2A message to agent |
| `async_delegate` | `/workspaces/:id/delegate` | POST | Fire-and-forget delegation |
| `check_delegations` | `/workspaces/:id/delegations` | GET | Check delegation status |
| `send_channel_message` | `/workspaces/:id/channels/:channelId/send` | POST | Send to social channel |
| `notify_user` | `/workspaces/:id/notify` | POST | Push notification to canvas |
| `list_peers` | `/registry/:id/peers` | GET | Find sibling/parent workspaces |
| `check_access` | `/registry/check-access` | POST | Check if two workspaces can communicate |

### Configuration

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `get_config` | `/workspaces/:id/config` | GET | Get workspace config.yaml |
| `update_config` | `/workspaces/:id/config` | PATCH | Update config fields |
| `get_model` | `/workspaces/:id/model` | GET | Get configured LLM model |

### Secrets

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_secrets` | `/workspaces/:id/secrets` | GET | List workspace secret keys |
| `set_secret` | `/workspaces/:id/secrets` | POST | Set a workspace secret |
| `delete_secret` | `/workspaces/:id/secrets/:key` | DELETE | Delete a secret |
| `list_global_secrets` | `/settings/secrets` | GET | List global secrets |
| `set_global_secret` | `/settings/secrets` | PUT | Set a global secret |
| `delete_global_secret` | `/settings/secrets/:key` | DELETE | Delete global secret |

### Memory

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `memory_list` | `/workspaces/:id/memory` | GET | List memory keys |
| `memory_get` | `/workspaces/:id/memory/:key` | GET | Get memory value |
| `memory_set` | `/workspaces/:id/memory` | POST | Set memory key-value |
| `memory_delete_kv` | `/workspaces/:id/memory/:key` | DELETE | Delete memory key |
| `search_memory` | `/workspaces/:id/memories` | GET | Full-text search memories |
| `commit_memory` | `/workspaces/:id/memories` | POST | Commit HMA memory |
| `delete_memory` | `/workspaces/:id/memories/:id` | DELETE | Delete HMA memory |

### Files

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_files` | `/workspaces/:id/files` | GET | List workspace files |
| `read_file` | `/workspaces/:id/files/*path` | GET | Read file content |
| `write_file` | `/workspaces/:id/files/*path` | PUT | Write/overwrite file |
| `delete_file` | `/workspaces/:id/files/*path` | DELETE | Delete file |
| `replace_all_files` | `/workspaces/:id/files` | PUT | Replace all files atomically |

### Schedules

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_schedules` | `/workspaces/:id/schedules` | GET | List cron schedules |
| `create_schedule` | `/workspaces/:id/schedules` | POST | Create cron schedule |
| `update_schedule` | `/workspaces/:id/schedules/:id` | PATCH | Update schedule |
| `delete_schedule` | `/workspaces/:id/schedules/:id` | DELETE | Delete schedule |
| `run_schedule` | `/workspaces/:id/schedules/:id/run` | POST | Trigger schedule now |
| `get_schedule_history` | `/workspaces/:id/schedules/:id/history` | GET | Past run history |

### Channels (Social Integrations)

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_channels` | `/workspaces/:id/channels` | GET | List configured channels |
| `add_channel` | `/workspaces/:id/channels` | POST | Add Telegram/Slack/Lark channel |
| `update_channel` | `/workspaces/:id/channels/:id` | PATCH | Update channel config |
| `remove_channel` | `/workspaces/:id/channels/:id` | DELETE | Remove channel |
| `test_channel` | `/workspaces/:id/channels/:id/test` | POST | Test channel connectivity |
| `list_channel_adapters` | `/channels/adapters` | GET | Available platforms |
| `discover_channel_chats` | `/channels/discover` | POST | Auto-detect chats for bot token |

### Plugins

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_installed_plugins` | `/workspaces/:id/plugins` | GET | List installed plugins |
| `install_plugin` | `/workspaces/:id/plugins` | POST | Install plugin from source |
| `uninstall_plugin` | `/workspaces/:id/plugins/:name` | DELETE | Uninstall plugin |
| `list_available_plugins` | `/workspaces/:id/plugins/available` | GET | Plugins matching runtime |
| `list_plugin_registry` | `/plugins` | GET | Full plugin registry |
| `list_plugin_sources` | `/plugins/sources` | GET | Registered source schemes |
| `check_plugin_compatibility` | `/workspaces/:id/plugins/compatibility` | GET | Preflight check |

### Teams / Hierarchy

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `expand_team` | `/workspaces/:id/expand` | POST | Expand team node |
| `collapse_team` | `/workspaces/:id/collapse` | POST | Collapse team node |

### Templates & Bundles

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_templates` | `/templates` | GET | Available templates |
| `import_template` | `/templates/import` | POST | Import template |
| `list_org_templates` | `/org/templates` | GET | Org template list |
| `import_org` | `/org/import` | POST | Import org template |
| `export_bundle` | `/bundles/export/:id` | GET | Export workspace bundle |
| `import_bundle` | `/bundles/import` | POST | Import workspace bundle |

### Tokens

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_tokens` | `/workspaces/:id/tokens` | GET | List workspace tokens |
| `create_token` | `/workspaces/:id/tokens` | POST | Create new bearer token |
| `revoke_token` | `/workspaces/:id/tokens/:id` | DELETE | Revoke specific token |

### Monitoring

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_activity` | `/workspaces/:id/activity` | GET | Activity log |
| `report_activity` | `/workspaces/:id/activity` | POST | Report agent activity |
| `list_events` | `/events` | GET | Platform event stream |
| `list_traces` | `/workspaces/:id/traces` | GET | LLM traces (Langfuse) |
| `session_search` | `/workspaces/:id/session-search` | GET | Search chat sessions |

### Approvals

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `create_approval` | `/workspaces/:id/approvals` | POST | Request approval |
| `get_workspace_approvals` | `/workspaces/:id/approvals` | GET | List approvals |
| `decide_approval` | `/workspaces/:id/approvals/:id/decide` | POST | Approve/reject |
| `list_pending_approvals` | `/approvals/pending` | GET | All pending approvals |

### Canvas

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `get_canvas_viewport` | `/canvas/viewport` | GET | Current viewport |
| `set_canvas_viewport` | `/canvas/viewport` | PUT | Set viewport position |

### Remote Agents

| MCP Tool | API Route | Method | Description |
|----------|-----------|--------|-------------|
| `list_remote_agents` | `/workspaces?runtime=external` | GET | List remote agents |
| `get_remote_agent_state` | `/registry/discover/:id` | GET | Remote agent status |
| `check_remote_agent_freshness` | `/registry/heartbeat` | POST | Check if agent is alive |
| `get_remote_agent_setup_command` | (local) | — | Get setup instructions |

## Authentication

Most routes require a bearer token:

```bash
curl -H "Authorization: Bearer <token>" http://localhost:8080/workspaces
```

Tokens are issued on workspace registration (`POST /registry/register`) or via the token management API (`POST /workspaces/:id/tokens`).

The MCP server handles auth automatically when configured with the correct `MOLECULE_URL`.

## Troubleshooting

| Issue | Fix |
|-------|-----|
| "Connection refused" | Check `MOLECULE_URL` points to running platform |
| "401 Unauthorized" | Token expired or revoked — create a new one |
| Tools not showing | Run `npx @molecule-ai/mcp-server` standalone to check for errors |
| Stale data | MCP server doesn't cache — check platform directly |