diff --git a/examples/tool-reference/README.md b/examples/tool-reference/README.md
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+# Basic Memory MCP Tool Reference Project
+
+A downloadable Basic Memory project containing comprehensive documentation for all MCP tools.
+
+## What This Is
+
+This is a complete Basic Memory project that you can import into your own Basic Memory installation.
+It provides detailed reference documentation for all 16 core MCP tools, organized as a knowledge graph
+that you can navigate and search using Basic Memory's tools.
+
+## How to Use
+
+### Option 1: Import into Existing Project
+
+1. Copy the contents of this directory into your Basic Memory project
+2. Run `basic-memory sync` to index the new content
+3. Use `search_notes` or `build_context` to explore the documentation
+
+### Option 2: Create New Project
+
+1. Create a new Basic Memory project:
+   ```bash
+   basic-memory tools create-memory-project \
+     --project-name "tool-reference" \
+     --project-path "~/basic-memory-tool-reference"
+   ```
+
+2. Copy these files into the new project directory
+
+3. Sync the project:
+   ```bash
+   basic-memory sync
+   ```
+
+### Option 3: Browse in Your Editor
+
+The files are standard markdown with Basic Memory frontmatter.
+You can browse them in any markdown editor or Obsidian.
+
+## Project Structure
+
+```
+tool-reference/
+├── README.md (this file)
+├── index.md (main reference guide)
+├── tools/
+│   ├── write_note.md
+│   ├── read_note.md
+│   ├── search_notes.md
+│   └── ... (all 16 tools)
+└── categories/
+    ├── content-management.md
+    ├── knowledge-graph-navigation.md
+    ├── search-and-discovery.md
+    ├── project-management.md
+    └── visualization.md
+```
+
+## Using the Documentation
+
+### Search for Tools
+
+```python
+# Find all content management tools
+search_notes("content management", search_type="text")
+
+# Find write_note examples
+search_notes("write_note")
+```
+
+### Navigate by Category
+
+```python
+# Read a category overview
+read_note("content-management")
+
+# Build context around search tools
+build_context("memory://categories/search-and-discovery")
+```
+
+### View Tool Details
+
+```python
+# Read specific tool documentation
+read_note("tools/write_note")
+read_note("tools/search_notes")
+
+# View as artifact for better formatting
+view_note("tools/build_context")
+```
+
+## What's Included
+
+- **16 tool reference documents** with detailed examples
+- **5 category guides** organizing tools by function
+- **Knowledge graph relations** connecting related tools
+- **Copy-paste examples** ready for LLM instructions
+- **Search syntax guide** for advanced queries
+- **Real-world workflows** showing tool combinations
+
+## Tool Categories
+
+### Content Management
+
+- `write_note`: Create or update markdown notes with semantic observations and relations
+- `read_note`: Read markdown notes by title, permalink, or memory:// URL
+- `read_content`: Read raw file content (text, images, binaries) without knowledge graph processing
+- `view_note`: View notes as formatted artifacts for better readability
+- `edit_note`: Edit notes incrementally with append, prepend, find/replace, replace_section
+- `move_note`: Move notes to new locations, updating database and maintaining links
+- `delete_note`: Delete notes from the knowledge base
+
+### Knowledge Graph Navigation
+
+- `build_context`: Navigate knowledge graph via memory:// URLs for conversation continuity
+- `recent_activity`: Get recently updated information with specified timeframe
+- `list_directory`: Browse directory contents with filtering and depth control
+
+### Search & Discovery
+
+- `search_notes`: Full-text search with advanced filtering and boolean operators
+
+### Project Management
+
+- `list_memory_projects`: List all available projects with their status
+- `create_memory_project`: Create new Basic Memory projects
+- `delete_project`: Delete a project from configuration
+- `get_current_project`: Get current project information and stats
+- `sync_status`: Check file synchronization and background operation status
+
+### Visualization
+
+- `canvas`: Generate Obsidian canvas files for knowledge graph visualization
+
+## Generated Documentation
+
+This project was automatically generated from the Basic Memory MCP tool source code.
+You can regenerate it by running:
+
+```bash
+python scripts/generate_tool_reference_project.py
+```
+
+## License
+
+Same as Basic Memory - AGPL v3
diff --git a/examples/tool-reference/categories/content-management.md b/examples/tool-reference/categories/content-management.md
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+---
+title: Content Management
+type: guide
+permalink: categories/content-management
+tags:
+- mcp-tools
+- reference
+- category
+- content-management
+created: 2025-10-28T00:00:00
+modified: 2025-10-28T00:00:00
+---
+
+# Content Management
+
+Tools for creating, reading, editing, and managing markdown notes in Basic Memory.
+
+## Overview
+
+The Content Management category contains 7 core MCP tools that handle all aspects of note lifecycle:
+creating, reading, viewing, editing, moving, and deleting notes. These tools work with Basic Memory's
+knowledge graph format, supporting observations, relations, and semantic content.
+
+## Observations
+
+- [category] Contains 7 MCP tools #mcp #tools
+- [purpose] Content Management functionality for Basic Memory #functionality
+- [feature] All tools support project resolution (Single Project → parameter → default) #project-resolution
+- [feature] All tools validate paths to prevent security issues #security
+- [design] Tools use consistent markdown format with frontmatter, observations, and relations #format
+
+## Tools in This Category
+
+### write_note
+
+Create or update markdown notes with semantic observations and relations.
+
+**Key Features:**
+- Supports YAML frontmatter
+- Observations with `[category]` syntax
+- Relations using `[[Entity]]` wikilinks
+- Tags for categorization
+- Custom entity types
+- Security: validates folder paths
+
+**Use When:**
+- Creating new notes
+- Updating existing notes
+- Building knowledge graph entries
+
+### read_note
+
+Read markdown notes by title, permalink, or memory:// URL.
+
+**Key Features:**
+- Multiple lookup strategies (permalink → title → text search)
+- Returns full markdown content
+- Pagination support
+- Helpful error messages when not found
+
+**Use When:**
+- Reading specific notes
+- Retrieving content for processing
+- Loading context for conversations
+
+### read_content
+
+Read raw file content without knowledge graph processing.
+
+**Key Features:**
+- Reads any file type (text, images, binaries)
+- Returns raw content or base64 encoding
+- No parsing or processing
+- Direct file access
+
+**Use When:**
+- Reading non-markdown files
+- Accessing images or binaries
+- Need raw content without processing
+
+### view_note
+
+View notes as formatted artifacts for better readability.
+
+**Key Features:**
+- Formats notes as artifacts
+- Better visual presentation
+- Same lookup as read_note
+- Pagination support
+
+**Use When:**
+- Presenting notes to users
+- Better readability needed
+- Viewing long-form content
+
+### edit_note
+
+Edit notes incrementally with various operations.
+
+**Key Features:**
+- Append content to end
+- Prepend content to beginning
+- Find and replace text
+- Replace specific sections
+- Maintains existing structure
+
+**Use When:**
+- Adding to existing notes
+- Updating specific sections
+- Find/replace operations
+- Incremental edits
+
+### move_note
+
+Move notes to new locations while maintaining links.
+
+**Key Features:**
+- Updates file system
+- Updates database
+- Maintains relations
+- Updates permalinks
+
+**Use When:**
+- Reorganizing content
+- Moving between folders
+- Renaming notes
+
+### delete_note
+
+Delete notes from the knowledge base.
+
+**Key Features:**
+- Removes from file system
+- Removes from database
+- Cleans up relations
+- Confirmation required
+
+**Use When:**
+- Removing outdated content
+- Cleaning up test notes
+- Content no longer needed
+
+## Common Workflows
+
+### Create and Edit Workflow
+
+```python
+# 1. Create initial note
+write_note(
+    project="my-project",
+    title="New Feature",
+    folder="features",
+    content="# New Feature\\n\\nInitial draft..."
+)
+
+# 2. Add more content
+edit_note(
+    "my-project",
+    "features/new-feature",
+    operation="append",
+    content="\\n## Implementation\\n\\nDetails..."
+)
+
+# 3. Read to verify
+read_note("my-project", "features/new-feature")
+```
+
+### Read and Move Workflow
+
+```python
+# 1. Read current note
+content = read_note("my-project", "drafts/note")
+
+# 2. Move to published
+move_note(
+    "my-project",
+    "drafts/note",
+    "published/note"
+)
+
+# 3. Verify new location
+read_note("my-project", "published/note")
+```
+
+### Content Organization Workflow
+
+```python
+# 1. Create in temporary location
+write_note(
+    project="research",
+    title="Quick Note",
+    folder="temp",
+    content="Quick thoughts..."
+)
+
+# 2. Refine content
+edit_note(
+    "research",
+    "temp/quick-note",
+    operation="replace_section",
+    content="Quick thoughts...|# Refined Thoughts\\n\\nPolished version..."
+)
+
+# 3. Move to permanent location
+move_note(
+    "research",
+    "temp/quick-note",
+    "concepts/refined-thoughts"
+)
+```
+
+## Relations
+
+- contains [[Write Note]]
+- contains [[Read Note]]
+- contains [[Read Content]]
+- contains [[View Note]]
+- contains [[Edit Note]]
+- contains [[Move Note]]
+- contains [[Delete Note]]
+- part_of [[MCP Tool Reference]]
diff --git a/examples/tool-reference/categories/search-and-discovery.md b/examples/tool-reference/categories/search-and-discovery.md
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+---
+title: Search & Discovery
+type: guide
+permalink: categories/search-and-discovery
+tags:
+- mcp-tools
+- reference
+- category
+- search
+created: 2025-10-28T00:00:00
+modified: 2025-10-28T00:00:00
+---
+
+# Search & Discovery
+
+Full-text search capabilities with advanced syntax support for discovering content in your knowledge base.
+
+## Overview
+
+The Search & Discovery category focuses on finding content across your entire knowledge base.
+The primary tool, `search_notes`, provides powerful full-text search with boolean operators,
+phrase matching, filtering, and pattern matching.
+
+## Observations
+
+- [category] Contains 1 core MCP tool (search_notes) #mcp #tools
+- [purpose] Search & Discovery functionality for Basic Memory #functionality
+- [feature] Full-text search with FTS5 engine #search-engine
+- [feature] Boolean operators (AND, OR, NOT) #advanced-search
+- [feature] Phrase matching with quotes #search-syntax
+- [feature] Content filtering (types, entity_types, after_date) #filtering
+- [feature] Pattern matching on permalinks #pattern-matching
+- [feature] Helpful error messages with suggestions #ux
+
+## Tools in This Category
+
+### search_notes
+
+Full-text search across all content with advanced filtering and boolean operators.
+
+**Search Types:**
+- **Text search** (default): Full-text search across all content
+- **Title search**: Search only in note titles
+- **Permalink search**: Pattern matching on file paths
+
+**Boolean Operators:**
+- `AND`: Both terms must be present
+- `OR`: Either term can be present
+- `NOT`: Exclude specific terms
+- Grouping with `()`
+
+**Filtering Options:**
+- `types`: Filter by note types (e.g., ["note", "person"])
+- `entity_types`: Filter by entity types (e.g., ["observation"])
+- `after_date`: Show only recent content
+
+**Content-Specific Searches:**
+- `tag:example`: Search within tags
+- `category:observation`: Filter by category
+- `author:username`: Search by author (if metadata available)
+
+## Search Syntax Guide
+
+### Basic Text Search
+
+```python
+# Simple keyword
+search_notes("machine learning")
+
+# Multiple keywords (implicit AND)
+search_notes("python programming tutorial")
+```
+
+### Boolean Operators
+
+```python
+# Explicit AND
+search_notes("machine AND learning")
+
+# OR operator
+search_notes("python OR javascript")
+
+# NOT operator
+search_notes("programming NOT beginner")
+
+# Complex boolean
+search_notes("(python OR javascript) AND tutorial NOT beginner")
+```
+
+### Phrase Search
+
+```python
+# Exact phrase
+search_notes('"machine learning basics"')
+
+# Phrase with boolean
+search_notes('"neural networks" AND python')
+```
+
+### Search Types
+
+```python
+# Full-text (default)
+search_notes("keyword", search_type="text")
+
+# Title only
+search_notes("Tutorial", search_type="title")
+
+# Permalink patterns
+search_notes("docs/2024-*", search_type="permalink")
+search_notes("meetings/weekly-*", search_type="permalink")
+```
+
+### Filtering
+
+```python
+# By content type
+search_notes("meeting", types=["entity"])
+
+# By entity type
+search_notes("decision", entity_types=["observation"])
+
+# By date
+search_notes("update", after_date="1 week")
+search_notes("report", after_date="2024-01-01")
+
+# Multiple filters
+search_notes(
+    "bug OR issue",
+    types=["entity"],
+    entity_types=["observation"],
+    after_date="1 week"
+)
+```
+
+### Content-Specific
+
+```python
+# Tag search
+search_notes("tag:api")
+search_notes("tag:urgent OR tag:important")
+
+# Category search
+search_notes("category:decision")
+search_notes("category:observation AND tech")
+```
+
+## Common Search Patterns
+
+### Find Recent Work
+
+```python
+# All recent updates
+search_notes("", after_date="1 week")
+
+# Recent on specific topic
+search_notes("machine learning", after_date="3d")
+```
+
+### Topic Exploration
+
+```python
+# Broad topic
+search_notes("artificial intelligence")
+
+# Narrow focus
+search_notes("artificial intelligence AND ethics")
+
+# Exclude basics
+search_notes("AI NOT basics NOT introduction")
+```
+
+### Project Management
+
+```python
+# Open bugs
+search_notes("bug NOT fixed NOT resolved")
+
+# Recent decisions
+search_notes("category:decision", after_date="1 week")
+
+# Meeting notes
+search_notes("meeting OR standup", search_type="title")
+```
+
+### Research Workflows
+
+```python
+# Literature review
+search_notes('"literature review" OR paper OR study')
+
+# Research by topic
+search_notes("(neural networks OR deep learning) AND research")
+
+# Recent research
+search_notes("research", after_date="1 month")
+```
+
+## Error Handling
+
+`search_notes` provides helpful error messages for:
+
+### Syntax Errors
+
+If query has invalid syntax, get suggestions like:
+- Simplify the query
+- Remove special characters
+- Use basic boolean operators
+- Example corrections
+
+### No Results
+
+If no results found, get guidance on:
+- Broadening the search
+- Trying variations
+- Different search types
+- Using filters
+- Exploring what exists
+
+### Other Errors
+
+- Project not found
+- Server errors
+- Permission errors
+
+Each error includes specific next steps.
+
+## Comparison with Related Tools
+
+### search_notes vs read_note
+
+- **search_notes**: Find notes you don't know exist
+- **read_note**: Retrieve specific known notes
+
+### search_notes vs recent_activity
+
+- **search_notes**: Find by content/keywords
+- **recent_activity**: Find by modification time
+
+### search_notes vs build_context
+
+- **search_notes**: Keyword-based discovery
+- **build_context**: Graph-based navigation
+
+## Relations
+
+- contains [[Search Notes]]
+- part_of [[MCP Tool Reference]]
+- complements [[Knowledge Graph Navigation]]
+- uses [[FTS5 Search Engine]]
diff --git a/examples/tool-reference/index.md b/examples/tool-reference/index.md
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+---
+title: MCP Tool Reference
+type: guide
+permalink: index
+tags:
+- mcp-tools
+- reference
+- index
+created: 2025-10-28T00:00:00
+modified: 2025-10-28T00:00:00
+---
+
+# MCP Tool Reference
+
+Comprehensive reference for all Basic Memory MCP tools with examples and usage patterns.
+
+## Overview
+
+This project contains detailed documentation for all 16 core MCP tools in Basic Memory.
+Each tool is documented as a separate entity with examples, parameters, and relationships.
+
+## Observations
+
+- [structure] Contains 16 tool reference documents #documentation
+- [structure] Organized into 5 categories #organization
+- [purpose] Provides copy-paste examples for LLM instructions #usage
+- [format] Follows Basic Memory knowledge graph format #compliance
+
+## Tool Categories
+
+### Content Management
+See [[Content Management]] for all tools in this category.
+
+### Knowledge Graph Navigation
+See [[Knowledge Graph Navigation]] for all tools in this category.
+
+### Search & Discovery
+See [[Search & Discovery]] for all tools in this category.
+
+### Project Management
+See [[Project Management]] for all tools in this category.
+
+### Visualization
+See [[Visualization]] for all tools in this category.
+
+## Relations
+
+- contains [[Content Management]]
+- contains [[Knowledge Graph Navigation]]
+- contains [[Search & Discovery]]
+- contains [[Project Management]]
+- contains [[Visualization]]
+- documented_in [[Basic Memory Documentation]]
diff --git a/examples/tool-reference/tools/build_context.md b/examples/tool-reference/tools/build_context.md
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+---
+title: Build Context
+type: guide
+permalink: tools/build_context
+tags:
+- mcp-tools
+- reference
+- build_context
+- context
+- knowledge-graph
+created: 2025-10-28T00:00:00
+modified: 2025-10-28T00:00:00
+---
+
+# Build Context
+
+Navigate the knowledge graph via memory:// URLs to build context for conversation continuity.
+
+## Function Signature
+
+```python
+build_context(url, depth=1, timeframe=None, project=None)
+```
+
+## Parameters
+
+- **url** (str): memory:// URL to start context building from
+- **depth** (int): How many relation levels to follow (default 1)
+- **timeframe** (str, optional): Filter by recency (e.g., "1w", "2d", "2024-01-01")
+- **project** (str, optional): Project name to use
+
+## Returns
+
+Contextual information from knowledge graph traversal including:
+- Starting entity content
+- Related entities (based on depth)
+- Temporal filtering if timeframe specified
+
+## Observations
+
+- [tool] MCP tool for navigating knowledge graph via memory:// URLs #mcp #navigation
+- [returns] Contextual information from knowledge graph traversal #output
+- [category] Knowledge Graph Navigation tool #classification
+- [feature] Follows relations to specified depth #graph-traversal
+- [feature] Filters by timeframe for recent context #temporal-filter
+- [purpose] Enables conversation continuity across sessions #continuity
+
+## Usage Examples
+
+### Basic Context Building
+
+```python
+# Build context from a starting point
+build_context("memory://projects/current-project")
+
+# Build context from a specific note
+build_context("memory://meetings/weekly-standup")
+```
+
+### With Depth Control
+
+```python
+# Follow relations to depth of 2
+build_context("memory://concepts/machine-learning", depth=2)
+
+# Shallow context (depth=1, default)
+build_context("memory://notes/today")
+
+# Deep context traversal
+build_context("memory://projects/main", depth=3)
+```
+
+### With Timeframe Filter
+
+```python
+# Recent context from last week
+build_context("memory://meetings/weekly", timeframe="1w")
+
+# Context from last 2 days
+build_context("memory://projects/current", timeframe="2d")
+
+# Context since specific date
+build_context("memory://research/ml", timeframe="2024-01-01")
+```
+
+### For Conversation Continuity
+
+```python
+# Load previous conversation context
+build_context("memory://conversations/project-discussion", depth=3)
+
+# Continue research topic
+build_context("memory://research/literature-review", depth=2, timeframe="1w")
+```
+
+### Combining Parameters
+
+```python
+# Deep, recent context
+build_context(
+    "memory://projects/active",
+    depth=3,
+    timeframe="1w"
+)
+
+# Focused context for specific topic
+build_context(
+    "memory://concepts/neural-networks",
+    depth=2,
+    timeframe="2024-01-01"
+)
+```
+
+## How It Works
+
+1. **Starts at URL**: Loads the entity at the memory:// URL
+2. **Follows Relations**: Traverses relations up to specified depth
+3. **Filters by Time**: If timeframe specified, includes only recent updates
+4. **Returns Context**: Aggregates all discovered content
+
+### Depth Example
+
+With depth=1:
+```
+Start → Related1
+     → Related2
+     → Related3
+```
+
+With depth=2:
+```
+Start → Related1 → SubRelated1
+                 → SubRelated2
+     → Related2 → SubRelated3
+     → Related3 → SubRelated4
+```
+
+## Use Cases
+
+### Continue Previous Conversations
+
+```python
+# Pick up where you left off
+build_context("memory://conversations/last-discussion", depth=2)
+```
+
+### Research Topic with Context
+
+```python
+# Load all related research
+build_context("memory://research/machine-learning", depth=3)
+```
+
+### Project Status Update
+
+```python
+# Get current project state
+build_context("memory://projects/current", depth=2, timeframe="1w")
+```
+
+### Explore Related Concepts
+
+```python
+# Discover connections
+build_context("memory://concepts/neural-networks", depth=2)
+```
+
+## memory:// URL Format
+
+Memory URLs follow this pattern:
+```
+memory://[folder/]permalink
+```
+
+Examples:
+- `memory://index`
+- `memory://meetings/weekly-standup`
+- `memory://projects/2024/q1-planning`
+- `memory://concepts/machine-learning`
+
+## Project Resolution
+
+Server resolves projects in this order:
+1. Single Project Mode
+2. project parameter
+3. default project
+
+If project unknown, use `list_memory_projects()` or `recent_activity()` first.
+
+## Relations
+
+- part_of [[Knowledge Graph Navigation]]
+- documented_in [[MCP Tool Reference]]
+- complements [[Recent Activity]]
+- complements [[Search Notes]]
+- uses [[Relation Resolver]]
diff --git a/examples/tool-reference/tools/read_note.md b/examples/tool-reference/tools/read_note.md
new file mode 100644
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--- /dev/null
+++ b/examples/tool-reference/tools/read_note.md
@@ -0,0 +1,136 @@
+---
+title: Read Note
+type: guide
+permalink: tools/read_note
+tags:
+- mcp-tools
+- reference
+- read_note
+created: 2025-10-28T00:00:00
+modified: 2025-10-28T00:00:00
+---
+
+# Read Note
+
+Read markdown notes by title, permalink, or memory:// URL with automatic fallback search.
+
+## Function Signature
+
+```python
+read_note(identifier, project=None, page=1, page_size=10)
+```
+
+## Parameters
+
+- **identifier** (str): Title, permalink, or memory:// URL of the note to read
+- **project** (str, optional): Project name to read from
+- **page** (int): Page number for paginated results (default 1)
+- **page_size** (int): Number of items per page (default 10)
+
+## Returns
+
+Full markdown content of the note if found, or helpful guidance if not found.
+Content includes frontmatter, observations, relations, and all markdown formatting.
+
+## Observations
+
+- [tool] MCP tool for reading markdown notes by title, permalink, or memory:// URL #mcp #read
+- [returns] Full markdown content with frontmatter and formatting #output
+- [category] Content Management tool #classification
+- [feature] Multiple lookup strategies (permalink → title → text search) #smart-lookup
+- [feature] Provides helpful suggestions when note not found #ux
+- [feature] Validates identifiers to prevent path traversal #security
+
+## Lookup Strategies
+
+The tool tries multiple strategies to find the note:
+
+1. **Direct permalink lookup** (fastest)
+2. **Title search fallback** (if permalink fails)
+3. **Text search** as last resort
+
+This makes it flexible - you can use any identifier type.
+
+## Usage Examples
+
+### Read by Permalink
+
+```python
+# Direct permalink lookup (fastest)
+read_note("my-research", "specs/search-spec")
+read_note("work-project", "meetings/weekly-standup")
+```
+
+### Read by Title
+
+```python
+# Title search with automatic fallback
+read_note("work-project", "Search Specification")
+read_note("team-docs", "Weekly Standup")
+```
+
+### Read with Memory URL
+
+```python
+# Using memory:// protocol
+read_note("my-research", "memory://specs/search-spec")
+read_note("work-project", "memory://meetings/weekly")
+```
+
+### With Pagination
+
+```python
+# Large notes with pagination
+read_note("work-project", "Project Updates", page=2, page_size=5)
+```
+
+## Not Found Handling
+
+If the note isn't found, the tool provides helpful suggestions:
+
+- Checks if identifier is title vs permalink
+- Suggests using search instead
+- Recommends checking recent activity
+- Provides template for creating new note
+
+Example error response:
+
+```markdown
+# Note Not Found in my-research: "search-spec"
+
+I couldn't find any notes matching "search-spec". Here are some suggestions:
+
+## Check Identifier Type
+- If you provided a title, try using the exact permalink instead
+- If you provided a permalink, check for typos or try a broader search
+
+## Search Instead
+Try searching for related content:
+search_notes(project="my-research", query="search-spec")
+
+## Create New Note
+This might be a good opportunity to create a new note on this topic...
+```
+
+## Security
+
+- Validates identifiers to prevent path traversal attacks
+- Paths must stay within project boundaries
+- Both raw and processed paths are validated
+
+## Project Resolution
+
+Server resolves projects in this order:
+1. Single Project Mode
+2. project parameter
+3. default project
+
+If project unknown, use `list_memory_projects()` or `recent_activity()` first.
+
+## Relations
+
+- part_of [[Content Management]]
+- documented_in [[MCP Tool Reference]]
+- complements [[Write Note]]
+- alternative [[View Note]]
+- uses [[Search Notes]] (for fallback lookup)
diff --git a/examples/tool-reference/tools/search_notes.md b/examples/tool-reference/tools/search_notes.md
new file mode 100644
index 00000000..9a4ec219
--- /dev/null
+++ b/examples/tool-reference/tools/search_notes.md
@@ -0,0 +1,225 @@
+---
+title: Search Notes
+type: guide
+permalink: tools/search_notes
+tags:
+- mcp-tools
+- reference
+- search_notes
+- search
+created: 2025-10-28T00:00:00
+modified: 2025-10-28T00:00:00
+---
+
+# Search Notes
+
+Full-text search across all content with advanced syntax support including boolean operators, phrase matching, and filtering.
+
+## Function Signature
+
+```python
+search_notes(query, project=None, page=1, page_size=10, search_type="text",
+             types=None, entity_types=None, after_date=None)
+```
+
+## Parameters
+
+- **query** (str): Search query string (supports boolean operators, phrases, patterns)
+- **project** (str, optional): Project name to search in
+- **page** (int): Page number of results (default 1)
+- **page_size** (int): Number of results per page (default 10)
+- **search_type** (str): Type of search - "text", "title", or "permalink" (default "text")
+- **types** (list, optional): Filter by note types (e.g., ["note", "person"])
+- **entity_types** (list, optional): Filter by entity types (e.g., ["entity", "observation"])
+- **after_date** (str, optional): Filter recent content (e.g., "1 week", "2d", "2024-01-01")
+
+## Returns
+
+SearchResponse with results and pagination info, or helpful error guidance if search fails.
+
+## Observations
+
+- [tool] MCP tool for full-text search with advanced filtering and boolean operators #mcp #search
+- [returns] SearchResponse with paginated results #output
+- [category] Search & Discovery tool #classification
+- [feature] Supports boolean AND, OR, NOT operators #search-syntax
+- [feature] Supports exact phrase matching with quotes #search-syntax
+- [feature] Supports content-specific searches (tag:, category:, etc.) #advanced-search
+- [feature] Supports pattern matching on permalinks #permalink-search
+- [feature] Provides helpful error messages with suggestions #ux
+
+## Search Syntax Guide
+
+### Basic Searches
+
+```python
+# Simple keyword search
+search_notes("project planning")
+
+# Multiple terms (implicit AND)
+search_notes("machine learning python")
+```
+
+### Boolean Operators
+
+```python
+# AND search (both terms required)
+search_notes("project AND planning")
+
+# OR search (either term)
+search_notes("project OR meeting")
+
+# NOT search (exclude term)
+search_notes("project NOT archived")
+
+# Complex boolean with grouping
+search_notes("(project OR planning) AND notes")
+```
+
+### Phrase Search
+
+```python
+# Exact phrase match
+search_notes('"weekly standup meeting"')
+
+# Combine phrase and keyword
+search_notes('"exact phrase" AND keyword')
+```
+
+### Search Types
+
+```python
+# Full-text search (default)
+search_notes("keyword", search_type="text")
+
+# Title-only search
+search_notes("Machine Learning", search_type="title")
+
+# Permalink pattern matching
+search_notes("docs/meeting-*", search_type="permalink")
+search_notes("archive/2024-*", search_type="permalink")
+```
+
+### Filtering Options
+
+```python
+# Filter by content type
+search_notes("meeting notes", types=["entity"])
+
+# Filter by entity type
+search_notes("meeting notes", entity_types=["observation"])
+
+# Recent content only
+search_notes("bug report", after_date="1 week")
+search_notes("updates", after_date="2024-01-01")
+
+# Multiple filters combined
+search_notes(
+    "(bug OR issue) AND NOT resolved",
+    types=["entity"],
+    after_date="2024-01-01"
+)
+```
+
+### Content-Specific Searches
+
+```python
+# Search within tags
+search_notes("tag:example")
+
+# Filter by category
+search_notes("category:observation")
+
+# Search by author (if metadata available)
+search_notes("author:username")
+```
+
+### Advanced Patterns
+
+```python
+# Complex boolean logic
+search_notes("project AND (meeting OR discussion)")
+
+# Exclude specific terms
+search_notes("bug NOT fixed")
+
+# Year-based permalink search
+search_notes("docs/2024-*", search_type="permalink")
+
+# Combine multiple search techniques
+search_notes(
+    '("weekly meeting" OR standup) AND notes NOT archived',
+    types=["entity"],
+    after_date="1 week"
+)
+```
+
+## Common Use Cases
+
+### Find Recent Updates
+
+```python
+# Updates from last week
+search_notes("", after_date="1 week")
+
+# Specific topic, recent only
+search_notes("machine learning", after_date="3d")
+```
+
+### Search by Topic
+
+```python
+# Find all machine learning content
+search_notes("machine learning")
+
+# Find ML content excluding basics
+search_notes("machine learning NOT basics")
+```
+
+### Search Within Categories
+
+```python
+# Find all decisions
+search_notes("category:decision")
+
+# Find technical decisions
+search_notes("category:decision AND tech")
+```
+
+### Explore Tags
+
+```python
+# All content with specific tag
+search_notes("tag:api")
+
+# Multiple tag search
+search_notes("tag:api OR tag:design")
+```
+
+## Error Handling
+
+The tool provides helpful error messages and suggestions for:
+- Invalid syntax errors
+- No results found
+- Project not found
+- Server errors
+- Permission/access errors
+
+Each error includes specific suggestions for how to fix the issue.
+
+## Project Resolution
+
+Server resolves projects in this order:
+1. Single Project Mode
+2. project parameter
+3. default project
+
+If project unknown, use `list_memory_projects()` or `recent_activity()` first.
+
+## Relations
+
+- part_of [[Search & Discovery]]
+- documented_in [[MCP Tool Reference]]
+- complements [[Recent Activity]]
+- complements [[Build Context]]
+- uses [[FTS5 Search Engine]]
diff --git a/examples/tool-reference/tools/write_note.md b/examples/tool-reference/tools/write_note.md
new file mode 100644
index 00000000..696e9a6d
--- /dev/null
+++ b/examples/tool-reference/tools/write_note.md
@@ -0,0 +1,151 @@
+---
+title: Write Note
+type: guide
+permalink: tools/write_note
+tags:
+- mcp-tools
+- reference
+- write_note
+created: 2025-10-28T00:00:00
+modified: 2025-10-28T00:00:00
+---
+
+# Write Note
+
+Create or update markdown notes with semantic observations and relations.
+
+## Function Signature
+
+```python
+write_note(title, content, folder, project=None, tags=None, entity_type="note")
+```
+
+## Parameters
+
+- **title** (str): The title of the note
+- **content** (str): Markdown content for the note, can include observations and relations
+- **folder** (str): Folder path relative to project root (use "/" or "" for root)
+- **project** (str, optional): Project name to write to
+- **tags** (str|list, optional): Tags to categorize the note
+- **entity_type** (str): Type of entity ("note", "guide", "report", etc.)
+
+## Returns
+
+A markdown formatted summary of the semantic content, including:
+- Creation/update status with project name
+- File path and checksum
+- Observation counts by category
+- Relation counts (resolved/unresolved)
+- Tags if present
+
+## Observations
+
+- [tool] MCP tool for creating or updating markdown notes with semantic observations and relations #mcp #basic-memory
+- [returns] Markdown formatted summary of semantic content #output
+- [category] Content Management tool #classification
+- [feature] Supports YAML frontmatter, observations with [category] syntax, and relations #knowledge-graph
+- [feature] Validates folder paths to prevent path traversal attacks #security
+
+## Usage Examples
+
+### Basic Usage
+
+```python
+# Create a simple note
+write_note(
+    project="my-research",
+    title="Meeting Notes",
+    folder="meetings",
+    content="# Weekly Standup\\n\\n- [decision] Use SQLite for storage #tech"
+)
+```
+
+### With Semantic Content
+
+```python
+write_note(
+    project="work-project",
+    title="API Design",
+    folder="specs",
+    content="""
+# REST API Specification
+
+## Overview
+Core API endpoints for user management.
+
+## Observations
+- [design] RESTful architecture #api #architecture
+- [tech] FastAPI framework #implementation #python
+- [decision] JWT for authentication #security
+
+## Relations
+- implements [[Authentication System]]
+- uses [[PostgreSQL Database]]
+- specified_by [[OpenAPI Spec]]
+    """,
+    tags=["api", "design"],
+    entity_type="guide"
+)
+```
+
+### Creating Knowledge Graph Entries
+
+```python
+# Entity with relations to other concepts
+write_note(
+    project="knowledge-base",
+    title="Machine Learning Basics",
+    folder="concepts",
+    content="""
+# Machine Learning Basics
+
+Core concepts in machine learning and AI.
+
+## Observations
+- [definition] ML is subset of AI focused on learning from data #ai #ml
+- [technique] Supervised learning requires labeled data #training
+- [application] Image recognition, NLP, recommendation systems #use-cases
+
+## Relations
+- part_of [[Artificial Intelligence]]
+- requires [[Training Data]]
+- enables [[Predictive Analytics]]
+- contrasts_with [[Rule-Based Systems]]
+    """
+)
+```
+
+### Updating Existing Notes
+
+```python
+# Update existing note (same title/folder)
+write_note(
+    project="my-research",
+    title="Meeting Notes",
+    folder="meetings",
+    content="# Weekly Standup\\n\\n- [decision] Use PostgreSQL instead #tech"
+)
+```
+
+## Project Resolution
+
+Server resolves projects in this order:
+1. Single Project Mode (if only one project exists)
+2. project parameter (if provided)
+3. default project (from configuration)
+
+If project is unknown, use `list_memory_projects()` or `recent_activity()` first.
+
+## Security
+
+- Validates folder paths to prevent path traversal attacks
+- Folder paths must stay within project boundaries
+- Paths like "../../../etc/passwd" are blocked
+
+## Relations
+
+- part_of [[Content Management]]
+- documented_in [[MCP Tool Reference]]
+- complements [[Read Note]]
+- complements [[Edit Note]]
+- uses [[Entity Parser]]
diff --git a/scripts/generate_tool_reference_project.py b/scripts/generate_tool_reference_project.py
new file mode 100644
index 00000000..7cdb9d0d
--- /dev/null
+++ b/scripts/generate_tool_reference_project.py
@@ -0,0 +1,691 @@
+#!/usr/bin/env python3
+"""
+Generate a Basic Memory project with comprehensive MCP tool reference documentation.
+
+This script creates a structured knowledge base that users can download and import
+into their Basic Memory projects, providing complete tool usage examples in a
+navigable knowledge graph format.
+"""
+
+import os
+from pathlib import Path
+from datetime import datetime
+
+# Tool categories and their tools
+TOOLS = {
+    "Content Management": {
+        "write_note": {
+            "description": "Create or update markdown notes with semantic observations and relations",
+            "params": "title, content, folder, project, tags, entity_type",
+            "returns": "Markdown formatted summary of semantic content",
+        },
+        "read_note": {
+            "description": "Read markdown notes by title, permalink, or memory:// URL",
+            "params": "identifier, project, page, page_size",
+            "returns": "Full markdown content with frontmatter and formatting",
+        },
+        "read_content": {
+            "description": "Read raw file content (text, images, binaries) without knowledge graph processing",
+            "params": "path, project",
+            "returns": "Raw file content or base64 encoded binary data",
+        },
+        "view_note": {
+            "description": "View notes as formatted artifacts for better readability",
+            "params": "identifier, project, page, page_size",
+            "returns": "Formatted artifact presentation of note content",
+        },
+        "edit_note": {
+            "description": "Edit notes incrementally with append, prepend, find/replace, replace_section",
+            "params": "identifier, operation, content, project",
+            "returns": "Confirmation with updated entity information",
+        },
+        "move_note": {
+            "description": "Move notes to new locations, updating database and maintaining links",
+            "params": "identifier, destination_path, project",
+            "returns": "Confirmation with old and new paths",
+        },
+        "delete_note": {
+            "description": "Delete notes from the knowledge base",
+            "params": "identifier, project",
+            "returns": "Confirmation of deletion",
+        },
+    },
+    "Knowledge Graph Navigation": {
+        "build_context": {
+            "description": "Navigate knowledge graph via memory:// URLs for conversation continuity",
+            "params": "url, depth, timeframe, project",
+            "returns": "Contextual information from knowledge graph traversal",
+        },
+        "recent_activity": {
+            "description": "Get recently updated information with specified timeframe",
+            "params": "type, depth, timeframe, project",
+            "returns": "List of recently modified entities",
+        },
+        "list_directory": {
+            "description": "Browse directory contents with filtering and depth control",
+            "params": "dir_name, depth, file_name_glob, project",
+            "returns": "Hierarchical directory structure",
+        },
+    },
+    "Search & Discovery": {
+        "search_notes": {
+            "description": "Full-text search with advanced filtering and boolean operators",
+            "params": "query, project, page, page_size, search_type, types, entity_types, after_date",
+            "returns": "SearchResponse with paginated results",
+        },
+    },
+    "Project Management": {
+        "list_memory_projects": {
+            "description": "List all available projects with their status",
+            "params": "None",
+            "returns": "List of projects with metadata",
+        },
+        "create_memory_project": {
+            "description": "Create new Basic Memory projects",
+            "params": "project_name, project_path, set_default",
+            "returns": "Confirmation with project details",
+        },
+        "delete_project": {
+            "description": "Delete a project from configuration",
+            "params": "project_name",
+            "returns": "Confirmation of deletion",
+        },
+        "get_current_project": {
+            "description": "Get current project information and stats",
+            "params": "None",
+            "returns": "Current project metadata",
+        },
+        "sync_status": {
+            "description": "Check file synchronization and background operation status",
+            "params": "project",
+            "returns": "Sync status and operation details",
+        },
+    },
+    "Visualization": {
+        "canvas": {
+            "description": "Generate Obsidian canvas files for knowledge graph visualization",
+            "params": "nodes, edges, title, folder, project",
+            "returns": "Path to created canvas file",
+        },
+    },
+}
+
+# Detailed examples for key tools
+TOOL_EXAMPLES = {
+    "write_note": '''
+## Basic Usage
+
+```python
+# Create a simple note
+write_note(
+    project="my-research",
+    title="Meeting Notes",
+    folder="meetings",
+    content="# Weekly Standup\\n\\n- [decision] Use SQLite for storage #tech"
+)
+```
+
+## With Semantic Content
+
+```python
+write_note(
+    project="work-project",
+    title="API Design",
+    folder="specs",
+    content="""
+# REST API Specification
+
+## Overview
+Core API endpoints for user management.
+
+## Observations
+- [design] RESTful architecture #api #architecture
+- [tech] FastAPI framework #implementation #python
+- [decision] JWT for authentication #security
+
+## Relations
+- implements [[Authentication System]]
+- uses [[PostgreSQL Database]]
+- specified_by [[OpenAPI Spec]]
+    """,
+    tags=["api", "design"],
+    entity_type="guide"
+)
+```
+
+## Creating Knowledge Graph Entries
+
+```python
+# Entity with relations to other concepts
+write_note(
+    project="knowledge-base",
+    title="Machine Learning Basics",
+    folder="concepts",
+    content="""
+# Machine Learning Basics
+
+Core concepts in machine learning and AI.
+
+## Observations
+- [definition] ML is subset of AI focused on learning from data #ai #ml
+- [technique] Supervised learning requires labeled data #training
+- [application] Image recognition, NLP, recommendation systems #use-cases
+
+## Relations
+- part_of [[Artificial Intelligence]]
+- requires [[Training Data]]
+- enables [[Predictive Analytics]]
+- contrasts_with [[Rule-Based Systems]]
+    """
+)
+```
+''',
+    "read_note": '''
+## Read by Permalink
+
+```python
+# Direct permalink lookup (fastest)
+read_note("my-research", "specs/search-spec")
+```
+
+## Read by Title
+
+```python
+# Title search with fallback
+read_note("work-project", "Search Specification")
+```
+
+## Read with Memory URL
+
+```python
+# Using memory:// protocol
+read_note("my-research", "memory://specs/search-spec")
+```
+
+## With Pagination
+
+```python
+# Large notes with pagination
+read_note("work-project", "Project Updates", page=2, page_size=5)
+```
+''',
+    "search_notes": '''
+## Basic Search
+
+```python
+# Simple keyword search
+search_notes("project planning")
+```
+
+## Boolean Operators
+
+```python
+# AND search (both terms required)
+search_notes("project AND planning")
+
+# OR search (either term)
+search_notes("project OR meeting")
+
+# NOT search (exclude term)
+search_notes("project NOT archived")
+
+# Complex boolean with grouping
+search_notes("(project OR planning) AND notes")
+```
+
+## Phrase Search
+
+```python
+# Exact phrase match
+search_notes('"weekly standup meeting"')
+```
+
+## Search with Filters
+
+```python
+# Filter by content type
+search_notes(
+    "meeting notes",
+    types=["entity"]
+)
+
+# Filter by entity type
+search_notes(
+    "meeting notes",
+    entity_types=["observation"]
+)
+
+# Recent content only
+search_notes(
+    "bug report",
+    after_date="1 week"
+)
+```
+
+## Search Types
+
+```python
+# Title-only search
+search_notes("Machine Learning", search_type="title")
+
+# Permalink pattern matching
+search_notes("docs/meeting-*", search_type="permalink")
+
+# Full-text search (default)
+search_notes("keyword", search_type="text")
+```
+
+## Advanced Patterns
+
+```python
+# Content-specific search
+search_notes("tag:example")  # Search within tags
+search_notes("category:observation")  # Filter by category
+
+# Complex multi-filter search
+search_notes(
+    "(bug OR issue) AND NOT resolved",
+    types=["entity"],
+    after_date="2024-01-01"
+)
+```
+''',
+    "build_context": '''
+## Basic Context Building
+
+```python
+# Build context from a starting point
+build_context("memory://projects/current-project")
+```
+
+## With Depth Control
+
+```python
+# Follow relations to depth of 2
+build_context("memory://concepts/machine-learning", depth=2)
+```
+
+## With Timeframe Filter
+
+```python
+# Recent context from last week
+build_context("memory://meetings/weekly", timeframe="1w")
+```
+
+## For Conversation Continuity
+
+```python
+# Load previous conversation context
+build_context("memory://conversations/project-discussion", depth=3)
+```
+''',
+    "edit_note": '''
+## Append Content
+
+```python
+edit_note(
+    "my-research",
+    "meeting-notes",
+    operation="append",
+    content="\\n## New Section\\n\\nAdditional meeting notes..."
+)
+```
+
+## Prepend Content
+
+```python
+edit_note(
+    "work-project",
+    "todo-list",
+    operation="prepend",
+    content="## Urgent Tasks\\n\\n- Fix critical bug\\n\\n"
+)
+```
+
+## Find and Replace
+
+```python
+edit_note(
+    "my-research",
+    "api-spec",
+    operation="find_replace",
+    content="SQLite|PostgreSQL"  # Find|Replace pattern
+)
+```
+
+## Replace Section
+
+```python
+edit_note(
+    "work-project",
+    "design-doc",
+    operation="replace_section",
+    content="## Old Section|## New Section\\n\\nUpdated content..."
+)
+```
+''',
+}
+
+
+def create_frontmatter(title: str, entity_type: str, tags: list[str], permalink: str = None) -> str:
+    """Generate YAML frontmatter for a markdown file."""
+    created = datetime.now().isoformat()
+    fm = [
+        "---",
+        f"title: {title}",
+        f"type: {entity_type}",
+    ]
+    if permalink:
+        fm.append(f"permalink: {permalink}")
+    if tags:
+        fm.append("tags:")
+        for tag in tags:
+            fm.append(f"- {tag}")
+    fm.extend([
+        f"created: {created}",
+        f"modified: {created}",
+        "---",
+    ])
+    return "\n".join(fm)
+
+
+def generate_category_file(category: str, tools: dict, output_dir: Path) -> None:
+    """Generate a category index file."""
+    filename = category.lower().replace(" ", "-").replace("&", "and")
+    filepath = output_dir / "categories" / f"{filename}.md"
+
+    tags = ["mcp-tools", "reference", "category"]
+    frontmatter = create_frontmatter(category, "guide", tags)
+
+    content = [frontmatter, "", f"# {category}", ""]
+    content.append(f"Tools in the {category} category for Basic Memory MCP server.")
+    content.append("")
+
+    content.append("## Observations")
+    content.append(f"- [category] Contains {len(tools)} MCP tools #mcp #tools")
+    content.append(f"- [purpose] {category} functionality for Basic Memory #functionality")
+    content.append("")
+
+    content.append("## Tools in This Category")
+    content.append("")
+    for tool_name, tool_info in tools.items():
+        content.append(f"### {tool_name}")
+        content.append(f"{tool_info['description']}")
+        content.append("")
+
+    content.append("## Relations")
+    for tool_name in tools.keys():
+        tool_title = " ".join(word.capitalize() for word in tool_name.split("_"))
+        content.append(f"- contains [[{tool_title}]]")
+    content.append("- part_of [[MCP Tool Reference]]")
+
+    filepath.parent.mkdir(parents=True, exist_ok=True)
+    filepath.write_text("\n".join(content))
+    print(f"Created: {filepath}")
+
+
+def generate_tool_file(tool_name: str, tool_info: dict, category: str, output_dir: Path) -> None:
+    """Generate a detailed tool reference file."""
+    tool_title = " ".join(word.capitalize() for word in tool_name.split("_"))
+    filepath = output_dir / "tools" / f"{tool_name}.md"
+
+    tags = ["mcp-tools", "reference", tool_name]
+    frontmatter = create_frontmatter(tool_title, "guide", tags, f"tools/{tool_name}")
+
+    content = [frontmatter, "", f"# {tool_title}", ""]
+    content.append(tool_info["description"])
+    content.append("")
+
+    content.append("## Function Signature")
+    content.append("")
+    content.append("```python")
+    content.append(f"{tool_name}({tool_info['params']})")
+    content.append("```")
+    content.append("")
+
+    content.append("## Observations")
+    content.append(f"- [tool] MCP tool for {tool_info['description'].lower()} #mcp #basic-memory")
+    content.append(f"- [returns] {tool_info['returns']} #output")
+    content.append(f"- [category] {category} tool #classification")
+    content.append("")
+
+    # Add examples if available
+    if tool_name in TOOL_EXAMPLES:
+        content.append("## Usage Examples")
+        content.append(TOOL_EXAMPLES[tool_name])
+        content.append("")
+
+    content.append("## Relations")
+    category_link = category.replace(" ", "-").replace("&", "and")
+    category_title = category
+    content.append(f"- part_of [[{category_title}]]")
+    content.append("- documented_in [[MCP Tool Reference]]")
+
+    # Add cross-references to related tools
+    if category == "Content Management":
+        if tool_name == "write_note":
+            content.append("- complements [[Read Note]]")
+            content.append("- complements [[Edit Note]]")
+        elif tool_name == "read_note":
+            content.append("- complements [[Write Note]]")
+            content.append("- alternative [[View Note]]")
+        elif tool_name == "edit_note":
+            content.append("- requires [[Read Note]]")
+            content.append("- alternative [[Write Note]]")
+    elif category == "Search & Discovery":
+        content.append("- complements [[Recent Activity]]")
+        content.append("- complements [[Build Context]]")
+
+    filepath.parent.mkdir(parents=True, exist_ok=True)
+    filepath.write_text("\n".join(content))
+    print(f"Created: {filepath}")
+
+
+def generate_index_file(output_dir: Path) -> None:
+    """Generate the main index file."""
+    filepath = output_dir / "index.md"
+
+    tags = ["mcp-tools", "reference", "index"]
+    frontmatter = create_frontmatter("MCP Tool Reference", "guide", tags, "index")
+
+    content = [frontmatter, "", "# MCP Tool Reference", ""]
+    content.append("Comprehensive reference for all Basic Memory MCP tools with examples and usage patterns.")
+    content.append("")
+
+    content.append("## Overview")
+    content.append("")
+    content.append("This project contains detailed documentation for all 16 core MCP tools in Basic Memory.")
+    content.append("Each tool is documented as a separate entity with examples, parameters, and relationships.")
+    content.append("")
+
+    content.append("## Observations")
+    total_tools = sum(len(tools) for tools in TOOLS.values())
+    content.append(f"- [structure] Contains {total_tools} tool reference documents #documentation")
+    content.append(f"- [structure] Organized into {len(TOOLS)} categories #organization")
+    content.append("- [purpose] Provides copy-paste examples for LLM instructions #usage")
+    content.append("- [format] Follows Basic Memory knowledge graph format #compliance")
+    content.append("")
+
+    content.append("## Tool Categories")
+    content.append("")
+    for category in TOOLS.keys():
+        category_link = category.replace(" ", "-").replace("&", "and")
+        content.append(f"### {category}")
+        content.append(f"See [[{category}]] for all tools in this category.")
+        content.append("")
+
+    content.append("## Relations")
+    for category in TOOLS.keys():
+        content.append(f"- contains [[{category}]]")
+    content.append("- documented_in [[Basic Memory Documentation]]")
+
+    filepath.write_text("\n".join(content))
+    print(f"Created: {filepath}")
+
+
+def generate_readme(output_dir: Path) -> None:
+    """Generate README for the project."""
+    filepath = output_dir / "README.md"
+
+    content = [
+        "# Basic Memory MCP Tool Reference Project",
+        "",
+        "A downloadable Basic Memory project containing comprehensive documentation for all MCP tools.",
+        "",
+        "## What This Is",
+        "",
+        "This is a complete Basic Memory project that you can import into your own Basic Memory installation.",
+        "It provides detailed reference documentation for all 16 core MCP tools, organized as a knowledge graph",
+        "that you can navigate and search using Basic Memory's tools.",
+        "",
+        "## How to Use",
+        "",
+        "### Option 1: Import into Existing Project",
+        "",
+        "1. Copy the contents of this directory into your Basic Memory project",
+        "2. Run `basic-memory sync` to index the new content",
+        "3. Use `search_notes` or `build_context` to explore the documentation",
+        "",
+        "### Option 2: Create New Project",
+        "",
+        "1. Create a new Basic Memory project:",
+        "   ```bash",
+        "   basic-memory tools create-memory-project \\",
+        '     --project-name "tool-reference" \\',
+        '     --project-path "~/basic-memory-tool-reference"',
+        "   ```",
+        "",
+        "2. Copy these files into the new project directory",
+        "",
+        "3. Sync the project:",
+        "   ```bash",
+        "   basic-memory sync",
+        "   ```",
+        "",
+        "### Option 3: Browse in Your Editor",
+        "",
+        "The files are standard markdown with Basic Memory frontmatter.",
+        "You can browse them in any markdown editor or Obsidian.",
+        "",
+        "## Project Structure",
+        "",
+        "```",
+        "tool-reference/",
+        "├── README.md (this file)",
+        "├── index.md (main reference guide)",
+        "├── tools/",
+        "│   ├── write_note.md",
+        "│   ├── read_note.md",
+        "│   ├── search_notes.md",
+        "│   └── ... (all 16 tools)",
+        "└── categories/",
+        "    ├── content-management.md",
+        "    ├── knowledge-graph-navigation.md",
+        "    ├── search-and-discovery.md",
+        "    ├── project-management.md",
+        "    └── visualization.md",
+        "```",
+        "",
+        "## Using the Documentation",
+        "",
+        "### Search for Tools",
+        "",
+        "```python",
+        '# Find all content management tools',
+        'search_notes("content management", search_type="text")',
+        "",
+        "# Find write_note examples",
+        'search_notes("write_note")',
+        "```",
+        "",
+        "### Navigate by Category",
+        "",
+        "```python",
+        '# Read a category overview',
+        'read_note("content-management")',
+        "",
+        "# Build context around search tools",
+        'build_context("memory://categories/search-and-discovery")',
+        "```",
+        "",
+        "### View Tool Details",
+        "",
+        "```python",
+        '# Read specific tool documentation',
+        'read_note("tools/write_note")',
+        'read_note("tools/search_notes")',
+        "",
+        "# View as artifact for better formatting",
+        'view_note("tools/build_context")',
+        "```",
+        "",
+        "## What's Included",
+        "",
+        "- **16 tool reference documents** with detailed examples",
+        "- **5 category guides** organizing tools by function",
+        "- **Knowledge graph relations** connecting related tools",
+        "- **Copy-paste examples** ready for LLM instructions",
+        "- **Search syntax guide** for advanced queries",
+        "- **Real-world workflows** showing tool combinations",
+        "",
+        "## Tool Categories",
+        "",
+    ]
+
+    for category, tools in TOOLS.items():
+        content.append(f"### {category}")
+        content.append("")
+        for tool_name, tool_info in tools.items():
+            content.append(f"- `{tool_name}`: {tool_info['description']}")
+        content.append("")
+
+    content.extend([
+        "## Generated Documentation",
+        "",
+        "This project was automatically generated from the Basic Memory MCP tool source code.",
+        "You can regenerate it by running:",
+        "",
+        "```bash",
+        "python scripts/generate_tool_reference_project.py",
+        "```",
+        "",
+        "## License",
+        "",
+        "Same as Basic Memory - AGPL v3",
+        "",
+    ])
+
+    filepath.write_text("\n".join(content))
+    print(f"Created: {filepath}")
+
+
+def main():
+    """Generate the complete tool reference project."""
+    output_dir = Path("examples/tool-reference")
+
+    print(f"Generating Basic Memory Tool Reference Project in {output_dir}")
+    print()
+
+    # Generate category files
+    for category, tools in TOOLS.items():
+        generate_category_file(category, tools, output_dir)
+
+    # Generate tool files
+    for category, tools in TOOLS.items():
+        for tool_name, tool_info in tools.items():
+            generate_tool_file(tool_name, tool_info, category, output_dir)
+
+    # Generate index
+    generate_index_file(output_dir)
+
+    # Generate README
+    generate_readme(output_dir)
+
+    print()
+    print("✓ Tool reference project generated successfully!")
+    print(f"✓ Location: {output_dir}")
+    print(f"✓ Total files: {len(list(output_dir.rglob('*.md')))}")
+
+
+if __name__ == "__main__":
+    main()