Get pending cluster analysis for structure note creation.

Clusters are groups of notes sharing tags but lacking a structure note. High-scoring clusters are good candidates for new structure notes.

Uses cached analysis by default. Set refresh=true to regenerate. Cluster analysis runs automatically via cron if configured.

Scoring factors:

• Note count (7-15 is ideal, >15 is overdue)

• Orphan ratio (more orphans = more urgent)

• Internal link density (fewer links = needs structure)

• Recency (recent activity = active domain)

Args: min_score: Minimum cluster score 0.0-1.0 (default: 0.5) limit: Maximum clusters to return (default: 5) include_notes: Include full note list per cluster (default: false) refresh: Force regeneration of cluster analysis (default: false)

Create a structure note from a detected cluster.

Generates a structure note organizing all notes in the cluster, with bidirectional links to each member note.

Run slipbox_get_cluster_report first to see available clusters and their IDs.

Args: cluster_id: ID from cluster report (e.g. "jackson-mac-low-chance-operations") title: Override the suggested title (optional) create_links: Create bidirectional links to member notes (default: true)

Regenerate cluster analysis and save report.

Analyzes all notes for emergent clusters based on:

• Tag co-occurrence (tags that frequently appear together)

• Connection patterns (notes that link to each other)

• Structure note coverage (which clusters already have structure notes)

Results saved to ~/.local/share/mcp/slipbox/cluster-analysis.json

Permanently dismiss a cluster from maintenance suggestions.

Use this when a cluster has been reviewed and determined not to need a structure note, or when the user doesn't want to be reminded about it.

Args: cluster_id: The cluster ID to dismiss (e.g. "poetry-craft-revision")

Create a semantic link between two notes.

Links are directional: source -> target. Use bidirectional=true for important relationships (automatically creates inverse link type).

Link Types:

• reference: Generic "see also" connection

• extends: Source builds upon target (inverse: extended_by)

• refines: Source clarifies or improves target (inverse: refined_by)

• contradicts: Source presents opposing view (inverse: contradicted_by)

• questions: Source raises questions about target (inverse: questioned_by)

• supports: Source provides evidence for target (inverse: supported_by)

• related: Loose thematic connection (symmetric)

Best Practices:

• Always add description explaining WHY notes are linked

• Use bidirectional=true for substantive relationships

• Create links immediately after creating notes

Args: source_id: ID of the source note (the note doing the linking) target_id: ID of the target note (the note being linked to) link_type: One of reference/extends/refines/contradicts/questions/supports/related description: Brief explanation of the relationship bidirectional: If true, creates inverse link from target to source

Remove a link between two notes.

Args: source_id: ID of the source note target_id: ID of the target note bidirectional: If true, removes links in both directions

Delete a specific link from one note to another.

Unlike slipbox_remove_link, this tool returns an error if no link exists between the two notes.

Args: source_id: ID of the source note (the note containing the link) target_id: ID of the target note (the note being linked to)

Get notes linked to or from a specific note.

Use this to explore the knowledge graph around a note.

Directions:

• outgoing: Notes this note links TO

• incoming: Notes that link TO this note

• both: All connected notes in either direction

Args: note_id: ID of the note to explore from direction: One of outgoing/incoming/both (default: both)

Get all tags in the Zettelkasten.

Returns alphabetically sorted list of all tags. Use this to find existing tags before creating new notes to maintain tag consistency across your knowledge base.

Create a new atomic Zettelkasten note.

    Each note should contain exactly one idea. After creating, immediately
    link to related notes using slipbox_create_link.

    Note Types:
    - fleeting: Quick captures, unprocessed thoughts (process within 24-48 hours)
    - literature: Ideas extracted from sources. REQUIRES at least one entry
      in references (citation or URL). If you don't yet have the citation,
      use 'fleeting' as a staging type and promote to 'literature' once
      the source is attached.
    - permanent: Refined ideas in the user's own words (the core of your Zettelkasten)
    - structure: Maps organizing 7-15 related notes on a topic
    - hub: Entry points into major knowledge domains

    Authoring:
    - Store `content` exactly as the user provided it. Do NOT rewrite,
      expand, or restructure their words. Compose or refine content only
      when explicitly asked (e.g. "draft", "refine", "make it standalone").

    Best Practices:
    - Title should express the idea in brief (understandable without reading content)
    - A refined permanent note typically runs 3-7 paragraphs and stands
      alone; match the length of what the user gave you, though — a
      one-line capture stays one line.
    - Use 2-5 specific tags; prefer existing tags when they fit
    - Search first (slipbox_search_notes) to avoid duplicating existing notes

    Args:
        title: Concise title expressing the core idea
        content: Full note content in markdown
        note_type: One of fleeting/literature/permanent/structure/hub (default: permanent)
        tags: Comma-separated tags, e.g. "poetry,revision,craft"
        references: Newline-separated citations to external sources (e.g. "Ahrens, S. (2017). How to Take Smart Notes.

https://zettelkasten.de")

Retrieve a note by ID or title.

Returns full note content including metadata, tags, and links. Use this to read note contents before creating links or updates.

Args: identifier: Either the note ID (e.g. "20251217T172432480464000") or exact title

Update an existing note.

Only provided fields are updated; omitted fields remain unchanged. Pass empty string for tags to clear all tags. Pass empty string for references to clear all references.

Constraint: notes with note_type='literature' must have at least one reference. If you are promoting a note to 'literature', pass the citation in references in the same call.

Args: note_id: The ID of the note to update title: New title (optional) content: New content (optional) note_type: New type: fleeting/literature/permanent/structure/hub (optional) tags: New comma-separated tags, or empty string to clear (optional) references: New newline-separated citations, or empty string to clear (optional)

Delete a note permanently.

Warning: This also removes all links to and from this note. Consider updating note_type to "fleeting" instead if uncertain.

Args: note_id: The ID of the note to delete

Search for notes by text, tags, or type.

Searches across titles and content. Combine parameters for precise filtering.

Examples:

• Search by topic: query="poetry revision"

• Filter by tag: tags="craft,poetry"

• Find structure notes: note_type="structure"

• Combined: query="metaphor" tags="poetry" limit=5

Args: query: Text to search in titles and content (optional) tags: Comma-separated tags to filter by, e.g. "poetry,craft" (optional) note_type: Filter by type: fleeting/literature/permanent/structure/hub (optional) limit: Maximum results to return (default: 10)

Find notes similar to a given note.

Similarity is based on shared tags, common links, and content overlap. Useful for discovering connections you might have missed.

Args: note_id: ID of the reference note threshold: Minimum similarity score 0.0-1.0 (default: 0.3) limit: Maximum results (default: 5)

Find the most connected notes in the Zettelkasten.

Central notes have the most incoming and outgoing links, making them key hubs in your knowledge network. Good candidates for hub notes.

Args: limit: Maximum results (default: 10)

Find notes with no connections to other notes.

Orphaned notes represent unintegrated knowledge. Review these periodically to either link them to existing notes or identify candidates for deletion.

List notes by creation or update date.

Useful for reviewing recent work or finding notes from a specific period.

Args: start_date: Start date in ISO format YYYY-MM-DD (optional) end_date: End date in ISO format YYYY-MM-DD (optional) use_updated: If true, filter by updated_at instead of created_at (default: false) limit: Maximum results (default: 10)

Rebuild the database index from markdown files.

Use this if notes were edited outside the MCP server or if the database seems out of sync with the filesystem.