@graphmemory/server 1.1.0 → 1.2.0

package/dist/ui/assets/{index-D6oxrVF7.js → index-0hRezICt.js}

@@ -579,8 +579,8 @@ Graph Memory maintains six separate but interconnected graphs:
 
 | Graph | What it indexes | Created from |
 |-------|----------------|--------------|
-| **DocGraph** | Markdown sections, headings, code blocks | Files matching \`graphs.docs.pattern\` |
-| **CodeGraph** | Functions, classes, methods, imports | Files matching \`graphs.code.pattern\` |
+| **DocGraph** | Markdown sections, headings, code blocks | Files matching \`graphs.docs.include\` |
+| **CodeGraph** | Functions, classes, methods, imports | Files matching \`graphs.code.include\` |
 | **FileIndexGraph** | All files and directories with metadata | Entire project directory |
 | **KnowledgeGraph** | User-created notes, facts, decisions | Manual creation via tools |
 | **TaskGraph** | Tasks with status, priority, dependencies | Manual creation via tools |
@@ -600,8 +600,7 @@ This means \`"how to authenticate users"\` will find documentation about auth ev
 
 ## Quick start workflow
 
-1. **Configure** your project in \`graph-memory.yaml\` with \`graphs.docs.pattern\` and \`graphs.code.pattern\`
-2. **Start** the server: \`graphmemory serve --config graph-memory.yaml\`
+1. **Start** the server: \`graphmemory serve\` (uses current directory as project, or \`--config graph-memory.yaml\` for custom config)
 3. **Browse** your indexed content in the UI
 4. **Search** across all graphs using natural language
 5. **Create notes** to capture knowledge and decisions
@@ -640,19 +639,19 @@ Each graph can use a different embedding model, configured in \`graph-memory.yam
 \`\`\`yaml
 projects:
   my-app:
-    embedding:
-      model: Xenova/bge-m3        # default for all graphs
+    model:
+      name: Xenova/bge-m3          # default for all graphs
     graphs:
       docs:
-        embedding:
-          model: Xenova/bge-m3    # override for docs (full config, no merge)
+        model:
+          name: Xenova/bge-m3      # override for docs (whole object, no merge)
       code:
-        embedding:
-          model: Xenova/bge-base-en-v1.5
-      # knowledge, tasks, files, skills inherit project.embedding
+        model:
+          name: Xenova/bge-base-en-v1.5
+      # knowledge, tasks, files, skills inherit project.model
 \`\`\`
 
-Resolution: \`graph.embedding → project.embedding → server.embedding → defaults\`. Each level is a complete config block — no field-by-field merge.
+Model resolution: \`graph.model → project.model → server.model → defaults\`. Each level is a complete config block — no field-by-field merge. Embedding config (\`batchSize\`, \`maxChars\`, etc.) is separate and merges field-by-field.
 
 ## Cosine similarity
 
@@ -873,54 +872,11 @@ This lets you create connections like:
 - Task "Update auth docs" → links to \`guide.md\` in DocGraph
 - Note "Config format" → links to \`src/config.ts\` in FileIndexGraph
 - Skill "Add REST endpoint" → links to \`auth.ts::AuthService\` in CodeGraph
-`},{id:`cross-graph`,title:`Cross-Graph Links`,summary:`How to link notes and tasks to code, docs, and files via proxy nodes.`,category:`concept`,relatedTools:[`create_relation`,`delete_relation`,`list_relations`,`create_task_link`,`delete_task_link`,`create_skill_link`,`delete_skill_link`,`find_linked_notes`,`find_linked_tasks`,`find_linked_skills`],content:'# Cross-Graph Links\n\nOne of Graph Memory\'s most powerful features is the ability to **link knowledge across different graphs**. A note can reference a code symbol, a task can link to documentation, and everything stays connected.\n\n## How it works\n\nWhen you create a cross-graph link (via `create_relation`, `create_task_link`, or `create_skill_link`), the system creates a **proxy node** — a lightweight placeholder in the source graph that represents a node from another graph.\n\nProxy node IDs follow the format `@{graph}::{nodeId}`:\n- `@docs::guide.md::Setup` — a doc section\n- `@code::auth.ts::AuthService` — a code symbol\n- `@files::src/config.ts` — a file\n- `@tasks::fix-auth-bug` — a task\n- `@knowledge::auth-architecture` — a note\n- `@skills::add-rest-endpoint` — a skill\n\n## Creating cross-graph links\n\n### From Knowledge (notes)\n\nUse `create_relation` with the `targetGraph` parameter:\n\n```\ncreate_relation({\n  fromId: "auth-architecture",\n  toId: "auth.ts::AuthService",\n  kind: "documents",\n  targetGraph: "code"\n})\n```\n\nSupported target graphs: `docs`, `code`, `files`, `tasks`, `skills`\n\n### From Tasks\n\nUse `create_task_link` with the `targetGraph` parameter:\n\n```\ncreate_task_link({\n  taskId: "update-auth-docs",\n  targetId: "guide.md::Authentication",\n  kind: "relates_to",\n  targetGraph: "docs"\n})\n```\n\nSupported target graphs: `docs`, `code`, `files`, `knowledge`, `skills`\n\n### From Skills\n\nUse `create_skill_link` with the `targetGraph` parameter:\n\n```\ncreate_skill_link({\n  skillId: "add-rest-endpoint",\n  targetId: "api-guide.md::REST",\n  kind: "relates_to",\n  targetGraph: "docs"\n})\n```\n\nSupported target graphs: `docs`, `code`, `files`, `knowledge`, `tasks`\n\n## Discovering cross-graph links\n\n- `find_linked_notes` — find all notes linked to a specific external node\n- `find_linked_tasks` — find all tasks linked to a specific external node\n- `find_linked_skills` — find all skills linked to a specific external node\n- `list_relations` — list all relations for a note (including cross-graph)\n- `get_task` — returns enriched task data including all cross-graph links\n- `get_skill` — returns enriched skill data including all cross-graph links\n\n## Proxy cleanup\n\nProxy nodes are automatically cleaned up when:\n- The source note, task, or skill is deleted (orphaned proxies removed)\n- The relation/link is explicitly deleted\n- During indexing, if the target file no longer exists\n\n## Use cases\n\n- **Architecture decisions**: Create notes documenting why code is structured a certain way, link to the actual code symbols\n- **Task context**: Link tasks to the files and docs they affect for quick navigation\n- **Knowledge mapping**: Build a web of connections between concepts, implementations, and documentation\n- **Reusable skills**: Link skills to the code, docs, and tasks they relate to so they can be recalled in context\n'},{id:`mcp-setup`,title:`Connecting MCP Clients`,summary:`How to connect Claude Desktop, Cursor, Windsurf, and other MCP clients via stdio or HTTP.`,category:`guide`,relatedTools:[`get_context`],content:`# Connecting MCP Clients
+`},{id:`cross-graph`,title:`Cross-Graph Links`,summary:`How to link notes and tasks to code, docs, and files via proxy nodes.`,category:`concept`,relatedTools:[`create_relation`,`delete_relation`,`list_relations`,`create_task_link`,`delete_task_link`,`create_skill_link`,`delete_skill_link`,`find_linked_notes`,`find_linked_tasks`,`find_linked_skills`],content:'# Cross-Graph Links\n\nOne of Graph Memory\'s most powerful features is the ability to **link knowledge across different graphs**. A note can reference a code symbol, a task can link to documentation, and everything stays connected.\n\n## How it works\n\nWhen you create a cross-graph link (via `create_relation`, `create_task_link`, or `create_skill_link`), the system creates a **proxy node** — a lightweight placeholder in the source graph that represents a node from another graph.\n\nProxy node IDs follow the format `@{graph}::{nodeId}`:\n- `@docs::guide.md::Setup` — a doc section\n- `@code::auth.ts::AuthService` — a code symbol\n- `@files::src/config.ts` — a file\n- `@tasks::fix-auth-bug` — a task\n- `@knowledge::auth-architecture` — a note\n- `@skills::add-rest-endpoint` — a skill\n\n## Creating cross-graph links\n\n### From Knowledge (notes)\n\nUse `create_relation` with the `targetGraph` parameter:\n\n```\ncreate_relation({\n  fromId: "auth-architecture",\n  toId: "auth.ts::AuthService",\n  kind: "documents",\n  targetGraph: "code"\n})\n```\n\nSupported target graphs: `docs`, `code`, `files`, `tasks`, `skills`\n\n### From Tasks\n\nUse `create_task_link` with the `targetGraph` parameter:\n\n```\ncreate_task_link({\n  taskId: "update-auth-docs",\n  targetId: "guide.md::Authentication",\n  kind: "relates_to",\n  targetGraph: "docs"\n})\n```\n\nSupported target graphs: `docs`, `code`, `files`, `knowledge`, `skills`\n\n### From Skills\n\nUse `create_skill_link` with the `targetGraph` parameter:\n\n```\ncreate_skill_link({\n  skillId: "add-rest-endpoint",\n  targetId: "api-guide.md::REST",\n  kind: "relates_to",\n  targetGraph: "docs"\n})\n```\n\nSupported target graphs: `docs`, `code`, `files`, `knowledge`, `tasks`\n\n## Discovering cross-graph links\n\n- `find_linked_notes` — find all notes linked to a specific external node\n- `find_linked_tasks` — find all tasks linked to a specific external node\n- `find_linked_skills` — find all skills linked to a specific external node\n- `list_relations` — list all relations for a note (including cross-graph)\n- `get_task` — returns enriched task data including all cross-graph links\n- `get_skill` — returns enriched skill data including all cross-graph links\n\n## Proxy cleanup\n\nProxy nodes are automatically cleaned up when:\n- The source note, task, or skill is deleted (orphaned proxies removed)\n- The relation/link is explicitly deleted\n- During indexing, if the target file no longer exists\n\n## Use cases\n\n- **Architecture decisions**: Create notes documenting why code is structured a certain way, link to the actual code symbols\n- **Task context**: Link tasks to the files and docs they affect for quick navigation\n- **Knowledge mapping**: Build a web of connections between concepts, implementations, and documentation\n- **Reusable skills**: Link skills to the code, docs, and tasks they relate to so they can be recalled in context\n'},{id:`mcp-setup`,title:`Connecting MCP Clients`,summary:`How to connect Claude Desktop, Cursor, Windsurf, and other MCP clients via HTTP.`,category:`guide`,relatedTools:[`get_context`],content:`# Connecting MCP Clients
 
-Graph Memory supports two transport modes for MCP clients: **stdio** (single project) and **HTTP** (multi-project). Choose the right one for your setup.
+Graph Memory uses HTTP transport for MCP clients. Start the server, then connect your client to the MCP endpoint.
 
-## Stdio transport
-
-Best for: single-project setups, IDE integrations where each project gets its own MCP server process.
-
-The MCP client launches the server as a subprocess. Communication happens over stdin/stdout.
-
-After \`npm install -g @graphmemory/server\`:
-
-### Claude Desktop (stdio)
-
-Add to your Claude Desktop config (\`claude_desktop_config.json\`):
-
-\`\`\`json
-{
-  "mcpServers": {
-    "graph-memory": {
-      "command": "graphmemory",
-      "args": ["mcp", "--config", "/path/to/graph-memory.yaml", "--project", "my-app"]
-    }
-  }
-}
-\`\`\`
-
-Replace \`my-app\` with the project ID from your \`graph-memory.yaml\`.
-
-### Claude Code (stdio)
-
-Add to your project's \`.mcp.json\`:
-
-\`\`\`json
-{
-  "mcpServers": {
-    "graph-memory": {
-      "type": "stdio",
-      "command": "graphmemory",
-      "args": ["mcp", "--config", "/path/to/graph-memory.yaml", "--project", "my-app"]
-    }
-  }
-}
-\`\`\`
-
-## HTTP transport
-
-Best for: multi-project setups, shared team servers, or when multiple clients need to access the same graphs simultaneously.
+## Setup
 
 Start the server first:
 
@@ -930,7 +886,7 @@ graphmemory serve --config graph-memory.yaml
 
 Each project gets its own MCP endpoint at \`http://localhost:3000/mcp/{projectId}\`.
 
-### Claude Desktop (HTTP)
+### Claude Desktop
 
 Add via **Settings > Connectors** in the Claude Desktop app, enter the URL:
 
@@ -938,7 +894,7 @@ Add via **Settings > Connectors** in the Claude Desktop app, enter the URL:
 http://localhost:3000/mcp/my-app
 \`\`\`
 
-### Claude Code (HTTP)
+### Claude Code
 
 Run in your project directory:
 
@@ -969,8 +925,6 @@ http://localhost:3000/mcp/{projectId}
 
 ## Docker
 
-When running via Docker, the HTTP transport is the only option (stdio requires a local process).
-
 \`\`\`bash
 docker run -d \\
   --name graph-memory \\
@@ -997,18 +951,6 @@ docker run --rm \\
 docker compose run --rm graph-memory index --config /data/config/graph-memory.yaml
 \`\`\`
 
-## Which transport to choose?
-
-| | Stdio | HTTP |
-|---|---|---|
-| **Projects** | One per process | Multiple from one server |
-| **Clients** | One client per server | Many clients share one server |
-| **Web UI** | Not available | Available at \`http://localhost:3000\` |
-| **REST API** | Not available | Available at \`/api/*\` |
-| **WebSocket** | Not available | Real-time updates via \`/api/ws\` |
-| **Setup** | Client manages process | You start the server separately |
-| **Best for** | IDE integration | Teams, multi-project, Docker |
-
 ## Troubleshooting
 
 **Model loading is slow on first start**: The embedding model (\`Xenova/bge-m3\`, ~560MB) is downloaded on first use. Subsequent starts use the cached model from \`~/.graph-memory/models/\` (or the configured \`modelsDir\`).
@@ -1017,7 +959,7 @@ docker compose run --rm graph-memory index --config /data/config/graph-memory.ya
 
 **Tools not showing up**: Make sure \`graphs.docs.include\` and/or \`graphs.code.include\` are set in your config (defaults: \`**/*.md\` and \`**/*.{js,ts,jsx,tsx}\`). If a graph is \`enabled: false\`, its tools won't be registered.
 
-**Config changes not taking effect**: The \`serve\` command watches \`graph-memory.yaml\` for changes automatically. For \`mcp\` (stdio), you need to restart the process.
+**Config changes not taking effect**: Restart the server process to apply changes to \`graph-memory.yaml\`.
 `},{id:`configuration`,title:`Configuration Guide`,summary:`All graph-memory.yaml settings: server, projects, workspaces, embedding models, and patterns.`,category:`guide`,relatedTools:[],content:`# Configuration Guide
 
 All configuration is done via a single \`graph-memory.yaml\` file. This guide covers every setting and common patterns.
@@ -1095,8 +1037,8 @@ projects:
         enabled: true                      # Set false to disable this graph
         include: "**/*.md"                 # Default — indexes all markdown files
         exclude: "**/archive/**"           # Glob to exclude
-        embedding:                          # Full embedding config (no merge with parent)
-          model: "Xenova/bge-m3"
+        model:                              # Full model config (whole object, no merge with parent)
+          name: "Xenova/bge-m3"
           pooling: "cls"
           normalize: true
         access:                             # Per-graph access control
@@ -1104,8 +1046,8 @@ projects:
       code:
         enabled: true
         include: "**/*.{js,ts,jsx,tsx}"    # Default — indexes all JS/TS files
-        embedding:
-          model: "Xenova/bge-base-en-v1.5"
+        model:
+          name: "Xenova/bge-base-en-v1.5"
       knowledge:
         access:
           bob: rw                           # bob gets rw on knowledge
@@ -1154,7 +1096,7 @@ workspaces:
 
 ## Users & authentication
 
-Define users for REST API and UI authentication. MCP stdio mode does not use authentication — identity comes from the \`author\` config.
+Define users for REST API and UI authentication.
 
 \`\`\`yaml
 users:
@@ -1296,8 +1238,9 @@ Instead of running the embedding model locally, delegate to a remote embedding A
 
 \`\`\`yaml
 server:
+  model:
+    name: "Xenova/bge-m3"
   embedding:
-    model: "Xenova/bge-m3"
     remote: "http://gpu-server:3000/api/embed"
     remoteApiKey: "emb-secret-key"
 \`\`\`
@@ -1372,16 +1315,16 @@ projects:
     projectDir: "/data/projects/my-app"
 \`\`\`
 
-## Hot reload
+## Applying config changes
 
-When using the \`serve\` command, the config file is watched for changes. You can add, remove, or update projects without restarting the server.
+Restart the server process to apply changes to \`graph-memory.yaml\`.
 
 ## Automatic re-indexing
 
 Each graph stores which embedding model was used. If you change the model in config, the graph is automatically discarded and re-indexed on next startup — no \`--reindex\` flag needed.
 `},{id:`docs-tools`,title:`Documentation Tools`,summary:`Search, browse, and navigate indexed markdown documentation.`,category:`guide`,relatedTools:[`list_topics`,`get_toc`,`search`,`get_node`,`search_topic_files`,`find_examples`,`search_snippets`,`list_snippets`,`explain_symbol`],content:`# Documentation Tools
 
-The docs tools let you search, browse, and navigate your indexed markdown documentation. They're available when \`graphs.docs.pattern\` (or legacy \`docsPattern\`) is configured in your project.
+The docs tools let you search, browse, and navigate your indexed markdown documentation. They're available when \`graphs.docs.include\` is configured in your project (default: \`**/*.md\`).
 
 ## Tool overview
 
@@ -1574,7 +1517,7 @@ Find documentation that explains a symbol — returns both code example and surr
 - Lower \`minScore\` to 0.3 when exploring unfamiliar codebases
 - Set \`bfsDepth: 0\` in \`search\` for pure vector search without graph expansion
 - Set \`bfsDepth: 2\` to discover more loosely related content
-`},{id:`code-tools`,title:`Code Tools`,summary:`Search and navigate TypeScript/JavaScript source code symbols.`,category:`guide`,relatedTools:[`list_files`,`get_file_symbols`,`search_code`,`get_symbol`,`search_files`],content:'# Code Tools\n\nThe code tools let you search and navigate your indexed TypeScript/JavaScript source code. They\'re available when `graphs.code.pattern` (or legacy `codePattern`) is configured in your project.\n\n## Tool overview\n\n| Tool | Purpose | When to use |\n|------|---------|-------------|\n| `list_files` | List all indexed source files | Get an overview of the codebase |\n| `get_file_symbols` | List symbols in a file | Explore a file\'s exports and structure |\n| `search_code` | Semantic search across code symbols | Find functions/classes by what they do |\n| `get_symbol` | Get full details of a symbol | Read signature, JSDoc, body, line numbers |\n| `search_files` | Search at file level | Find which files are relevant to a topic |\n\n## What gets indexed\n\nThe code parser uses tree-sitter to extract:\n- **Functions** — name, signature, JSDoc, line range, exported flag\n- **Classes** — name, methods, extends/implements relationships\n- **Interfaces** and **Types** — name, signature\n- **Enums** — name, members\n- **Variables** (exported) — name, type\n- **Methods** — as children of their parent class\n\nEdges capture structural relationships:\n- `contains` — file → symbol, class → method\n- `imports` — file → imported file (resolved by import resolver)\n- `extends` — class → base class\n- `implements` — class → interface\n\n## Node ID format\n\nCode graph node IDs follow a hierarchical pattern:\n- `"src/auth.ts"` — file node\n- `"src/auth.ts::createUser"` — top-level symbol in file\n- `"src/auth.ts::AuthService::login"` — method within a class\n\n## Typical workflow\n\n### 1. Find code by meaning\n\nUse `search_code` with a description of what you\'re looking for:\n- `"user authentication"` — finds auth-related functions and classes\n- `"parse markdown into sections"` — finds parsing logic\n\nUnlike grep, this finds code by **what it does**, not by exact text matches.\n\n### 2. Explore a symbol\n\nUse `get_symbol` with the symbol ID from search results. This returns the full picture: signature, JSDoc comment, body text, file location, line numbers, export status.\n\n### 3. Understand file structure\n\nUse `get_file_symbols` to see all symbols in a file — helpful for understanding module organization. The result includes `isExported` flag to distinguish public API from internal helpers.\n\n### 4. Discover relevant files\n\nUse `search_files` for a quick file-level search before diving into symbols. Lighter than `search_code` when you just need to identify which files to explore.\n\n### 5. Cross-reference with docs\n\nUse `cross_references` (requires both `docsPattern` and `codePattern`) to find everywhere a symbol appears — in both code definitions and documentation examples. See the dedicated guide for details.\n\n## Tool reference\n\n### list_files\n\nList indexed source files with optional filtering.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `filter` | string | No | — | Case-insensitive substring to match against file paths, e.g. `"graph"` or `"src/lib"` |\n| `limit` | number | No | 20 | Maximum number of results |\n\n**Returns:** `[{ fileId, symbolCount }]`\n\n### get_file_symbols\n\nReturn all symbols declared in a specific file.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fileId` | string | Yes | File path, e.g. `"src/lib/graph.ts"` |\n\n**Returns:** `[{ id, kind, name, signature, startLine, endLine, isExported }]`\n\nSymbol kinds: `function`, `class`, `interface`, `type`, `enum`, `variable`, `method`, `property`.\n\n### search_code\n\nSemantic search over code symbols. Matches against signatures and doc comments using vector similarity, then expands through graph edges.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Natural language or code search query |\n| `topK` | number | No | 5 | Number of seed nodes from vector search |\n| `bfsDepth` | number | No | 1 | Hops to follow graph edges (imports, contains, extends) from each seed. 0 = no expansion |\n| `maxResults` | number | No | 20 | Maximum results to return |\n| `minScore` | number | No | 0.5 | Minimum relevance score (0–1) |\n| `bfsDecay` | number | No | 0.8 | Score multiplier per graph hop |\n\n**Returns:** `[{ id, fileId, kind, name, signature, docComment, startLine, endLine, score }]`\n\n### get_symbol\n\nReturn full details of a specific code symbol.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `nodeId` | string | Yes | Symbol ID, e.g. `"src/lib/graph.ts::updateFile"` or `"src/auth.ts::AuthService::login"` |\n\n**Returns:** `{ id, fileId, kind, name, signature, docComment, body, startLine, endLine, isExported }`\n\nThe `body` field contains the full implementation text. `docComment` contains the JSDoc comment if present.\n\n### search_files\n\nSemantic search at file level using file path embeddings.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Natural language or path search query |\n| `topK` | number | No | 10 | Maximum results |\n| `minScore` | number | No | 0.3 | Minimum relevance score (0–1) |\n\n**Returns:** `[{ fileId, symbolCount, score }]`\n\n## Tips\n\n- `search_code` works best with descriptive queries about **what the code does**, not exact symbol names\n- For exact name lookup, use `get_symbol` directly with the node ID\n- `get_file_symbols` shows `isExported` — useful for distinguishing public API from internals\n- `search_files` is useful as a first step when exploring unfamiliar codebases\n- The `cross_references` tool (see dedicated guide) is the most comprehensive way to understand a symbol\n- BFS expansion in `search_code` follows `imports`, `contains`, and `extends` edges — set `bfsDepth: 2` to discover related modules\n- Code graph edges track `imports` for relative imports only (`./ ../` paths); external packages are skipped\n'},{id:`knowledge-tools`,title:`Knowledge Tools`,summary:`Create and manage notes, facts, and decisions in a persistent knowledge graph.`,category:`guide`,relatedTools:[`create_note`,`update_note`,`delete_note`,`get_note`,`list_notes`,`search_notes`,`create_relation`,`delete_relation`,`list_relations`,`find_linked_notes`,`add_note_attachment`,`remove_note_attachment`],content:'# Knowledge Tools\n\nThe knowledge tools manage a persistent graph of **notes, facts, and decisions**. Unlike docs and code tools that index existing files, the knowledge graph is built manually — capturing information that lives in people\'s heads.\n\n## Why use a knowledge graph?\n\nCode and docs tell you **what** exists. The knowledge graph captures **why** — architectural decisions, domain knowledge, gotchas, context that doesn\'t belong in code comments.\n\nExamples:\n- "We use JWT instead of sessions because the mobile app needs stateless auth"\n- "The billing service has a 30-second timeout — don\'t chain more than 3 API calls"\n- "Users in the \'legacy\' tier have different rate limits, check `isLegacy` flag"\n\n## Tool overview\n\n| Tool | Purpose | Type |\n|------|---------|------|\n| `create_note` | Create a new note with title, content, tags | Mutation |\n| `update_note` | Update an existing note | Mutation |\n| `delete_note` | Remove a note and all its relations | Mutation |\n| `get_note` | Read a single note by ID | Read |\n| `list_notes` | List notes with optional filters | Read |\n| `search_notes` | Semantic search across notes | Read |\n| `create_relation` | Link a note to another note or external node | Mutation |\n| `delete_relation` | Remove a link | Mutation |\n| `list_relations` | List all relations for a note | Read |\n| `find_linked_notes` | Reverse lookup: find notes that link to an external node | Read |\n| `add_note_attachment` | Attach a file to a note | Mutation |\n| `remove_note_attachment` | Remove an attachment from a note | Mutation |\n\n> **Mutation tools** are serialized through a queue to prevent concurrent graph modifications.\n\n## Note ID generation\n\nNote IDs are slugified from the title:\n- "Auth Architecture" → `auth-architecture`\n- "JWT Token Format" → `jwt-token-format`\n\nDuplicate titles get a suffix: `auth-architecture::2`, `auth-architecture::3`.\n\n## Tool reference\n\n### create_note\n\nCreate a new note. Automatically embedded for semantic search.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `title` | string | Yes | Short title, e.g. `"Auth uses JWT tokens"` |\n| `content` | string | Yes | Full text content |\n| `tags` | string[] | No | Tags for filtering, e.g. `["architecture", "decision"]` |\n\n**Returns:** `{ noteId }` — the generated slug ID\n\n### update_note\n\nUpdate an existing note. Only provided fields change. Re-embeds automatically if title or content changes.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | ID of the note to update |\n| `title` | string | No | New title |\n| `content` | string | No | New content |\n| `tags` | string[] | No | New tags (replaces existing array entirely) |\n\n**Returns:** `{ noteId, updated: true }`\n\n### delete_note\n\nDelete a note and all its connected edges (relations, cross-graph links). Orphaned proxy nodes are cleaned up automatically.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | ID of the note to delete |\n\n**Returns:** `{ noteId, deleted: true }`\n\n### get_note\n\nReturn the full content of a note.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | Note ID, e.g. `"auth-uses-jwt-tokens"` |\n\n**Returns:** `{ id, title, content, tags, createdAt, updatedAt }`\n\n### list_notes\n\nList notes with optional filtering. Sorted by most recently updated.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `filter` | string | No | — | Case-insensitive substring match on title or ID |\n| `tag` | string | No | — | Filter by tag (exact match, case-insensitive) |\n| `limit` | number | No | 20 | Maximum results |\n\n**Returns:** `[{ id, title, tags, updatedAt }]`\n\n### search_notes\n\nSemantic search over the knowledge graph with BFS expansion through note relations.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Natural language search query |\n| `topK` | number | No | 5 | Number of seed nodes from vector search |\n| `bfsDepth` | number | No | 1 | Hops to follow relations from each seed (0 = no expansion) |\n| `maxResults` | number | No | 20 | Maximum results |\n| `minScore` | number | No | 0.5 | Minimum relevance score (0–1) |\n| `bfsDecay` | number | No | 0.8 | Score multiplier per hop |\n\n**Returns:** `[{ id, title, content, tags, score }]`\n\n### create_relation\n\nCreate a directed edge from a note to another note or to an external graph node.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fromId` | string | Yes | Source note ID |\n| `toId` | string | Yes | Target note ID, or target node ID in external graph |\n| `kind` | string | Yes | Relation type: `"relates_to"`, `"depends_on"`, `"contradicts"`, `"supports"`, `"part_of"`, `"references"`, etc. |\n| `targetGraph` | `"docs"` \\| `"code"` \\| `"files"` \\| `"tasks"` \\| `"skills"` | No | Set to create a cross-graph link instead of note-to-note |\n\n**Returns:** `{ fromId, toId, kind, targetGraph, created: true }`\n\n**Cross-graph examples:**\n```\ncreate_relation({ fromId: "auth-arch", toId: "auth.ts::AuthService", kind: "documents", targetGraph: "code" })\ncreate_relation({ fromId: "config-note", toId: "src/config.ts", kind: "references", targetGraph: "files" })\ncreate_relation({ fromId: "api-decision", toId: "api-guide.md::Endpoints", kind: "explains", targetGraph: "docs" })\ncreate_relation({ fromId: "my-note", toId: "fix-auth-bug", kind: "tracks", targetGraph: "tasks" })\n```\n\n### delete_relation\n\nRemove a directed edge.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fromId` | string | Yes | Source note ID |\n| `toId` | string | Yes | Target note ID or external node ID |\n| `targetGraph` | `"docs"` \\| `"code"` \\| `"files"` \\| `"tasks"` \\| `"skills"` | No | Set when deleting a cross-graph link |\n\n**Returns:** `{ fromId, toId, targetGraph, deleted: true }`\n\n### list_relations\n\nList all relations (both incoming and outgoing) for a note. Cross-graph links include `targetGraph` field and resolve the real node ID (not the proxy ID).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | Note ID to list relations for |\n\n**Returns:** `[{ fromId, toId, kind, targetGraph? }]`\n\n### find_linked_notes\n\nReverse lookup: given a node in an external graph, find all notes that link to it.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `targetId` | string | Yes | Target node ID in the external graph, e.g. `"src/config.ts"`, `"auth.ts::login"`, `"api.md::Setup"` |\n| `targetGraph` | `"docs"` \\| `"code"` \\| `"files"` \\| `"tasks"` \\| `"skills"` | Yes | Which graph the target belongs to |\n| `kind` | string | No | Filter by relation kind. If omitted, returns all relations |\n\n**Returns:** `[{ noteId, title, kind, tags }]`\n\n**Use case:** When working on a code file, call `find_linked_notes({ targetId: "src/auth.ts", targetGraph: "code" })` to discover what knowledge notes reference that file.\n\n### add_note_attachment\n\nAttach a file to a note. The file is copied into the note\'s directory (`.notes/{noteId}/`).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | Note ID to attach the file to |\n| `filePath` | string | Yes | Absolute path to the file on disk |\n\n**Returns:** `{ noteId, attachment: { filename, mimeType, size } }`\n\n### remove_note_attachment\n\nRemove an attachment from a note. Deletes the file from disk.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | Note ID |\n| `filename` | string | Yes | Filename of the attachment to remove |\n\n**Returns:** `{ noteId, filename, deleted: true }`\n\n## Tips\n\n- Use tags consistently for easy filtering (e.g., `decision`, `gotcha`, `todo`, `architecture`)\n- Link notes to the code they describe — this creates a navigable knowledge web\n- `find_linked_notes` is useful to discover what knowledge exists about a specific code symbol or file\n- Notes persist across server restarts (saved as `knowledge.json`)\n- The `kind` field on relations is free-form — use whatever makes sense for your domain\n- `update_note` with `tags` replaces the entire array — include all tags you want to keep\n- `search_notes` with `bfsDepth: 2` will traverse through related notes to find loosely connected knowledge\n- Notes support file attachments — attach images, logs, or any file via `add_note_attachment`\n- Attachments are stored in `.notes/{noteId}/` alongside the note\'s markdown file\n'},{id:`task-tools`,title:`Task Tools`,summary:`Kanban task management with priorities, dependencies, and cross-graph links.`,category:`guide`,relatedTools:[`create_task`,`update_task`,`delete_task`,`get_task`,`list_tasks`,`search_tasks`,`move_task`,`link_task`,`create_task_link`,`delete_task_link`,`find_linked_tasks`,`add_task_attachment`,`remove_task_attachment`],content:'# Task Tools\n\nThe task tools provide a full **kanban-style task management** system within Graph Memory. Tasks have status, priority, due dates, estimates, and can link to any other graph.\n\n## Why tasks in Graph Memory?\n\nTasks here are tightly integrated with your project\'s knowledge graph:\n- Link a task to the code files it affects\n- Link a task to documentation that needs updating\n- Link a task to knowledge notes for context\n- Track dependencies between tasks (subtasks, blockers)\n\n## Tool overview\n\n| Tool | Purpose | Type |\n|------|---------|------|\n| `create_task` | Create a task | Mutation |\n| `update_task` | Modify task fields | Mutation |\n| `delete_task` | Remove a task and all its edges | Mutation |\n| `get_task` | Read a task with all relations | Read |\n| `list_tasks` | List tasks with filters | Read |\n| `search_tasks` | Semantic search across tasks | Read |\n| `move_task` | Change task status (kanban move) | Mutation |\n| `link_task` | Create task-to-task relation | Mutation |\n| `create_task_link` | Link task to external graph node | Mutation |\n| `delete_task_link` | Remove cross-graph link | Mutation |\n| `find_linked_tasks` | Reverse lookup: find tasks linked to an external node | Read |\n| `add_task_attachment` | Attach a file to a task | Mutation |\n| `remove_task_attachment` | Remove an attachment from a task | Mutation |\n\n> **Mutation tools** are serialized through a queue to prevent concurrent graph modifications.\n\n## Task properties\n\n| Property | Type | Values / Format | Notes |\n|----------|------|-----------------|-------|\n| `title` | string | Free text | Becomes slug ID |\n| `description` | string | Markdown | Full task description |\n| `status` | enum | `backlog`, `todo`, `in_progress`, `review`, `done`, `cancelled` | Use `move_task` to change |\n| `priority` | enum | `critical`, `high`, `medium`, `low` | Affects sort order |\n| `tags` | string[] | Free-form | For filtering |\n| `dueDate` | number | Unix timestamp in milliseconds | Optional deadline |\n| `estimate` | number | Hours | Optional effort estimate |\n| `assignee` | string \\| null | Team member ID | Optional assignee from `users:` config |\n| `completedAt` | number | Unix timestamp (auto-managed) | Set on done/cancelled, cleared on reopen |\n| `createdAt` | number | Unix timestamp (auto) | Set at creation |\n| `updatedAt` | number | Unix timestamp (auto) | Updated on every change |\n\n## Task ID generation\n\nLike notes, task IDs are slugified from the title:\n- "Fix auth redirect loop" → `fix-auth-redirect-loop`\n- Duplicates get suffixes: `fix-auth-redirect-loop::2`\n\n## Tool reference\n\n### create_task\n\nCreate a new task. Automatically embedded for semantic search.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `title` | string | Yes | — | Short title, e.g. `"Fix auth redirect loop"` |\n| `description` | string | Yes | — | Full description (markdown) |\n| `priority` | enum | Yes | — | `"critical"`, `"high"`, `"medium"`, `"low"` |\n| `status` | enum | No | `"backlog"` | `"backlog"`, `"todo"`, `"in_progress"`, `"review"`, `"done"`, `"cancelled"` |\n| `tags` | string[] | No | `[]` | Tags for filtering |\n| `dueDate` | number | No | — | Due date as Unix timestamp in milliseconds |\n| `estimate` | number | No | — | Estimated effort in hours |\n| `assignee` | string | No | — | Team member ID to assign the task to |\n\n**Returns:** `{ taskId }`\n\n### update_task\n\nUpdate an existing task. Only provided fields change. Re-embeds if title or description changes. Status changes auto-manage `completedAt`.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to update |\n| `title` | string | No | New title |\n| `description` | string | No | New description |\n| `status` | enum | No | New status |\n| `priority` | enum | No | New priority |\n| `tags` | string[] | No | Replace tags array (include all you want to keep) |\n| `dueDate` | number \\| null | No | New due date (ms timestamp), or `null` to clear |\n| `estimate` | number \\| null | No | New estimate (hours), or `null` to clear |\n| `assignee` | string \\| null | No | Team member ID to assign, or `null` to unassign |\n\n**Returns:** `{ taskId, updated: true }`\n\n> Use `move_task` for a simpler status-only change — it\'s more explicit about `completedAt` management.\n\n### delete_task\n\nDelete a task and all its edges (relations + cross-graph links). Orphaned proxy nodes cleaned up automatically. **Irreversible.**\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to delete |\n\n**Returns:** `{ taskId, deleted: true }`\n\n### get_task\n\nReturn full task details including all relations. This is the most complete view of a task.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to retrieve |\n\n**Returns:**\n```\n{\n  id, title, description, status, priority, tags, assignee,\n  dueDate, estimate, completedAt, createdAt, updatedAt,\n  subtasks: [{ id, title, status }],\n  blockedBy: [{ id, title, status }],\n  blocks: [{ id, title, status }],\n  related: [{ id, title, status }]\n}\n```\n\nThe `subtasks`, `blockedBy`, `blocks`, and `related` arrays are automatically populated from task-to-task edges.\n\n### list_tasks\n\nList tasks with optional filters. Sorted by priority (critical → low) then due date (earliest first, nulls last).\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `status` | enum | No | — | Filter by status |\n| `priority` | enum | No | — | Filter by priority |\n| `tag` | string | No | — | Filter by tag (exact match, case-insensitive) |\n| `filter` | string | No | — | Substring match on title or ID |\n| `assignee` | string | No | — | Filter by assignee (team member ID) |\n| `limit` | number | No | 50 | Maximum results |\n\n**Returns:** `[{ id, title, description, status, priority, tags, dueDate, estimate, assignee, completedAt, createdAt, updatedAt }]`\n\n### search_tasks\n\nSemantic search over the task graph with BFS expansion.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Natural language search query |\n| `topK` | number | No | 5 | Seed nodes from vector search |\n| `bfsDepth` | number | No | 1 | Hops to follow relations (0 = no expansion) |\n| `maxResults` | number | No | 20 | Maximum results |\n| `minScore` | number | No | 0.5 | Minimum relevance score (0–1) |\n| `bfsDecay` | number | No | 0.8 | Score multiplier per hop |\n\n**Returns:** `[{ id, title, description, status, priority, tags, score }]`\n\n### move_task\n\nChange task status. The preferred way to move tasks through the kanban workflow.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to move |\n| `status` | enum | Yes | New status: `"backlog"`, `"todo"`, `"in_progress"`, `"review"`, `"done"`, `"cancelled"` |\n\n**Returns:** `{ taskId, status, completedAt }`\n\n**Automatic behavior:**\n- Moving to `done` or `cancelled` → sets `completedAt` to current time\n- Moving from `done`/`cancelled` to any other status → clears `completedAt`\n\n### link_task\n\nCreate a directed relation between two tasks.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fromId` | string | Yes | Source task ID |\n| `toId` | string | Yes | Target task ID |\n| `kind` | enum | Yes | `"subtask_of"`, `"blocks"`, `"related_to"` |\n\n**Returns:** `{ fromId, toId, kind, created: true }`\n\n**Semantics:**\n- `subtask_of` — `fromId` is a subtask of `toId` (child → parent)\n- `blocks` — `fromId` blocks `toId` (blocker → blocked task)\n- `related_to` — free association between tasks\n\n### create_task_link\n\nLink a task to a node in another graph (docs, code, files, or knowledge).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Source task ID |\n| `targetId` | string | Yes | Target node ID in the external graph |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"skills"` |\n| `kind` | string | Yes | Relation type: `"references"`, `"fixes"`, `"implements"`, `"documents"`, etc. |\n\n**Returns:** `{ taskId, targetId, targetGraph, kind, created: true }`\n\n**Examples:**\n```\ncreate_task_link({ taskId: "fix-auth", targetId: "src/auth.ts::login", targetGraph: "code", kind: "fixes" })\ncreate_task_link({ taskId: "update-docs", targetId: "guide.md::Authentication", targetGraph: "docs", kind: "updates" })\ncreate_task_link({ taskId: "review-config", targetId: "src/config.ts", targetGraph: "files", kind: "references" })\ncreate_task_link({ taskId: "implement-arch", targetId: "auth-architecture", targetGraph: "knowledge", kind: "implements" })\n```\n\n### delete_task_link\n\nRemove a cross-graph link from a task. Orphaned proxy nodes cleaned up automatically.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Source task ID |\n| `targetId` | string | Yes | Target node ID in the external graph |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"skills"` |\n\n**Returns:** `{ taskId, targetId, targetGraph, deleted: true }`\n\n### find_linked_tasks\n\nReverse lookup: given a node in an external graph, find all tasks that link to it.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `targetId` | string | Yes | Target node ID, e.g. `"src/auth.ts"`, `"guide.md::Setup"`, `"my-note"` |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"skills"` |\n| `kind` | string | No | Filter by relation kind. Omit for all relations |\n\n**Returns:** `[{ taskId, title, kind, status, priority, tags }]`\n\n**Use case:** When working on a file, call `find_linked_tasks({ targetId: "src/auth.ts", targetGraph: "code" })` to see all tasks related to that file.\n\n### add_task_attachment\n\nAttach a file to a task. The file is copied into the task\'s directory (`.tasks/{taskId}/`).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to attach the file to |\n| `filePath` | string | Yes | Absolute path to the file on disk |\n\n**Returns:** `{ taskId, attachment: { filename, mimeType, size } }`\n\n### remove_task_attachment\n\nRemove an attachment from a task. Deletes the file from disk.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID |\n| `filename` | string | Yes | Filename of the attachment to remove |\n\n**Returns:** `{ taskId, filename, deleted: true }`\n\n## Kanban board UI\n\nThe Tasks page provides a visual kanban board with these features:\n\n- **Column visibility** — toggle which status columns are shown via the column icon in the top bar; saved in localStorage\n- **Drag-and-drop** — drag task cards between columns to change status; drop-zone highlights on hover\n- **Inline task creation** — click "+" in a column header to quickly create a task in that status\n- **Filter bar** — search tasks by text, filter by priority or tag\n- **Due date indicators** — overdue tasks show a red badge, approaching deadlines (≤3 days) show yellow\n- **Estimate badges** — tasks with estimates show hours on the card\n- **Quick actions** — hover a card to see edit and delete buttons\n- **Scrollable columns** — columns scroll independently when content overflows\n\n## Tips\n\n- Use `move_task` instead of `update_task` for status changes — it explicitly handles `completedAt`\n- `get_task` returns the richest data — includes subtasks, blockers, and related tasks\n- `list_tasks` is sorted by priority then due date — critical overdue tasks appear first\n- Link tasks to code files they affect — makes it easy to find related tasks when working on code\n- Use `search_tasks` to find tasks by meaning, not just title keywords\n- `update_task` with `dueDate: null` or `estimate: null` clears those fields\n- `update_task` with `tags` replaces the entire array — include all tags you want to keep\n- Task-to-task `kind` values are a fixed enum (`subtask_of`, `blocks`, `related_to`), unlike knowledge relations which are free-form\n- Tasks support file attachments — attach screenshots, logs, or any file via `add_task_attachment`\n- Attachments are stored in `.tasks/{taskId}/` alongside the task\'s markdown file\n'},{id:`skill-tools`,title:`Skill Tools`,summary:`Create and manage reusable skills, recipes, and procedures with triggers and usage tracking.`,category:`guide`,relatedTools:[`create_skill`,`update_skill`,`delete_skill`,`get_skill`,`list_skills`,`search_skills`,`link_skill`,`create_skill_link`,`delete_skill_link`,`find_linked_skills`,`add_skill_attachment`,`remove_skill_attachment`,`recall_skills`,`bump_skill_usage`],content:'# Skill Tools\n\nThe skill tools provide a **recipe/procedure management** system within Graph Memory. Skills capture reusable knowledge — step-by-step procedures, patterns, and best practices — with triggers, usage tracking, and cross-graph links.\n\n## Why skills in Graph Memory?\n\nSkills here are tightly integrated with your project\'s knowledge graph:\n- Link a skill to the code files it applies to\n- Link a skill to documentation that describes the pattern\n- Link a skill to knowledge notes for context\n- Link a skill to tasks that use the procedure\n- Track dependencies and variants between skills\n\n## Tool overview\n\n| Tool | Purpose | Type |\n|------|---------|------|\n| `create_skill` | Create a skill with steps, triggers, and metadata | Mutation |\n| `update_skill` | Modify skill fields (partial update) | Mutation |\n| `delete_skill` | Remove a skill and all its edges | Mutation |\n| `get_skill` | Read a skill with all relations | Read |\n| `list_skills` | List skills with filters | Read |\n| `search_skills` | Semantic search across skills | Read |\n| `link_skill` | Create skill-to-skill relation | Mutation |\n| `create_skill_link` | Link skill to external graph node | Mutation |\n| `delete_skill_link` | Remove cross-graph link | Mutation |\n| `find_linked_skills` | Reverse lookup: find skills linked to an external node | Read |\n| `add_skill_attachment` | Attach a file to a skill | Mutation |\n| `remove_skill_attachment` | Remove an attachment from a skill | Mutation |\n| `recall_skills` | Recall relevant skills for a task context | Read |\n| `bump_skill_usage` | Increment usage counter + set lastUsedAt | Mutation |\n\n> **Mutation tools** are serialized through a queue to prevent concurrent graph modifications.\n\n## Skill properties\n\n| Property | Type | Values / Format | Notes |\n|----------|------|-----------------|-------|\n| `title` | string | Free text | Becomes slug ID |\n| `description` | string | Markdown | Full skill description |\n| `steps` | string[] | Ordered list | Step-by-step procedure |\n| `triggers` | string[] | Free-form | When to apply this skill |\n| `source` | enum | `user`, `learned` | How the skill was created |\n| `tags` | string[] | Free-form | For filtering |\n| `usageCount` | number | Auto-managed | Incremented by `bump_skill_usage` |\n| `lastUsedAt` | number | Unix timestamp (auto) | Set by `bump_skill_usage` |\n| `createdAt` | number | Unix timestamp (auto) | Set at creation |\n| `updatedAt` | number | Unix timestamp (auto) | Updated on every change |\n\n## Skill ID generation\n\nLike notes and tasks, skill IDs are slugified from the title:\n- "Add REST Endpoint" -> `add-rest-endpoint`\n- Duplicates get suffixes: `add-rest-endpoint::2`\n\n## Tool reference\n\n### create_skill\n\nCreate a new skill. Automatically embedded for semantic search.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `title` | string | Yes | -- | Short title, e.g. `"Add REST Endpoint"` |\n| `description` | string | Yes | -- | Full description (markdown) |\n| `steps` | string[] | No | `[]` | Ordered steps of the procedure |\n| `triggers` | string[] | No | `[]` | When this skill should be applied |\n| `source` | enum | No | `"user"` | `"user"`, `"learned"` |\n| `tags` | string[] | No | `[]` | Tags for filtering |\n\n**Returns:** `{ skillId }`\n\n### update_skill\n\nUpdate an existing skill. Only provided fields change. Re-embeds if title, description, or triggers change.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to update |\n| `title` | string | No | New title |\n| `description` | string | No | New description |\n| `steps` | string[] | No | Replace steps array |\n| `triggers` | string[] | No | Replace triggers array |\n| `source` | enum | No | New source |\n| `tags` | string[] | No | Replace tags array (include all you want to keep) |\n\n**Returns:** `{ skillId, updated: true }`\n\n### delete_skill\n\nDelete a skill and all its edges (relations + cross-graph links). Orphaned proxy nodes cleaned up automatically. **Irreversible.**\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to delete |\n\n**Returns:** `{ skillId, deleted: true }`\n\n### get_skill\n\nReturn full skill details including all relations. This is the most complete view of a skill.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to retrieve |\n\n**Returns:**\n```\n{\n  id, title, description, steps, triggers, source, tags,\n  usageCount, lastUsedAt, createdAt, updatedAt,\n  dependsOn: [{ id, title }],\n  dependedBy: [{ id, title }],\n  related: [{ id, title }],\n  variants: [{ id, title }]\n}\n```\n\nThe `dependsOn`, `dependedBy`, `related`, and `variants` arrays are automatically populated from skill-to-skill edges.\n\n### list_skills\n\nList skills with optional filters. Sorted by usage count (most used first).\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `source` | enum | No | -- | Filter by source (`user`, `learned`) |\n| `tag` | string | No | -- | Filter by tag (exact match, case-insensitive) |\n| `filter` | string | No | -- | Substring match on title or ID |\n| `limit` | number | No | 50 | Maximum results |\n\n**Returns:** `[{ id, title, description, steps, triggers, source, tags, usageCount, lastUsedAt, createdAt, updatedAt }]`\n\n### search_skills\n\nSemantic search over the skill graph with BFS expansion.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | -- | Natural language search query |\n| `topK` | number | No | 5 | Seed nodes from vector search |\n| `bfsDepth` | number | No | 1 | Hops to follow relations (0 = no expansion) |\n| `maxResults` | number | No | 20 | Maximum results |\n| `minScore` | number | No | 0.5 | Minimum relevance score (0-1) |\n| `bfsDecay` | number | No | 0.8 | Score multiplier per hop |\n\n**Returns:** `[{ id, title, description, steps, triggers, source, tags, score }]`\n\n### recall_skills\n\nRecall relevant skills for a task context. Uses a lower default `minScore` (0.3) for higher recall.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | -- | Task context or description |\n| `topK` | number | No | 10 | Maximum results |\n| `minScore` | number | No | 0.3 | Minimum relevance score (0-1) |\n\n**Returns:** `[{ id, title, description, steps, triggers, source, tags, score, usageCount }]`\n\n### bump_skill_usage\n\nRecord that a skill was used. Increments `usageCount` and sets `lastUsedAt` to the current time.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to bump |\n\n**Returns:** `{ skillId, usageCount, lastUsedAt }`\n\n### link_skill\n\nCreate a directed relation between two skills.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fromId` | string | Yes | Source skill ID |\n| `toId` | string | Yes | Target skill ID |\n| `kind` | enum | Yes | `"depends_on"`, `"related_to"`, `"variant_of"` |\n\n**Returns:** `{ fromId, toId, kind, created: true }`\n\n**Semantics:**\n- `depends_on` -- `fromId` depends on `toId` (prerequisite)\n- `related_to` -- free association between skills\n- `variant_of` -- `fromId` is a variation of `toId`\n\n### create_skill_link\n\nLink a skill to a node in another graph (docs, code, files, knowledge, or tasks).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Source skill ID |\n| `targetId` | string | Yes | Target node ID in the external graph |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"tasks"` |\n| `kind` | string | Yes | Relation type: `"applies_to"`, `"documented_in"`, `"used_by"`, etc. |\n\n**Returns:** `{ skillId, targetId, targetGraph, kind, created: true }`\n\n**Examples:**\n```\ncreate_skill_link({ skillId: "add-rest-endpoint", targetId: "src/routes/index.ts", targetGraph: "code", kind: "applies_to" })\ncreate_skill_link({ skillId: "add-rest-endpoint", targetId: "guide.md::REST API", targetGraph: "docs", kind: "documented_in" })\ncreate_skill_link({ skillId: "add-rest-endpoint", targetId: "implement-api", targetGraph: "tasks", kind: "used_by" })\n```\n\n### delete_skill_link\n\nRemove a cross-graph link from a skill. Orphaned proxy nodes cleaned up automatically.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Source skill ID |\n| `targetId` | string | Yes | Target node ID in the external graph |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"tasks"` |\n\n**Returns:** `{ skillId, targetId, targetGraph, deleted: true }`\n\n### find_linked_skills\n\nReverse lookup: given a node in an external graph, find all skills that link to it.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `targetId` | string | Yes | Target node ID, e.g. `"src/auth.ts"`, `"guide.md::Setup"`, `"my-task"` |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"tasks"` |\n| `kind` | string | No | Filter by relation kind. Omit for all relations |\n\n**Returns:** `[{ skillId, title, kind, source, tags }]`\n\n**Use case:** When working on a file, call `find_linked_skills({ targetId: "src/routes/index.ts", targetGraph: "code" })` to see all skills related to that file.\n\n### add_skill_attachment\n\nAttach a file to a skill. The file is copied into the skill\'s directory (`.skills/{skillId}/`).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to attach the file to |\n| `filePath` | string | Yes | Absolute path to the file on disk |\n\n**Returns:** `{ skillId, attachment: { filename, mimeType, size } }`\n\n### remove_skill_attachment\n\nRemove an attachment from a skill. Deletes the file from disk.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID |\n| `filename` | string | Yes | Filename of the attachment to remove |\n\n**Returns:** `{ skillId, filename, deleted: true }`\n\n## Tips\n\n- Use `recall_skills` when starting a task to find relevant procedures -- it uses a lower threshold for better recall\n- Call `bump_skill_usage` after applying a skill to track which skills are most useful\n- Skills with `source: "learned"` are typically created by AI agents that discover patterns\n- Skills with `source: "user"` are created by humans documenting their procedures\n- Link skills to code files they apply to -- makes it easy to find relevant skills when working on code\n- Use `search_skills` to find skills by meaning, not just title keywords\n- `update_skill` with `tags` replaces the entire array -- include all tags you want to keep\n- Skill-to-skill `kind` values are a fixed enum (`depends_on`, `related_to`, `variant_of`)\n- Skills support file attachments -- attach templates, examples, or reference files via `add_skill_attachment`\n- Attachments are stored in `.skills/{skillId}/` alongside the skill\'s markdown file\n'},{id:`files-tools`,title:`File Index Tools`,summary:`Browse and search metadata for every file and directory in your project.`,category:`guide`,relatedTools:[`list_all_files`,`search_all_files`,`get_file_info`],content:'# File Index Tools\n\nThe file index tools provide access to metadata about **every file and directory** in your project. Unlike docs and code tools which only index pattern-matched files, the file index covers the entire project tree.\n\n## Tool overview\n\n| Tool | Purpose | When to use |\n|------|---------|-------------|\n| `list_all_files` | List files/directories with filters | Browse project structure, filter by extension/language |\n| `search_all_files` | Semantic search by file path | Find files by what they might contain |\n| `get_file_info` | Get metadata for a specific path | Check size, language, modification date |\n\n## What gets indexed\n\nFor every file in the project directory:\n- **Path** (relative to project root)\n- **File name** and **extension**\n- **Size** in bytes\n- **Language** (detected from extension: `.ts` → TypeScript, `.md` → Markdown, `.json` → JSON, etc.)\n- **MIME type** (e.g., `application/json`, `text/markdown`, `image/png`)\n- **Modification time** (`mtime`)\n\nFor directories:\n- **Aggregate size** (sum of all contained files)\n- **File count** (total files in subtree)\n- Directory → child edges (`contains`)\n\n## Browsing vs searching\n\n### Directory browsing\n\n`list_all_files` with the `directory` parameter returns **immediate children** (files + subdirectories) of that directory. This is how you browse the project tree:\n\n```\nlist_all_files({ directory: "." })           → root contents\nlist_all_files({ directory: "src" })         → src/ contents\nlist_all_files({ directory: "src/api" })     → src/api/ contents\n```\n\nWithout `directory`, it returns all files matching filters (flat list, no directories).\n\n### File search\n\n`search_all_files` embeds file paths for semantic search. You can search by:\n- Partial paths: `"config"` finds configuration files\n- Concepts: `"authentication"` finds files in auth-related directories\n- File types: `"typescript source"` finds `.ts` files\n\nThe `minScore` default is **0.3** (lower than node search) because file path embeddings are less semantically rich than content embeddings.\n\n## Tool reference\n\n### list_all_files\n\nList project files and directories with optional filters.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `directory` | string | No | — | List immediate children of this directory (e.g. `"."`, `"src/lib"`). Without this, returns all files matching filters |\n| `extension` | string | No | — | Filter by extension (e.g. `".ts"`, `".md"`, `".png"`) |\n| `language` | string | No | — | Filter by detected language (e.g. `"typescript"`, `"markdown"`, `"json"`) |\n| `filter` | string | No | — | Substring match on file path (case-insensitive) |\n| `limit` | number | No | 50 | Maximum results |\n\n**Returns:** `[{ filePath, kind, fileName, extension, language, mimeType, size, fileCount }]`\n\n- `kind` is `"file"` or `"directory"`\n- `fileCount` is present for directories (number of files in subtree)\n- `language` and `mimeType` are present for files\n\n**Behavior differences:**\n- With `directory` set: returns both files and subdirectories (immediate children only)\n- Without `directory`: returns only files (no directories), across the entire project\n\n### search_all_files\n\nSemantic search over file nodes by path embedding. Searches files only (not directories).\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Search query (natural language or path fragment) |\n| `topK` | number | No | 10 | Maximum results |\n| `minScore` | number | No | 0.3 | Minimum cosine similarity score (0–1) |\n\n**Returns:** `[{ filePath, fileName, extension, language, size, score }]`\n\n### get_file_info\n\nGet full metadata for a specific file or directory. Use `"."` for the project root.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `filePath` | string | Yes | Relative file or directory path (e.g. `"src/lib/config.ts"`, `"src/lib"`, `"."`) |\n\n**Returns for files:**\n```\n{ filePath, kind: "file", fileName, directory, extension, language, mimeType, size, mtime }\n```\n\n**Returns for directories:**\n```\n{ filePath, kind: "directory", fileName, directory, fileCount, size }\n```\n\n- `size` for directories is the total size of all direct children\n- `fileCount` for directories is the total number of files in the subtree\n- `mtime` is the last modification timestamp (files only)\n\n## Cross-graph links\n\nFiles can be linked from notes and tasks:\n\n```\n// From a knowledge note\ncreate_relation({ fromId: "config-format", toId: "src/config.ts", kind: "documents", targetGraph: "files" })\n\n// From a task\ncreate_task_link({ taskId: "refactor-config", targetId: "src/config.ts", targetGraph: "files", kind: "affects" })\n```\n\nUse `find_linked_notes` or `find_linked_tasks` with `targetGraph: "files"` to discover what knowledge or tasks reference a specific file:\n\n```\nfind_linked_notes({ targetId: "src/auth.ts", targetGraph: "files" })\nfind_linked_tasks({ targetId: "src/auth.ts", targetGraph: "files" })\n```\n\n## Tips\n\n- Use `list_all_files` with `directory` to browse top-down through the project tree\n- Use `list_all_files` with `extension: ".ts"` or `language: "typescript"` to find all files of a type\n- `get_file_info` on `"."` gives project-level stats (total size, file count)\n- `search_all_files` works better with path-like queries than abstract concepts\n- File index is always active — no `docsPattern` or `codePattern` configuration needed\n- The `language` filter in `list_all_files` uses detected language names like `"typescript"`, `"javascript"`, `"markdown"`, `"json"`, `"yaml"`, `"css"`, `"html"`, `"python"`, etc.\n'},{id:`cross-references`,title:`Cross References Tool`,summary:`Bridge code definitions and documentation examples for any symbol.`,category:`guide`,relatedTools:[`cross_references`],content:`# Cross References Tool
+`},{id:`code-tools`,title:`Code Tools`,summary:`Search and navigate TypeScript/JavaScript source code symbols.`,category:`guide`,relatedTools:[`list_files`,`get_file_symbols`,`search_code`,`get_symbol`,`search_files`],content:'# Code Tools\n\nThe code tools let you search and navigate your indexed TypeScript/JavaScript source code. They\'re available when `graphs.code.include` is configured in your project (default: `**/*.{js,ts,jsx,tsx}`).\n\n## Tool overview\n\n| Tool | Purpose | When to use |\n|------|---------|-------------|\n| `list_files` | List all indexed source files | Get an overview of the codebase |\n| `get_file_symbols` | List symbols in a file | Explore a file\'s exports and structure |\n| `search_code` | Semantic search across code symbols | Find functions/classes by what they do |\n| `get_symbol` | Get full details of a symbol | Read signature, JSDoc, body, line numbers |\n| `search_files` | Search at file level | Find which files are relevant to a topic |\n\n## What gets indexed\n\nThe code parser uses tree-sitter to extract:\n- **Functions** — name, signature, JSDoc, line range, exported flag\n- **Classes** — name, methods, extends/implements relationships\n- **Interfaces** and **Types** — name, signature\n- **Enums** — name, members\n- **Variables** (exported) — name, type\n- **Methods** — as children of their parent class\n\nEdges capture structural relationships:\n- `contains` — file → symbol, class → method\n- `imports` — file → imported file (resolved by import resolver)\n- `extends` — class → base class\n- `implements` — class → interface\n\n## Node ID format\n\nCode graph node IDs follow a hierarchical pattern:\n- `"src/auth.ts"` — file node\n- `"src/auth.ts::createUser"` — top-level symbol in file\n- `"src/auth.ts::AuthService::login"` — method within a class\n\n## Typical workflow\n\n### 1. Find code by meaning\n\nUse `search_code` with a description of what you\'re looking for:\n- `"user authentication"` — finds auth-related functions and classes\n- `"parse markdown into sections"` — finds parsing logic\n\nUnlike grep, this finds code by **what it does**, not by exact text matches.\n\n### 2. Explore a symbol\n\nUse `get_symbol` with the symbol ID from search results. This returns the full picture: signature, JSDoc comment, body text, file location, line numbers, export status.\n\n### 3. Understand file structure\n\nUse `get_file_symbols` to see all symbols in a file — helpful for understanding module organization. The result includes `isExported` flag to distinguish public API from internal helpers.\n\n### 4. Discover relevant files\n\nUse `search_files` for a quick file-level search before diving into symbols. Lighter than `search_code` when you just need to identify which files to explore.\n\n### 5. Cross-reference with docs\n\nUse `cross_references` (requires both `graphs.docs.include` and `graphs.code.include`) to find everywhere a symbol appears — in both code definitions and documentation examples. See the dedicated guide for details.\n\n## Tool reference\n\n### list_files\n\nList indexed source files with optional filtering.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `filter` | string | No | — | Case-insensitive substring to match against file paths, e.g. `"graph"` or `"src/lib"` |\n| `limit` | number | No | 20 | Maximum number of results |\n\n**Returns:** `[{ fileId, symbolCount }]`\n\n### get_file_symbols\n\nReturn all symbols declared in a specific file.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fileId` | string | Yes | File path, e.g. `"src/lib/graph.ts"` |\n\n**Returns:** `[{ id, kind, name, signature, startLine, endLine, isExported }]`\n\nSymbol kinds: `function`, `class`, `interface`, `type`, `enum`, `variable`, `method`, `property`.\n\n### search_code\n\nSemantic search over code symbols. Matches against signatures and doc comments using vector similarity, then expands through graph edges.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Natural language or code search query |\n| `topK` | number | No | 5 | Number of seed nodes from vector search |\n| `bfsDepth` | number | No | 1 | Hops to follow graph edges (imports, contains, extends) from each seed. 0 = no expansion |\n| `maxResults` | number | No | 20 | Maximum results to return |\n| `minScore` | number | No | 0.5 | Minimum relevance score (0–1) |\n| `bfsDecay` | number | No | 0.8 | Score multiplier per graph hop |\n\n**Returns:** `[{ id, fileId, kind, name, signature, docComment, startLine, endLine, score }]`\n\n### get_symbol\n\nReturn full details of a specific code symbol.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `nodeId` | string | Yes | Symbol ID, e.g. `"src/lib/graph.ts::updateFile"` or `"src/auth.ts::AuthService::login"` |\n\n**Returns:** `{ id, fileId, kind, name, signature, docComment, body, startLine, endLine, isExported }`\n\nThe `body` field contains the full implementation text. `docComment` contains the JSDoc comment if present.\n\n### search_files\n\nSemantic search at file level using file path embeddings.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Natural language or path search query |\n| `topK` | number | No | 10 | Maximum results |\n| `minScore` | number | No | 0.3 | Minimum relevance score (0–1) |\n\n**Returns:** `[{ fileId, symbolCount, score }]`\n\n## Tips\n\n- `search_code` works best with descriptive queries about **what the code does**, not exact symbol names\n- For exact name lookup, use `get_symbol` directly with the node ID\n- `get_file_symbols` shows `isExported` — useful for distinguishing public API from internals\n- `search_files` is useful as a first step when exploring unfamiliar codebases\n- The `cross_references` tool (see dedicated guide) is the most comprehensive way to understand a symbol\n- BFS expansion in `search_code` follows `imports`, `contains`, and `extends` edges — set `bfsDepth: 2` to discover related modules\n- Code graph edges track `imports` for relative imports only (`./ ../` paths); external packages are skipped\n'},{id:`knowledge-tools`,title:`Knowledge Tools`,summary:`Create and manage notes, facts, and decisions in a persistent knowledge graph.`,category:`guide`,relatedTools:[`create_note`,`update_note`,`delete_note`,`get_note`,`list_notes`,`search_notes`,`create_relation`,`delete_relation`,`list_relations`,`find_linked_notes`,`add_note_attachment`,`remove_note_attachment`],content:'# Knowledge Tools\n\nThe knowledge tools manage a persistent graph of **notes, facts, and decisions**. Unlike docs and code tools that index existing files, the knowledge graph is built manually — capturing information that lives in people\'s heads.\n\n## Why use a knowledge graph?\n\nCode and docs tell you **what** exists. The knowledge graph captures **why** — architectural decisions, domain knowledge, gotchas, context that doesn\'t belong in code comments.\n\nExamples:\n- "We use JWT instead of sessions because the mobile app needs stateless auth"\n- "The billing service has a 30-second timeout — don\'t chain more than 3 API calls"\n- "Users in the \'legacy\' tier have different rate limits, check `isLegacy` flag"\n\n## Tool overview\n\n| Tool | Purpose | Type |\n|------|---------|------|\n| `create_note` | Create a new note with title, content, tags | Mutation |\n| `update_note` | Update an existing note | Mutation |\n| `delete_note` | Remove a note and all its relations | Mutation |\n| `get_note` | Read a single note by ID | Read |\n| `list_notes` | List notes with optional filters | Read |\n| `search_notes` | Semantic search across notes | Read |\n| `create_relation` | Link a note to another note or external node | Mutation |\n| `delete_relation` | Remove a link | Mutation |\n| `list_relations` | List all relations for a note | Read |\n| `find_linked_notes` | Reverse lookup: find notes that link to an external node | Read |\n| `add_note_attachment` | Attach a file to a note | Mutation |\n| `remove_note_attachment` | Remove an attachment from a note | Mutation |\n\n> **Mutation tools** are serialized through a queue to prevent concurrent graph modifications.\n\n## Note ID generation\n\nNote IDs are slugified from the title:\n- "Auth Architecture" → `auth-architecture`\n- "JWT Token Format" → `jwt-token-format`\n\nDuplicate titles get a suffix: `auth-architecture::2`, `auth-architecture::3`.\n\n## Tool reference\n\n### create_note\n\nCreate a new note. Automatically embedded for semantic search.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `title` | string | Yes | Short title, e.g. `"Auth uses JWT tokens"` |\n| `content` | string | Yes | Full text content |\n| `tags` | string[] | No | Tags for filtering, e.g. `["architecture", "decision"]` |\n\n**Returns:** `{ noteId }` — the generated slug ID\n\n### update_note\n\nUpdate an existing note. Only provided fields change. Re-embeds automatically if title or content changes.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | ID of the note to update |\n| `title` | string | No | New title |\n| `content` | string | No | New content |\n| `tags` | string[] | No | New tags (replaces existing array entirely) |\n\n**Returns:** `{ noteId, updated: true }`\n\n### delete_note\n\nDelete a note and all its connected edges (relations, cross-graph links). Orphaned proxy nodes are cleaned up automatically.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | ID of the note to delete |\n\n**Returns:** `{ noteId, deleted: true }`\n\n### get_note\n\nReturn the full content of a note.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | Note ID, e.g. `"auth-uses-jwt-tokens"` |\n\n**Returns:** `{ id, title, content, tags, createdAt, updatedAt }`\n\n### list_notes\n\nList notes with optional filtering. Sorted by most recently updated.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `filter` | string | No | — | Case-insensitive substring match on title or ID |\n| `tag` | string | No | — | Filter by tag (exact match, case-insensitive) |\n| `limit` | number | No | 20 | Maximum results |\n\n**Returns:** `[{ id, title, tags, updatedAt }]`\n\n### search_notes\n\nSemantic search over the knowledge graph with BFS expansion through note relations.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Natural language search query |\n| `topK` | number | No | 5 | Number of seed nodes from vector search |\n| `bfsDepth` | number | No | 1 | Hops to follow relations from each seed (0 = no expansion) |\n| `maxResults` | number | No | 20 | Maximum results |\n| `minScore` | number | No | 0.5 | Minimum relevance score (0–1) |\n| `bfsDecay` | number | No | 0.8 | Score multiplier per hop |\n\n**Returns:** `[{ id, title, content, tags, score }]`\n\n### create_relation\n\nCreate a directed edge from a note to another note or to an external graph node.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fromId` | string | Yes | Source note ID |\n| `toId` | string | Yes | Target note ID, or target node ID in external graph |\n| `kind` | string | Yes | Relation type: `"relates_to"`, `"depends_on"`, `"contradicts"`, `"supports"`, `"part_of"`, `"references"`, etc. |\n| `targetGraph` | `"docs"` \\| `"code"` \\| `"files"` \\| `"tasks"` \\| `"skills"` | No | Set to create a cross-graph link instead of note-to-note |\n\n**Returns:** `{ fromId, toId, kind, targetGraph, created: true }`\n\n**Cross-graph examples:**\n```\ncreate_relation({ fromId: "auth-arch", toId: "auth.ts::AuthService", kind: "documents", targetGraph: "code" })\ncreate_relation({ fromId: "config-note", toId: "src/config.ts", kind: "references", targetGraph: "files" })\ncreate_relation({ fromId: "api-decision", toId: "api-guide.md::Endpoints", kind: "explains", targetGraph: "docs" })\ncreate_relation({ fromId: "my-note", toId: "fix-auth-bug", kind: "tracks", targetGraph: "tasks" })\n```\n\n### delete_relation\n\nRemove a directed edge.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fromId` | string | Yes | Source note ID |\n| `toId` | string | Yes | Target note ID or external node ID |\n| `targetGraph` | `"docs"` \\| `"code"` \\| `"files"` \\| `"tasks"` \\| `"skills"` | No | Set when deleting a cross-graph link |\n\n**Returns:** `{ fromId, toId, targetGraph, deleted: true }`\n\n### list_relations\n\nList all relations (both incoming and outgoing) for a note. Cross-graph links include `targetGraph` field and resolve the real node ID (not the proxy ID).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | Note ID to list relations for |\n\n**Returns:** `[{ fromId, toId, kind, targetGraph? }]`\n\n### find_linked_notes\n\nReverse lookup: given a node in an external graph, find all notes that link to it.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `targetId` | string | Yes | Target node ID in the external graph, e.g. `"src/config.ts"`, `"auth.ts::login"`, `"api.md::Setup"` |\n| `targetGraph` | `"docs"` \\| `"code"` \\| `"files"` \\| `"tasks"` \\| `"skills"` | Yes | Which graph the target belongs to |\n| `kind` | string | No | Filter by relation kind. If omitted, returns all relations |\n\n**Returns:** `[{ noteId, title, kind, tags }]`\n\n**Use case:** When working on a code file, call `find_linked_notes({ targetId: "src/auth.ts", targetGraph: "code" })` to discover what knowledge notes reference that file.\n\n### add_note_attachment\n\nAttach a file to a note. The file is copied into the note\'s directory (`.notes/{noteId}/`).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | Note ID to attach the file to |\n| `filePath` | string | Yes | Absolute path to the file on disk |\n\n**Returns:** `{ noteId, attachment: { filename, mimeType, size } }`\n\n### remove_note_attachment\n\nRemove an attachment from a note. Deletes the file from disk.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `noteId` | string | Yes | Note ID |\n| `filename` | string | Yes | Filename of the attachment to remove |\n\n**Returns:** `{ noteId, filename, deleted: true }`\n\n## Tips\n\n- Use tags consistently for easy filtering (e.g., `decision`, `gotcha`, `todo`, `architecture`)\n- Link notes to the code they describe — this creates a navigable knowledge web\n- `find_linked_notes` is useful to discover what knowledge exists about a specific code symbol or file\n- Notes persist across server restarts (saved as `knowledge.json`)\n- The `kind` field on relations is free-form — use whatever makes sense for your domain\n- `update_note` with `tags` replaces the entire array — include all tags you want to keep\n- `search_notes` with `bfsDepth: 2` will traverse through related notes to find loosely connected knowledge\n- Notes support file attachments — attach images, logs, or any file via `add_note_attachment`\n- Attachments are stored in `.notes/{noteId}/` alongside the note\'s markdown file\n'},{id:`task-tools`,title:`Task Tools`,summary:`Kanban task management with priorities, dependencies, and cross-graph links.`,category:`guide`,relatedTools:[`create_task`,`update_task`,`delete_task`,`get_task`,`list_tasks`,`search_tasks`,`move_task`,`link_task`,`create_task_link`,`delete_task_link`,`find_linked_tasks`,`add_task_attachment`,`remove_task_attachment`],content:'# Task Tools\n\nThe task tools provide a full **kanban-style task management** system within Graph Memory. Tasks have status, priority, due dates, estimates, and can link to any other graph.\n\n## Why tasks in Graph Memory?\n\nTasks here are tightly integrated with your project\'s knowledge graph:\n- Link a task to the code files it affects\n- Link a task to documentation that needs updating\n- Link a task to knowledge notes for context\n- Track dependencies between tasks (subtasks, blockers)\n\n## Tool overview\n\n| Tool | Purpose | Type |\n|------|---------|------|\n| `create_task` | Create a task | Mutation |\n| `update_task` | Modify task fields | Mutation |\n| `delete_task` | Remove a task and all its edges | Mutation |\n| `get_task` | Read a task with all relations | Read |\n| `list_tasks` | List tasks with filters | Read |\n| `search_tasks` | Semantic search across tasks | Read |\n| `move_task` | Change task status (kanban move) | Mutation |\n| `link_task` | Create task-to-task relation | Mutation |\n| `create_task_link` | Link task to external graph node | Mutation |\n| `delete_task_link` | Remove cross-graph link | Mutation |\n| `find_linked_tasks` | Reverse lookup: find tasks linked to an external node | Read |\n| `add_task_attachment` | Attach a file to a task | Mutation |\n| `remove_task_attachment` | Remove an attachment from a task | Mutation |\n\n> **Mutation tools** are serialized through a queue to prevent concurrent graph modifications.\n\n## Task properties\n\n| Property | Type | Values / Format | Notes |\n|----------|------|-----------------|-------|\n| `title` | string | Free text | Becomes slug ID |\n| `description` | string | Markdown | Full task description |\n| `status` | enum | `backlog`, `todo`, `in_progress`, `review`, `done`, `cancelled` | Use `move_task` to change |\n| `priority` | enum | `critical`, `high`, `medium`, `low` | Affects sort order |\n| `tags` | string[] | Free-form | For filtering |\n| `dueDate` | number | Unix timestamp in milliseconds | Optional deadline |\n| `estimate` | number | Hours | Optional effort estimate |\n| `assignee` | string \\| null | Team member ID | Optional assignee from `users:` config |\n| `completedAt` | number | Unix timestamp (auto-managed) | Set on done/cancelled, cleared on reopen |\n| `createdAt` | number | Unix timestamp (auto) | Set at creation |\n| `updatedAt` | number | Unix timestamp (auto) | Updated on every change |\n\n## Task ID generation\n\nLike notes, task IDs are slugified from the title:\n- "Fix auth redirect loop" → `fix-auth-redirect-loop`\n- Duplicates get suffixes: `fix-auth-redirect-loop::2`\n\n## Tool reference\n\n### create_task\n\nCreate a new task. Automatically embedded for semantic search.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `title` | string | Yes | — | Short title, e.g. `"Fix auth redirect loop"` |\n| `description` | string | Yes | — | Full description (markdown) |\n| `priority` | enum | Yes | — | `"critical"`, `"high"`, `"medium"`, `"low"` |\n| `status` | enum | No | `"backlog"` | `"backlog"`, `"todo"`, `"in_progress"`, `"review"`, `"done"`, `"cancelled"` |\n| `tags` | string[] | No | `[]` | Tags for filtering |\n| `dueDate` | number | No | — | Due date as Unix timestamp in milliseconds |\n| `estimate` | number | No | — | Estimated effort in hours |\n| `assignee` | string | No | — | Team member ID to assign the task to |\n\n**Returns:** `{ taskId }`\n\n### update_task\n\nUpdate an existing task. Only provided fields change. Re-embeds if title or description changes. Status changes auto-manage `completedAt`.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to update |\n| `title` | string | No | New title |\n| `description` | string | No | New description |\n| `status` | enum | No | New status |\n| `priority` | enum | No | New priority |\n| `tags` | string[] | No | Replace tags array (include all you want to keep) |\n| `dueDate` | number \\| null | No | New due date (ms timestamp), or `null` to clear |\n| `estimate` | number \\| null | No | New estimate (hours), or `null` to clear |\n| `assignee` | string \\| null | No | Team member ID to assign, or `null` to unassign |\n\n**Returns:** `{ taskId, updated: true }`\n\n> Use `move_task` for a simpler status-only change — it\'s more explicit about `completedAt` management.\n\n### delete_task\n\nDelete a task and all its edges (relations + cross-graph links). Orphaned proxy nodes cleaned up automatically. **Irreversible.**\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to delete |\n\n**Returns:** `{ taskId, deleted: true }`\n\n### get_task\n\nReturn full task details including all relations. This is the most complete view of a task.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to retrieve |\n\n**Returns:**\n```\n{\n  id, title, description, status, priority, tags, assignee,\n  dueDate, estimate, completedAt, createdAt, updatedAt,\n  subtasks: [{ id, title, status }],\n  blockedBy: [{ id, title, status }],\n  blocks: [{ id, title, status }],\n  related: [{ id, title, status }]\n}\n```\n\nThe `subtasks`, `blockedBy`, `blocks`, and `related` arrays are automatically populated from task-to-task edges.\n\n### list_tasks\n\nList tasks with optional filters. Sorted by priority (critical → low) then due date (earliest first, nulls last).\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `status` | enum | No | — | Filter by status |\n| `priority` | enum | No | — | Filter by priority |\n| `tag` | string | No | — | Filter by tag (exact match, case-insensitive) |\n| `filter` | string | No | — | Substring match on title or ID |\n| `assignee` | string | No | — | Filter by assignee (team member ID) |\n| `limit` | number | No | 50 | Maximum results |\n\n**Returns:** `[{ id, title, description, status, priority, tags, dueDate, estimate, assignee, completedAt, createdAt, updatedAt }]`\n\n### search_tasks\n\nSemantic search over the task graph with BFS expansion.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Natural language search query |\n| `topK` | number | No | 5 | Seed nodes from vector search |\n| `bfsDepth` | number | No | 1 | Hops to follow relations (0 = no expansion) |\n| `maxResults` | number | No | 20 | Maximum results |\n| `minScore` | number | No | 0.5 | Minimum relevance score (0–1) |\n| `bfsDecay` | number | No | 0.8 | Score multiplier per hop |\n\n**Returns:** `[{ id, title, description, status, priority, tags, score }]`\n\n### move_task\n\nChange task status. The preferred way to move tasks through the kanban workflow.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to move |\n| `status` | enum | Yes | New status: `"backlog"`, `"todo"`, `"in_progress"`, `"review"`, `"done"`, `"cancelled"` |\n\n**Returns:** `{ taskId, status, completedAt }`\n\n**Automatic behavior:**\n- Moving to `done` or `cancelled` → sets `completedAt` to current time\n- Moving from `done`/`cancelled` to any other status → clears `completedAt`\n\n### link_task\n\nCreate a directed relation between two tasks.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fromId` | string | Yes | Source task ID |\n| `toId` | string | Yes | Target task ID |\n| `kind` | enum | Yes | `"subtask_of"`, `"blocks"`, `"related_to"` |\n\n**Returns:** `{ fromId, toId, kind, created: true }`\n\n**Semantics:**\n- `subtask_of` — `fromId` is a subtask of `toId` (child → parent)\n- `blocks` — `fromId` blocks `toId` (blocker → blocked task)\n- `related_to` — free association between tasks\n\n### create_task_link\n\nLink a task to a node in another graph (docs, code, files, or knowledge).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Source task ID |\n| `targetId` | string | Yes | Target node ID in the external graph |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"skills"` |\n| `kind` | string | Yes | Relation type: `"references"`, `"fixes"`, `"implements"`, `"documents"`, etc. |\n\n**Returns:** `{ taskId, targetId, targetGraph, kind, created: true }`\n\n**Examples:**\n```\ncreate_task_link({ taskId: "fix-auth", targetId: "src/auth.ts::login", targetGraph: "code", kind: "fixes" })\ncreate_task_link({ taskId: "update-docs", targetId: "guide.md::Authentication", targetGraph: "docs", kind: "updates" })\ncreate_task_link({ taskId: "review-config", targetId: "src/config.ts", targetGraph: "files", kind: "references" })\ncreate_task_link({ taskId: "implement-arch", targetId: "auth-architecture", targetGraph: "knowledge", kind: "implements" })\n```\n\n### delete_task_link\n\nRemove a cross-graph link from a task. Orphaned proxy nodes cleaned up automatically.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Source task ID |\n| `targetId` | string | Yes | Target node ID in the external graph |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"skills"` |\n\n**Returns:** `{ taskId, targetId, targetGraph, deleted: true }`\n\n### find_linked_tasks\n\nReverse lookup: given a node in an external graph, find all tasks that link to it.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `targetId` | string | Yes | Target node ID, e.g. `"src/auth.ts"`, `"guide.md::Setup"`, `"my-note"` |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"skills"` |\n| `kind` | string | No | Filter by relation kind. Omit for all relations |\n\n**Returns:** `[{ taskId, title, kind, status, priority, tags }]`\n\n**Use case:** When working on a file, call `find_linked_tasks({ targetId: "src/auth.ts", targetGraph: "code" })` to see all tasks related to that file.\n\n### add_task_attachment\n\nAttach a file to a task. The file is copied into the task\'s directory (`.tasks/{taskId}/`).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID to attach the file to |\n| `filePath` | string | Yes | Absolute path to the file on disk |\n\n**Returns:** `{ taskId, attachment: { filename, mimeType, size } }`\n\n### remove_task_attachment\n\nRemove an attachment from a task. Deletes the file from disk.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `taskId` | string | Yes | Task ID |\n| `filename` | string | Yes | Filename of the attachment to remove |\n\n**Returns:** `{ taskId, filename, deleted: true }`\n\n## Kanban board UI\n\nThe Tasks page provides a visual kanban board with these features:\n\n- **Column visibility** — toggle which status columns are shown via the column icon in the top bar; saved in localStorage\n- **Drag-and-drop** — drag task cards between columns to change status; drop-zone highlights on hover\n- **Inline task creation** — click "+" in a column header to quickly create a task in that status\n- **Filter bar** — search tasks by text, filter by priority or tag\n- **Due date indicators** — overdue tasks show a red badge, approaching deadlines (≤3 days) show yellow\n- **Estimate badges** — tasks with estimates show hours on the card\n- **Quick actions** — hover a card to see edit and delete buttons\n- **Scrollable columns** — columns scroll independently when content overflows\n\n## Tips\n\n- Use `move_task` instead of `update_task` for status changes — it explicitly handles `completedAt`\n- `get_task` returns the richest data — includes subtasks, blockers, and related tasks\n- `list_tasks` is sorted by priority then due date — critical overdue tasks appear first\n- Link tasks to code files they affect — makes it easy to find related tasks when working on code\n- Use `search_tasks` to find tasks by meaning, not just title keywords\n- `update_task` with `dueDate: null` or `estimate: null` clears those fields\n- `update_task` with `tags` replaces the entire array — include all tags you want to keep\n- Task-to-task `kind` values are a fixed enum (`subtask_of`, `blocks`, `related_to`), unlike knowledge relations which are free-form\n- Tasks support file attachments — attach screenshots, logs, or any file via `add_task_attachment`\n- Attachments are stored in `.tasks/{taskId}/` alongside the task\'s markdown file\n'},{id:`skill-tools`,title:`Skill Tools`,summary:`Create and manage reusable skills, recipes, and procedures with triggers and usage tracking.`,category:`guide`,relatedTools:[`create_skill`,`update_skill`,`delete_skill`,`get_skill`,`list_skills`,`search_skills`,`link_skill`,`create_skill_link`,`delete_skill_link`,`find_linked_skills`,`add_skill_attachment`,`remove_skill_attachment`,`recall_skills`,`bump_skill_usage`],content:'# Skill Tools\n\nThe skill tools provide a **recipe/procedure management** system within Graph Memory. Skills capture reusable knowledge — step-by-step procedures, patterns, and best practices — with triggers, usage tracking, and cross-graph links.\n\n## Why skills in Graph Memory?\n\nSkills here are tightly integrated with your project\'s knowledge graph:\n- Link a skill to the code files it applies to\n- Link a skill to documentation that describes the pattern\n- Link a skill to knowledge notes for context\n- Link a skill to tasks that use the procedure\n- Track dependencies and variants between skills\n\n## Tool overview\n\n| Tool | Purpose | Type |\n|------|---------|------|\n| `create_skill` | Create a skill with steps, triggers, and metadata | Mutation |\n| `update_skill` | Modify skill fields (partial update) | Mutation |\n| `delete_skill` | Remove a skill and all its edges | Mutation |\n| `get_skill` | Read a skill with all relations | Read |\n| `list_skills` | List skills with filters | Read |\n| `search_skills` | Semantic search across skills | Read |\n| `link_skill` | Create skill-to-skill relation | Mutation |\n| `create_skill_link` | Link skill to external graph node | Mutation |\n| `delete_skill_link` | Remove cross-graph link | Mutation |\n| `find_linked_skills` | Reverse lookup: find skills linked to an external node | Read |\n| `add_skill_attachment` | Attach a file to a skill | Mutation |\n| `remove_skill_attachment` | Remove an attachment from a skill | Mutation |\n| `recall_skills` | Recall relevant skills for a task context | Read |\n| `bump_skill_usage` | Increment usage counter + set lastUsedAt | Mutation |\n\n> **Mutation tools** are serialized through a queue to prevent concurrent graph modifications.\n\n## Skill properties\n\n| Property | Type | Values / Format | Notes |\n|----------|------|-----------------|-------|\n| `title` | string | Free text | Becomes slug ID |\n| `description` | string | Markdown | Full skill description |\n| `steps` | string[] | Ordered list | Step-by-step procedure |\n| `triggers` | string[] | Free-form | When to apply this skill |\n| `source` | enum | `user`, `learned` | How the skill was created |\n| `tags` | string[] | Free-form | For filtering |\n| `usageCount` | number | Auto-managed | Incremented by `bump_skill_usage` |\n| `lastUsedAt` | number | Unix timestamp (auto) | Set by `bump_skill_usage` |\n| `createdAt` | number | Unix timestamp (auto) | Set at creation |\n| `updatedAt` | number | Unix timestamp (auto) | Updated on every change |\n\n## Skill ID generation\n\nLike notes and tasks, skill IDs are slugified from the title:\n- "Add REST Endpoint" -> `add-rest-endpoint`\n- Duplicates get suffixes: `add-rest-endpoint::2`\n\n## Tool reference\n\n### create_skill\n\nCreate a new skill. Automatically embedded for semantic search.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `title` | string | Yes | -- | Short title, e.g. `"Add REST Endpoint"` |\n| `description` | string | Yes | -- | Full description (markdown) |\n| `steps` | string[] | No | `[]` | Ordered steps of the procedure |\n| `triggers` | string[] | No | `[]` | When this skill should be applied |\n| `source` | enum | No | `"user"` | `"user"`, `"learned"` |\n| `tags` | string[] | No | `[]` | Tags for filtering |\n\n**Returns:** `{ skillId }`\n\n### update_skill\n\nUpdate an existing skill. Only provided fields change. Re-embeds if title, description, or triggers change.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to update |\n| `title` | string | No | New title |\n| `description` | string | No | New description |\n| `steps` | string[] | No | Replace steps array |\n| `triggers` | string[] | No | Replace triggers array |\n| `source` | enum | No | New source |\n| `tags` | string[] | No | Replace tags array (include all you want to keep) |\n\n**Returns:** `{ skillId, updated: true }`\n\n### delete_skill\n\nDelete a skill and all its edges (relations + cross-graph links). Orphaned proxy nodes cleaned up automatically. **Irreversible.**\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to delete |\n\n**Returns:** `{ skillId, deleted: true }`\n\n### get_skill\n\nReturn full skill details including all relations. This is the most complete view of a skill.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to retrieve |\n\n**Returns:**\n```\n{\n  id, title, description, steps, triggers, source, tags,\n  usageCount, lastUsedAt, createdAt, updatedAt,\n  dependsOn: [{ id, title }],\n  dependedBy: [{ id, title }],\n  related: [{ id, title }],\n  variants: [{ id, title }]\n}\n```\n\nThe `dependsOn`, `dependedBy`, `related`, and `variants` arrays are automatically populated from skill-to-skill edges.\n\n### list_skills\n\nList skills with optional filters. Sorted by usage count (most used first).\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `source` | enum | No | -- | Filter by source (`user`, `learned`) |\n| `tag` | string | No | -- | Filter by tag (exact match, case-insensitive) |\n| `filter` | string | No | -- | Substring match on title or ID |\n| `limit` | number | No | 50 | Maximum results |\n\n**Returns:** `[{ id, title, description, steps, triggers, source, tags, usageCount, lastUsedAt, createdAt, updatedAt }]`\n\n### search_skills\n\nSemantic search over the skill graph with BFS expansion.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | -- | Natural language search query |\n| `topK` | number | No | 5 | Seed nodes from vector search |\n| `bfsDepth` | number | No | 1 | Hops to follow relations (0 = no expansion) |\n| `maxResults` | number | No | 20 | Maximum results |\n| `minScore` | number | No | 0.5 | Minimum relevance score (0-1) |\n| `bfsDecay` | number | No | 0.8 | Score multiplier per hop |\n\n**Returns:** `[{ id, title, description, steps, triggers, source, tags, score }]`\n\n### recall_skills\n\nRecall relevant skills for a task context. Uses a lower default `minScore` (0.3) for higher recall.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | -- | Task context or description |\n| `topK` | number | No | 10 | Maximum results |\n| `minScore` | number | No | 0.3 | Minimum relevance score (0-1) |\n\n**Returns:** `[{ id, title, description, steps, triggers, source, tags, score, usageCount }]`\n\n### bump_skill_usage\n\nRecord that a skill was used. Increments `usageCount` and sets `lastUsedAt` to the current time.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to bump |\n\n**Returns:** `{ skillId, usageCount, lastUsedAt }`\n\n### link_skill\n\nCreate a directed relation between two skills.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `fromId` | string | Yes | Source skill ID |\n| `toId` | string | Yes | Target skill ID |\n| `kind` | enum | Yes | `"depends_on"`, `"related_to"`, `"variant_of"` |\n\n**Returns:** `{ fromId, toId, kind, created: true }`\n\n**Semantics:**\n- `depends_on` -- `fromId` depends on `toId` (prerequisite)\n- `related_to` -- free association between skills\n- `variant_of` -- `fromId` is a variation of `toId`\n\n### create_skill_link\n\nLink a skill to a node in another graph (docs, code, files, knowledge, or tasks).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Source skill ID |\n| `targetId` | string | Yes | Target node ID in the external graph |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"tasks"` |\n| `kind` | string | Yes | Relation type: `"applies_to"`, `"documented_in"`, `"used_by"`, etc. |\n\n**Returns:** `{ skillId, targetId, targetGraph, kind, created: true }`\n\n**Examples:**\n```\ncreate_skill_link({ skillId: "add-rest-endpoint", targetId: "src/routes/index.ts", targetGraph: "code", kind: "applies_to" })\ncreate_skill_link({ skillId: "add-rest-endpoint", targetId: "guide.md::REST API", targetGraph: "docs", kind: "documented_in" })\ncreate_skill_link({ skillId: "add-rest-endpoint", targetId: "implement-api", targetGraph: "tasks", kind: "used_by" })\n```\n\n### delete_skill_link\n\nRemove a cross-graph link from a skill. Orphaned proxy nodes cleaned up automatically.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Source skill ID |\n| `targetId` | string | Yes | Target node ID in the external graph |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"tasks"` |\n\n**Returns:** `{ skillId, targetId, targetGraph, deleted: true }`\n\n### find_linked_skills\n\nReverse lookup: given a node in an external graph, find all skills that link to it.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `targetId` | string | Yes | Target node ID, e.g. `"src/auth.ts"`, `"guide.md::Setup"`, `"my-task"` |\n| `targetGraph` | enum | Yes | `"docs"`, `"code"`, `"files"`, `"knowledge"`, `"tasks"` |\n| `kind` | string | No | Filter by relation kind. Omit for all relations |\n\n**Returns:** `[{ skillId, title, kind, source, tags }]`\n\n**Use case:** When working on a file, call `find_linked_skills({ targetId: "src/routes/index.ts", targetGraph: "code" })` to see all skills related to that file.\n\n### add_skill_attachment\n\nAttach a file to a skill. The file is copied into the skill\'s directory (`.skills/{skillId}/`).\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID to attach the file to |\n| `filePath` | string | Yes | Absolute path to the file on disk |\n\n**Returns:** `{ skillId, attachment: { filename, mimeType, size } }`\n\n### remove_skill_attachment\n\nRemove an attachment from a skill. Deletes the file from disk.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `skillId` | string | Yes | Skill ID |\n| `filename` | string | Yes | Filename of the attachment to remove |\n\n**Returns:** `{ skillId, filename, deleted: true }`\n\n## Tips\n\n- Use `recall_skills` when starting a task to find relevant procedures -- it uses a lower threshold for better recall\n- Call `bump_skill_usage` after applying a skill to track which skills are most useful\n- Skills with `source: "learned"` are typically created by AI agents that discover patterns\n- Skills with `source: "user"` are created by humans documenting their procedures\n- Link skills to code files they apply to -- makes it easy to find relevant skills when working on code\n- Use `search_skills` to find skills by meaning, not just title keywords\n- `update_skill` with `tags` replaces the entire array -- include all tags you want to keep\n- Skill-to-skill `kind` values are a fixed enum (`depends_on`, `related_to`, `variant_of`)\n- Skills support file attachments -- attach templates, examples, or reference files via `add_skill_attachment`\n- Attachments are stored in `.skills/{skillId}/` alongside the skill\'s markdown file\n'},{id:`files-tools`,title:`File Index Tools`,summary:`Browse and search metadata for every file and directory in your project.`,category:`guide`,relatedTools:[`list_all_files`,`search_all_files`,`get_file_info`],content:'# File Index Tools\n\nThe file index tools provide access to metadata about **every file and directory** in your project. Unlike docs and code tools which only index pattern-matched files, the file index covers the entire project tree.\n\n## Tool overview\n\n| Tool | Purpose | When to use |\n|------|---------|-------------|\n| `list_all_files` | List files/directories with filters | Browse project structure, filter by extension/language |\n| `search_all_files` | Semantic search by file path | Find files by what they might contain |\n| `get_file_info` | Get metadata for a specific path | Check size, language, modification date |\n\n## What gets indexed\n\nFor every file in the project directory:\n- **Path** (relative to project root)\n- **File name** and **extension**\n- **Size** in bytes\n- **Language** (detected from extension: `.ts` → TypeScript, `.md` → Markdown, `.json` → JSON, etc.)\n- **MIME type** (e.g., `application/json`, `text/markdown`, `image/png`)\n- **Modification time** (`mtime`)\n\nFor directories:\n- **Aggregate size** (sum of all contained files)\n- **File count** (total files in subtree)\n- Directory → child edges (`contains`)\n\n## Browsing vs searching\n\n### Directory browsing\n\n`list_all_files` with the `directory` parameter returns **immediate children** (files + subdirectories) of that directory. This is how you browse the project tree:\n\n```\nlist_all_files({ directory: "." })           → root contents\nlist_all_files({ directory: "src" })         → src/ contents\nlist_all_files({ directory: "src/api" })     → src/api/ contents\n```\n\nWithout `directory`, it returns all files matching filters (flat list, no directories).\n\n### File search\n\n`search_all_files` embeds file paths for semantic search. You can search by:\n- Partial paths: `"config"` finds configuration files\n- Concepts: `"authentication"` finds files in auth-related directories\n- File types: `"typescript source"` finds `.ts` files\n\nThe `minScore` default is **0.3** (lower than node search) because file path embeddings are less semantically rich than content embeddings.\n\n## Tool reference\n\n### list_all_files\n\nList project files and directories with optional filters.\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `directory` | string | No | — | List immediate children of this directory (e.g. `"."`, `"src/lib"`). Without this, returns all files matching filters |\n| `extension` | string | No | — | Filter by extension (e.g. `".ts"`, `".md"`, `".png"`) |\n| `language` | string | No | — | Filter by detected language (e.g. `"typescript"`, `"markdown"`, `"json"`) |\n| `filter` | string | No | — | Substring match on file path (case-insensitive) |\n| `limit` | number | No | 50 | Maximum results |\n\n**Returns:** `[{ filePath, kind, fileName, extension, language, mimeType, size, fileCount }]`\n\n- `kind` is `"file"` or `"directory"`\n- `fileCount` is present for directories (number of files in subtree)\n- `language` and `mimeType` are present for files\n\n**Behavior differences:**\n- With `directory` set: returns both files and subdirectories (immediate children only)\n- Without `directory`: returns only files (no directories), across the entire project\n\n### search_all_files\n\nSemantic search over file nodes by path embedding. Searches files only (not directories).\n\n| Parameter | Type | Required | Default | Description |\n|-----------|------|----------|---------|-------------|\n| `query` | string | Yes | — | Search query (natural language or path fragment) |\n| `topK` | number | No | 10 | Maximum results |\n| `minScore` | number | No | 0.3 | Minimum cosine similarity score (0–1) |\n\n**Returns:** `[{ filePath, fileName, extension, language, size, score }]`\n\n### get_file_info\n\nGet full metadata for a specific file or directory. Use `"."` for the project root.\n\n| Parameter | Type | Required | Description |\n|-----------|------|----------|-------------|\n| `filePath` | string | Yes | Relative file or directory path (e.g. `"src/lib/config.ts"`, `"src/lib"`, `"."`) |\n\n**Returns for files:**\n```\n{ filePath, kind: "file", fileName, directory, extension, language, mimeType, size, mtime }\n```\n\n**Returns for directories:**\n```\n{ filePath, kind: "directory", fileName, directory, fileCount, size }\n```\n\n- `size` for directories is the total size of all direct children\n- `fileCount` for directories is the total number of files in the subtree\n- `mtime` is the last modification timestamp (files only)\n\n## Cross-graph links\n\nFiles can be linked from notes and tasks:\n\n```\n// From a knowledge note\ncreate_relation({ fromId: "config-format", toId: "src/config.ts", kind: "documents", targetGraph: "files" })\n\n// From a task\ncreate_task_link({ taskId: "refactor-config", targetId: "src/config.ts", targetGraph: "files", kind: "affects" })\n```\n\nUse `find_linked_notes` or `find_linked_tasks` with `targetGraph: "files"` to discover what knowledge or tasks reference a specific file:\n\n```\nfind_linked_notes({ targetId: "src/auth.ts", targetGraph: "files" })\nfind_linked_tasks({ targetId: "src/auth.ts", targetGraph: "files" })\n```\n\n## Tips\n\n- Use `list_all_files` with `directory` to browse top-down through the project tree\n- Use `list_all_files` with `extension: ".ts"` or `language: "typescript"` to find all files of a type\n- `get_file_info` on `"."` gives project-level stats (total size, file count)\n- `search_all_files` works better with path-like queries than abstract concepts\n- File index is always active — no `graphs.docs.include` or `graphs.code.include` configuration needed\n- The `language` filter in `list_all_files` uses detected language names like `"typescript"`, `"javascript"`, `"markdown"`, `"json"`, `"yaml"`, `"css"`, `"html"`, `"python"`, etc.\n'},{id:`cross-references`,title:`Cross References Tool`,summary:`Bridge code definitions and documentation examples for any symbol.`,category:`guide`,relatedTools:[`cross_references`],content:`# Cross References Tool
 
 \`cross_references\` is the only tool that works across **both** the CodeGraph and DocGraph simultaneously. It's the most comprehensive way to understand a symbol — combining source code definitions, documentation context, and usage examples.
 
@@ -1587,7 +1530,7 @@ Use \`cross_references\` when you want to fully understand a symbol:
 
 ## Requirements
 
-This tool is **only available** when both \`docsPattern\` and \`codePattern\` are configured in the project. It needs both graphs to bridge definitions and documentation.
+This tool is **only available** when both \`graphs.docs.include\` and \`graphs.code.include\` are configured in the project. It needs both graphs to bridge definitions and documentation.
 
 ## Tool reference
 
@@ -1696,7 +1639,7 @@ Calling \`cross_references({ symbol: "createUser" })\` returns:
 ## Tips
 
 - Use exact symbol names (case-sensitive match)
-- If you get no results, check that both \`docsPattern\` and \`codePattern\` are configured
+- If you get no results, check that both \`graphs.docs.include\` and \`graphs.code.include\` are configured
 - Empty \`definitions\` + non-empty \`examples\` means the symbol is documented but not in your indexed code
 - Empty \`examples\` + non-empty \`definitions\` means the symbol exists in code but isn't documented with examples
 - Combine with \`get_symbol\` to read the full implementation body (which \`cross_references\` doesn't include)

package/dist/ui/index.html

@@ -5,7 +5,7 @@
     <link rel="icon" type="image/svg+xml" href="/favicon.svg" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>ui</title>
-    <script type="module" crossorigin src="/assets/index-D6oxrVF7.js"></script>
+    <script type="module" crossorigin src="/assets/index-0hRezICt.js"></script>
     <link rel="stylesheet" crossorigin href="/assets/index-kKd4mVrh.css">
   </head>
   <body>

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@graphmemory/server",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "description": "MCP server for semantic graph memory from markdown files",
   "main": "dist/cli/index.js",
   "bin": {