feat: Add knowledge-organizer skill for maintaining knowledge graph

New skill to help users organize and maintain their knowledge base:

Capabilities:
- Find orphan notes (no relations to other notes)
- Suggest relations based on content similarity
- Identify duplicate or overlapping notes
- Review and suggest folder organization
- Normalize inconsistent tags
- Create index/hub notes for topic navigation
- Enrich sparse notes with observations and structure

Includes workflows for:
- Quick health check (overview of KB status)
- Deep organization session (thorough review)
- Topic-focused organization (organize around a subject)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
Signed-off-by: phernandez <paul@basicmachines.co>

Author: phernandez

PLUGIN.md

@@ -168,6 +168,28 @@ Edit notes directly as local markdown files with automatic sync.
 
 **Best for:** Local users who want full file access and git integration.
 
+### knowledge-organizer
+
+Help organize, link, and maintain the knowledge graph.
+
+**Triggers when:**
+- User wants to organize their notes
+- User asks about orphan or unlinked notes
+- User wants to find connections between notes
+- User mentions duplicates or similar notes
+- User asks for help with folder organization
+
+**Capabilities:**
+- **Find orphan notes** - Identify notes with no relations
+- **Suggest relations** - Propose meaningful links between notes
+- **Identify duplicates** - Find notes covering similar topics
+- **Folder organization** - Review and suggest folder structure
+- **Tag consistency** - Normalize and improve tagging
+- **Create index notes** - Generate hub notes linking related topics
+- **Enrich sparse notes** - Suggest observations and structure
+
+**Best for:** Periodic knowledge base maintenance and improving discoverability.
+
 ---
 
 ## Hooks
@@ -216,7 +238,8 @@ basic-memory/
 │   ├── continue-conversation/
 │   ├── spec-driven-development/
 │   ├── edit-note/
-│   └── edit-note-local/
+│   ├── edit-note-local/
+│   └── knowledge-organizer/
 ├── hooks/
 │   └── hooks.json           # Hook definitions
 └── PLUGIN.md                # This file

skills/knowledge-organizer/SKILL.md

@@ -0,0 +1,283 @@
+---
+name: knowledge-organizer
+description: Help organize, link, and maintain the Basic Memory knowledge graph - find orphan notes, suggest relations, identify duplicates, and improve overall knowledge structure
+---
+
+# Knowledge Organizer
+
+This skill helps users maintain a healthy, well-connected knowledge graph. As notes accumulate, it becomes valuable to periodically organize, link, and curate the knowledge base.
+
+## When to Use
+
+Use this skill when:
+- User asks to organize their notes
+- User wants to find connections between notes
+- User mentions orphan or unlinked notes
+- User wants to clean up or improve their knowledge base
+- User asks about duplicate or similar notes
+- User wants help with folder organization
+- User asks to review or audit their notes
+- Phrases like "help me organize", "find related notes", "what's not linked", "clean up my notes"
+
+## Organization Capabilities
+
+### 1. Find Orphan Notes
+
+Identify notes that have no relations to other notes - they're isolated in the knowledge graph.
+
+```python
+# Get all notes
+mcp__basic-memory__search_notes(
+    query="*",
+    page_size=50,
+    project="main"
+)
+
+# For each note, check if it has relations
+# Orphans have empty Relations sections
+```
+
+**What to do with orphans:**
+- Suggest potential relations based on content similarity
+- Ask if they should be linked to existing topics
+- Propose creating hub notes to connect related orphans
+
+### 2. Suggest Relations
+
+Analyze note content and suggest meaningful connections.
+
+```python
+# Read a note
+mcp__basic-memory__read_note(
+    identifier="note-to-analyze",
+    project="main"
+)
+
+# Search for potentially related notes
+mcp__basic-memory__search_notes(
+    query="key terms from the note",
+    project="main"
+)
+
+# Suggest relations based on:
+# - Shared topics or concepts
+# - Complementary content (problem/solution, question/answer)
+# - Sequential relationship (part 1, part 2)
+# - Hierarchical (parent concept, child detail)
+```
+
+**Relation types to suggest:**
+- `relates-to` - General topical connection
+- `extends` - Builds upon or expands
+- `implements` - Realizes a concept
+- `depends-on` - Requires understanding of
+- `contradicts` - Presents alternative view
+- `learned-from` - Source of insight
+- `enables` - Makes something possible
+
+### 3. Identify Similar/Duplicate Notes
+
+Find notes that may cover the same topic.
+
+```python
+# Search for notes with similar titles or content
+mcp__basic-memory__search_notes(
+    query="topic keywords",
+    project="main"
+)
+
+# Compare results for overlap
+# Look for:
+# - Similar titles
+# - Overlapping observations
+# - Same tags
+# - Related timestamps (created around same time)
+```
+
+**Actions for duplicates:**
+- Merge into a single comprehensive note
+- Link them with `supersedes` or `updates` relations
+- Differentiate by adding context about their distinct focus
+
+### 4. Folder Organization Review
+
+Analyze folder structure and suggest improvements.
+
+```python
+# List directory structure
+mcp__basic-memory__list_directory(
+    dir_name="/",
+    depth=3,
+    project="main"
+)
+
+# Identify:
+# - Overcrowded folders
+# - Single-note folders
+# - Inconsistent naming
+# - Notes that might belong elsewhere
+```
+
+**Organization suggestions:**
+- Group related notes into topic folders
+- Create subfolders for large categories
+- Suggest consistent naming conventions
+- Move misplaced notes
+
+### 5. Tag Consistency
+
+Review and normalize tags across notes.
+
+```python
+# Search notes to analyze tag patterns
+mcp__basic-memory__search_notes(
+    query="*",
+    page_size=100,
+    project="main"
+)
+
+# Look for:
+# - Similar tags (architecture vs arch)
+# - Unused tags
+# - Over-used generic tags
+# - Missing tags on relevant notes
+```
+
+**Tag improvements:**
+- Suggest tag standardization (pick one variant)
+- Propose new tags for common themes
+- Identify notes missing obvious tags
+
+### 6. Create Index/Hub Notes
+
+Generate notes that serve as navigation hubs for related topics.
+
+```python
+# After identifying a cluster of related notes
+mcp__basic-memory__write_note(
+    title="Architecture Decisions Index",
+    content="""---
+title: Architecture Decisions Index
+type: index
+tags:
+- architecture
+- index
+---
+
+# Architecture Decisions Index
+
+A hub linking all architecture-related decisions and patterns.
+
+## Decisions
+
+- [[Database Selection Decision]]
+- [[API Design Patterns]]
+- [[Authentication Architecture]]
+
+## Patterns
+
+- [[Repository Pattern]]
+- [[Async Client Pattern]]
+
+## Observations
+
+- [index] Central hub for architecture knowledge #navigation
+
+## Relations
+
+- indexes [[Architecture]]
+""",
+    folder="indexes",
+    project="main"
+)
+```
+
+### 7. Enrich Sparse Notes
+
+Find notes lacking observations or structure and suggest improvements.
+
+```python
+# Read a sparse note
+mcp__basic-memory__read_note(
+    identifier="sparse-note",
+    project="main"
+)
+
+# If missing:
+# - Observations section → suggest categories
+# - Relations section → suggest links
+# - Tags → suggest relevant tags
+# - Context → suggest adding background
+```
+
+## Organization Workflows
+
+### Quick Health Check
+
+A fast overview of knowledge base status:
+
+1. Count total notes
+2. Identify orphan count
+3. List recently modified
+4. Check for obvious duplicates
+5. Report folder distribution
+
+### Deep Organization Session
+
+Thorough review and improvement:
+
+1. **Audit phase** - Catalog all notes, identify issues
+2. **Orphan phase** - Address unlinked notes
+3. **Relation phase** - Suggest new connections
+4. **Duplicate phase** - Merge or differentiate similar notes
+5. **Structure phase** - Reorganize folders if needed
+6. **Index phase** - Create hub notes for major topics
+
+### Topic-Focused Organization
+
+Organize around a specific subject:
+
+1. Find all notes related to topic
+2. Map existing relations
+3. Identify gaps in the topic graph
+4. Suggest new notes to fill gaps
+5. Create topic index note
+
+## Best Practices
+
+1. **Work incrementally** - Don't reorganize everything at once
+2. **Confirm before changing** - Always ask before moving/editing notes
+3. **Preserve permalinks** - Moving is okay, changing permalinks breaks links
+4. **Show the graph** - Help user visualize connections
+5. **Explain suggestions** - Say why a relation makes sense
+6. **Respect user's system** - Enhance their organization, don't impose a new one
+
+## Example Conversations
+
+**User:** "Help me organize my notes"
+
+**Claude:**
+1. Runs health check on the knowledge base
+2. Reports: "You have 47 notes. I found 12 orphan notes and 3 potential duplicates."
+3. Asks: "Would you like to start by connecting the orphan notes, or review the duplicates first?"
+
+**User:** "Find notes that should be linked to my API design note"
+
+**Claude:**
+1. Reads the API design note
+2. Searches for related content
+3. Suggests: "I found 5 notes that could relate:
+   - 'REST Best Practices' → relates-to
+   - 'Authentication Flow' → implements
+   - 'Rate Limiting Decision' → extends
+   Would you like me to add any of these relations?"
+
+**User:** "Are there any notes about similar topics?"
+
+**Claude:**
+1. Analyzes note titles and content
+2. Identifies clusters of similar notes
+3. Reports: "I found these potential overlaps:
+   - 'Auth Flow' and 'Authentication Design' cover similar ground
+   - 'DB Schema v1' and 'DB Schema v2' might need a 'supersedes' relation
+   Would you like to review any of these?"