Add MCP server for Claude Code memory integration

- Create stdio MCP server wrapping core memory functions (query, show, list, children, add, link)
- Add CLAUDE.md with memory-querying instructions for Claude
- Register MCP server in .mcp.json
- Document MCP setup and tools in USAGE.md

.mcp.json

@@ -0,0 +1,8 @@
+{
+  "mcpServers": {
+    "memory": {
+      "command": "node",
+      "args": ["./dist/mcp/index.js"]
+    }
+  }
+}

CLAUDE.md

@@ -0,0 +1,23 @@
+# Project Memory Guidelines
+
+## Before Making Changes
+- **Always query memory** before modifying code or making architectural decisions: use `memory_query` to search for relevant context.
+- Use `memory_show` to check existing context on a specific topic before acting.
+- Check for existing decisions, gotchas, and component info that may affect your changes.
+
+## After Making Changes
+- **Store new decisions** as memory nodes (kind: `decision`) when architectural choices are made.
+- **Store gotchas** as memory nodes (kind: `memory`) when you discover non-obvious behavior.
+- **Store component info** (kind: `component`) when creating or significantly modifying a module.
+- Tag nodes appropriately for future retrieval.
+
+## Memory Tools (MCP)
+- `memory_query` — search memory by text
+- `memory_show` — show a node by ID or prefix
+- `memory_list` — list nodes filtered by kind/status/tags
+- `memory_children` — list children of a node
+- `memory_add` — add a new memory node
+- `memory_link` — create a relationship between nodes
+
+## Git Preferences
+- Do not add `Co-Authored-By` lines to commits.

USAGE.md

@@ -260,3 +260,44 @@ The web server exposes these endpoints under `/api`:
 | `DELETE` | `/api/edges/:id` | Delete edge |
 | `GET` | `/api/graph` | Get full graph (nodes + edges) for visualization |
 | `POST` | `/api/search` | Search. Body: `{ text, options?: { kind?, tags?, limit?, includeStale? } }` |
+
+---
+
+## MCP Server (Claude Code Integration)
+
+Cortex includes an MCP (Model Context Protocol) server that exposes memory tools directly to Claude Code.
+
+### Setup
+
+1. Build the project: `npm run build`
+2. Ensure `.mcp.json` exists in the project root:
+
+```json
+{
+  "mcpServers": {
+    "memory": {
+      "command": "node",
+      "args": ["./dist/mcp/index.js"]
+    }
+  }
+}
+```
+
+3. Restart Claude Code — the memory tools will appear automatically.
+
+### MCP Tools
+
+| Tool | Description | Parameters |
+|---|---|---|
+| `memory_query` | Hybrid search (BM25 + vector + freshness) | `text`, `kind?`, `limit?` |
+| `memory_show` | Show node by ID or prefix with connections | `id` |
+| `memory_list` | List nodes with filters | `kind?`, `status?`, `tags?`, `limit?` |
+| `memory_children` | List children of a node | `id`, `kind?` |
+| `memory_add` | Add a new node | `kind`, `title`, `content?`, `tags?`, `status?`, `sections?` |
+| `memory_link` | Create an edge between nodes | `fromId`, `toId`, `type` |
+
+### Manual Testing
+
+```bash
+echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"test","version":"0.1"}}}' | node dist/mcp/index.js
+```

package-lock.json

@@ -9,15 +9,18 @@
       "version": "1.0.0",
       "license": "ISC",
       "dependencies": {
+        "@modelcontextprotocol/sdk": "^1.25.3",
         "better-sqlite3": "^12.6.2",
         "chalk": "^4.1.2",
         "commander": "^14.0.3",
         "cors": "^2.8.6",
         "express": "^5.2.1",
-        "uuid": "^13.0.0"
+        "uuid": "^13.0.0",
+        "zod": "^4.3.6"
       },
       "bin": {
-        "memory": "dist/cli/index.js"
+        "memory": "dist/cli/index.js",
+        "memory-mcp": "dist/mcp/index.js"
       },
       "devDependencies": {
         "@types/better-sqlite3": "^7.6.13",
@@ -28,6 +31,57 @@
         "typescript": "^5.9.3"
       }
     },
+    "node_modules/@hono/node-server": {
+      "version": "1.19.9",
+      "resolved": "https://registry.npmjs.org/@hono/node-server/-/node-server-1.19.9.tgz",
+      "integrity": "sha512-vHL6w3ecZsky+8P5MD+eFfaGTyCeOHUIFYMGpQGbrBTSmNNoxv0if69rEZ5giu36weC5saFuznL411gRX7bJDw==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=18.14.1"
+      },
+      "peerDependencies": {
+        "hono": "^4"
+      }
+    },
+    "node_modules/@modelcontextprotocol/sdk": {
+      "version": "1.25.3",
+      "resolved": "https://registry.npmjs.org/@modelcontextprotocol/sdk/-/sdk-1.25.3.tgz",
+      "integrity": "sha512-vsAMBMERybvYgKbg/l4L1rhS7VXV1c0CtyJg72vwxONVX0l4ZfKVAnZEWTQixJGTzKnELjQ59e4NbdFDALRiAQ==",
+      "license": "MIT",
+      "dependencies": {
+        "@hono/node-server": "^1.19.9",
+        "ajv": "^8.17.1",
+        "ajv-formats": "^3.0.1",
+        "content-type": "^1.0.5",
+        "cors": "^2.8.5",
+        "cross-spawn": "^7.0.5",
+        "eventsource": "^3.0.2",
+        "eventsource-parser": "^3.0.0",
+        "express": "^5.0.1",
+        "express-rate-limit": "^7.5.0",
+        "jose": "^6.1.1",
+        "json-schema-typed": "^8.0.2",
+        "pkce-challenge": "^5.0.0",
+        "raw-body": "^3.0.0",
+        "zod": "^3.25 || ^4.0",
+        "zod-to-json-schema": "^3.25.0"
+      },
+      "engines": {
+        "node": ">=18"
+      },
+      "peerDependencies": {
+        "@cfworker/json-schema": "^4.1.1",
+        "zod": "^3.25 || ^4.0"
+      },
+      "peerDependenciesMeta": {
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+        "zod": {
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+        }
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@@ -166,6 +220,39 @@
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+      "license": "MIT",
+      "dependencies": {
+        "fast-deep-equal": "^3.1.3",
+        "fast-uri": "^3.0.1",
+        "json-schema-traverse": "^1.0.0",
+        "require-from-string": "^2.0.2"
+      },
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/epoberezkin"
+      }
+    },
+    "node_modules/ajv-formats": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/ajv-formats/-/ajv-formats-3.0.1.tgz",
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+      "dependencies": {
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       "version": "4.3.0",
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@@ -427,6 +514,20 @@
         "url": "https://opencollective.com/express"
       }
     },
+    "node_modules/cross-spawn": {
+      "version": "7.0.6",
+      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.6.tgz",
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+      "license": "MIT",
+      "dependencies": {
+        "path-key": "^3.1.0",
+        "shebang-command": "^2.0.0",
+        "which": "^2.0.1"
+      },
+      "engines": {
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+      }
+    },
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       "version": "4.4.3",
       "resolved": "https://registry.npmjs.org/debug/-/debug-4.4.3.tgz",
@@ -569,6 +670,27 @@
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       }
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+    "node_modules/eventsource": {
+      "version": "3.0.7",
+      "resolved": "https://registry.npmjs.org/eventsource/-/eventsource-3.0.7.tgz",
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+      "license": "MIT",
+      "dependencies": {
+        "eventsource-parser": "^3.0.1"
+      },
+      "engines": {
+        "node": ">=18.0.0"
+      }
+    },
+    "node_modules/eventsource-parser": {
+      "version": "3.0.6",
+      "resolved": "https://registry.npmjs.org/eventsource-parser/-/eventsource-parser-3.0.6.tgz",
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+      "license": "MIT",
+      "engines": {
+        "node": ">=18.0.0"
+      }
+    },
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       "version": "2.0.3",
       "resolved": "https://registry.npmjs.org/expand-template/-/expand-template-2.0.3.tgz",
@@ -621,6 +743,43 @@
         "url": "https://opencollective.com/express"
       }
     },
+    "node_modules/express-rate-limit": {
+      "version": "7.5.1",
+      "resolved": "https://registry.npmjs.org/express-rate-limit/-/express-rate-limit-7.5.1.tgz",
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+      "license": "MIT",
+      "engines": {
+        "node": ">= 16"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/express-rate-limit"
+      },
+      "peerDependencies": {
+        "express": ">= 4.11"
+      }
+    },
+    "node_modules/fast-deep-equal": {
+      "version": "3.1.3",
+      "resolved": "https://registry.npmjs.org/fast-deep-equal/-/fast-deep-equal-3.1.3.tgz",
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+      "resolved": "https://registry.npmjs.org/fast-uri/-/fast-uri-3.1.0.tgz",
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+      "funding": [
+        {
+          "type": "github",
+          "url": "https://github.com/sponsors/fastify"
+        },
+        {
+          "type": "opencollective",
+          "url": "https://opencollective.com/fastify"
+        }
+      ],
+      "license": "BSD-3-Clause"
+    },
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       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/file-uri-to-path/-/file-uri-to-path-1.0.0.tgz",
@@ -769,6 +928,16 @@
         "node": ">= 0.4"
       }
     },
+    "node_modules/hono": {
+      "version": "4.11.7",
+      "resolved": "https://registry.npmjs.org/hono/-/hono-4.11.7.tgz",
+      "integrity": "sha512-l7qMiNee7t82bH3SeyUCt9UF15EVmaBvsppY2zQtrbIhl/yzBTny+YUxsVjSjQ6gaqaeVtZmGocom8TzBlA4Yw==",
+      "license": "MIT",
+      "peer": true,
+      "engines": {
+        "node": ">=16.9.0"
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+    },
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       "license": "MIT"
     },
+    "node_modules/isexe": {
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/isexe/-/isexe-2.0.0.tgz",
+      "integrity": "sha512-RHxMLp9lnKHGHRng9QFhRCMbYAcVpn69smSGcq3f36xjgVVWThj4qqLbTLlq7Ssj8B+fIQ1EuCEGI2lKsyQeIw==",
+      "license": "ISC"
+    },
+    "node_modules/jose": {
+      "version": "6.1.3",
+      "resolved": "https://registry.npmjs.org/jose/-/jose-6.1.3.tgz",
+      "integrity": "sha512-0TpaTfihd4QMNwrz/ob2Bp7X04yuxJkjRGi4aKmOqwhov54i6u79oCv7T+C7lo70MKH6BesI3vscD1yb/yzKXQ==",
+      "license": "MIT",
+      "funding": {
+        "url": "https://github.com/sponsors/panva"
+      }
+    },
+    "node_modules/json-schema-traverse": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-1.0.0.tgz",
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+      "license": "MIT"
+    },
+    "node_modules/json-schema-typed": {
+      "version": "8.0.2",
+      "resolved": "https://registry.npmjs.org/json-schema-typed/-/json-schema-typed-8.0.2.tgz",
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+      "license": "BSD-2-Clause"
+    },
     "node_modules/math-intrinsics": {
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       "resolved": "https://registry.npmjs.org/math-intrinsics/-/math-intrinsics-1.1.0.tgz",
@@ -1018,6 +1214,15 @@
         "node": ">= 0.8"
       }
     },
+    "node_modules/path-key": {
+      "version": "3.1.1",
+      "resolved": "https://registry.npmjs.org/path-key/-/path-key-3.1.1.tgz",
+      "integrity": "sha512-ojmeN0qd+y0jszEtoY48r0Peq5dwMEkIlCOu6Q5f41lfkswXuKtYrhgoTpLnyIcHm24Uhqx+5Tqm2InSwLhE6Q==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=8"
+      }
+    },
     "node_modules/path-to-regexp": {
       "version": "8.3.0",
       "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-8.3.0.tgz",
@@ -1028,6 +1233,15 @@
         "url": "https://opencollective.com/express"
       }
     },
+    "node_modules/pkce-challenge": {
+      "version": "5.0.1",
+      "resolved": "https://registry.npmjs.org/pkce-challenge/-/pkce-challenge-5.0.1.tgz",
+      "integrity": "sha512-wQ0b/W4Fr01qtpHlqSqspcj3EhBvimsdh0KlHhH8HRZnMsEa0ea2fTULOXOS9ccQr3om+GcGRk4e+isrZWV8qQ==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=16.20.0"
+      }
+    },
     "node_modules/prebuild-install": {
       "version": "7.1.3",
       "resolved": "https://registry.npmjs.org/prebuild-install/-/prebuild-install-7.1.3.tgz",
@@ -1145,6 +1359,15 @@
         "node": ">= 6"
       }
     },
+    "node_modules/require-from-string": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/require-from-string/-/require-from-string-2.0.2.tgz",
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+      "license": "MIT",
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
     "node_modules/router": {
       "version": "2.2.0",
       "resolved": "https://registry.npmjs.org/router/-/router-2.2.0.tgz",
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       "license": "ISC"
     },
+    "node_modules/shebang-command": {
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/shebang-command/-/shebang-command-2.0.0.tgz",
+      "integrity": "sha512-kHxr2zZpYtdmrN1qDjrrX/Z1rR1kG8Dx+gkpK1G4eXmvXswmcE1hTWBWYUzlraYw1/yZp6YuDY77YtvbN0dmDA==",
+      "license": "MIT",
+      "dependencies": {
+        "shebang-regex": "^3.0.0"
+      },
+      "engines": {
+        "node": ">=8"
+      }
+    },
+    "node_modules/shebang-regex": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/shebang-regex/-/shebang-regex-3.0.0.tgz",
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+      "license": "MIT",
+      "engines": {
+        "node": ">=8"
+      }
+    },
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       "resolved": "https://registry.npmjs.org/side-channel/-/side-channel-1.1.0.tgz",
@@ -1527,11 +1771,44 @@
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       }
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+    "node_modules/which": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
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+      "license": "ISC",
+      "dependencies": {
+        "isexe": "^2.0.0"
+      },
+      "bin": {
+        "node-which": "bin/node-which"
+      },
+      "engines": {
+        "node": ">= 8"
+      }
+    },
     "node_modules/wrappy": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
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       "license": "ISC"
+    },
+    "node_modules/zod": {
+      "version": "4.3.6",
+      "resolved": "https://registry.npmjs.org/zod/-/zod-4.3.6.tgz",
+      "integrity": "sha512-rftlrkhHZOcjDwkGlnUtZZkvaPHCsDATp4pGpuOOMDaTdDDXF91wuVDJoWoPsKX/3YPQ5fHuF3STjcYyKr+Qhg==",
+      "license": "MIT",
+      "funding": {
+        "url": "https://github.com/sponsors/colinhacks"
+      }
+    },
+    "node_modules/zod-to-json-schema": {
+      "version": "3.25.1",
+      "resolved": "https://registry.npmjs.org/zod-to-json-schema/-/zod-to-json-schema-3.25.1.tgz",
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+      "license": "ISC",
+      "peerDependencies": {
+        "zod": "^3.25 || ^4"
+      }
     }
   }
 }

package.json

@@ -12,15 +12,18 @@
   "license": "ISC",
   "description": "AI project memory - knowledge graph backed by SQLite + Ollama embeddings",
   "bin": {
-    "memory": "./dist/cli/index.js"
+    "memory": "./dist/cli/index.js",
+    "memory-mcp": "./dist/mcp/index.js"
   },
   "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.25.3",
     "better-sqlite3": "^12.6.2",
     "chalk": "^4.1.2",
     "commander": "^14.0.3",
     "cors": "^2.8.6",
     "express": "^5.2.1",
-    "uuid": "^13.0.0"
+    "uuid": "^13.0.0",
+    "zod": "^4.3.6"
   },
   "devDependencies": {
     "@types/better-sqlite3": "^7.6.13",

src/mcp/index.ts

@@ -0,0 +1,121 @@
+import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { z } from 'zod/v3';
+import { query, listNodes, getNode, findNodeByPrefix, addNode, addEdge } from '../core/store';
+import { getConnections } from '../core/graph';
+import { NodeKind, EdgeType } from '../types';
+
+const server = new McpServer({
+  name: 'memory',
+  version: '1.0.0',
+});
+
+server.tool(
+  'memory_query',
+  'Search memory nodes by text (hybrid BM25 + vector search)',
+  {
+    text: z.string().describe('Search query text'),
+    kind: z.enum(['memory', 'component', 'task', 'decision']).optional().describe('Filter by node kind'),
+    limit: z.number().optional().describe('Max results (default 10)'),
+  },
+  async ({ text, kind, limit }) => {
+    const results = await query(text, { kind: kind as NodeKind, limit });
+    return { content: [{ type: 'text' as const, text: JSON.stringify(results, null, 2) }] };
+  }
+);
+
+server.tool(
+  'memory_show',
+  'Show a memory node by ID or ID prefix',
+  {
+    id: z.string().describe('Full node ID or prefix'),
+  },
+  async ({ id }) => {
+    const node = getNode(id) ?? findNodeByPrefix(id);
+    if (!node) {
+      return { content: [{ type: 'text' as const, text: JSON.stringify({ error: 'Node not found' }) }], isError: true };
+    }
+    const connections = getConnections(node.id);
+    return { content: [{ type: 'text' as const, text: JSON.stringify({ node, connections }, null, 2) }] };
+  }
+);
+
+server.tool(
+  'memory_list',
+  'List memory nodes with optional filters',
+  {
+    kind: z.enum(['memory', 'component', 'task', 'decision']).optional().describe('Filter by node kind'),
+    status: z.string().optional().describe('Filter by status'),
+    tags: z.array(z.string()).optional().describe('Filter by tags'),
+    limit: z.number().optional().describe('Max results'),
+  },
+  async ({ kind, status, tags, limit }) => {
+    const nodes = listNodes({ kind: kind as NodeKind, status, tags, limit });
+    return { content: [{ type: 'text' as const, text: JSON.stringify(nodes, null, 2) }] };
+  }
+);
+
+server.tool(
+  'memory_children',
+  'List children of a memory node (outgoing "contains" edges)',
+  {
+    id: z.string().describe('Parent node ID or prefix'),
+    kind: z.enum(['memory', 'component', 'task', 'decision']).optional().describe('Filter children by kind'),
+  },
+  async ({ id, kind }) => {
+    const node = getNode(id) ?? findNodeByPrefix(id);
+    if (!node) {
+      return { content: [{ type: 'text' as const, text: JSON.stringify({ error: 'Node not found' }) }], isError: true };
+    }
+    const { outgoing } = getConnections(node.id);
+    let children = outgoing.filter(e => e.type === 'contains').map(e => (e as any).node);
+    if (kind) {
+      children = children.filter((n: any) => n.kind === kind);
+    }
+    return { content: [{ type: 'text' as const, text: JSON.stringify(children, null, 2) }] };
+  }
+);
+
+server.tool(
+  'memory_add',
+  'Add a new memory node',
+  {
+    kind: z.enum(['memory', 'component', 'task', 'decision']).describe('Node kind'),
+    title: z.string().describe('Node title'),
+    content: z.string().optional().describe('Node content/body'),
+    tags: z.array(z.string()).optional().describe('Tags'),
+    status: z.string().optional().describe('Status (e.g. active, todo, done)'),
+    sections: z.array(z.object({ label: z.string(), body: z.string() })).optional().describe('Structured sections'),
+  },
+  async ({ kind, title, content, tags, status, sections }) => {
+    const metadata: Record<string, any> = {};
+    if (sections) metadata.sections = sections;
+    const node = await addNode({ kind: kind as NodeKind, title, content, tags, status, metadata });
+    return { content: [{ type: 'text' as const, text: JSON.stringify(node, null, 2) }] };
+  }
+);
+
+server.tool(
+  'memory_link',
+  'Create an edge between two memory nodes',
+  {
+    fromId: z.string().describe('Source node ID'),
+    toId: z.string().describe('Target node ID'),
+    type: z.enum(['depends_on', 'contains', 'implements', 'blocked_by', 'subtask_of', 'relates_to', 'supersedes', 'about']).describe('Edge type'),
+  },
+  async ({ fromId, toId, type }) => {
+    const edge = addEdge(fromId, toId, type as EdgeType);
+    return { content: [{ type: 'text' as const, text: JSON.stringify(edge, null, 2) }] };
+  }
+);
+
+async function main() {
+  const transport = new StdioServerTransport();
+  await server.connect(transport);
+  console.error('Memory MCP server running on stdio');
+}
+
+main().catch((err) => {
+  console.error('Fatal error:', err);
+  process.exit(1);
+});