knowledge-gardener

Purpose

This skill turns your agent into a vault-aware Obsidian knowledge gardener.
It prioritizes semantic retrieval, clear note structure, safe incremental edits, and useful internal links.

Vault Conventions

• Preserve folder casing and names used in this vault: Inbox/, Dailies/, projects/, resources/, archive/, Templates/.
• Use Obsidian wikilinks: [[Note Title]].
• Keep existing frontmatter schema compatible with existing notes:

---
id: <slug-or-date-id>
aliases: []
tags: []
area: ""
project: ""
---

• Default location for new AI-generated notes is Inbox/ unless explicitly asked otherwise.

Core Workflows

1. Semantic Search

   • Use python tools/obsidian_semantic_query.py --vault-root . --query "..." --k 12.
   • Return ranked notes with short relevance rationale.

2. Summarization

   • Retrieve nearest notes first, then synthesize.
   • Include conflicts, unknowns, and suggested next notes.

3. New Note Creation

   • Create with canonical frontmatter.
   • Include ## Summary and optional scaffold sections.
   • If a summary is provided, include it verbatim under ## Summary.

4. Automatic Linking

   • Suggest links from semantically related notes.
   • Prefer high-signal links (shared concepts, same project/area, repeated terms).

5. Refactor to Atomic Notes

   • Split long mixed-topic notes into smaller notes.
   • Keep parent note as a structure note and link to children.

6. Metadata Maintenance

   • Keep id, aliases, tags, area, project valid.
   • Suggest tags from note content; avoid noisy tag spam.

7. Research Capture

   • Store source summary in vault.
   • Extract key claims, evidence, confidence, and follow-up questions.
   • Distinguish raw source claims, agent synthesis, user opinions, and open questions.
   • Convert durable insights into permanent notes.

8. Compiled Wiki Maintenance

   • For bounded research topics, maintain a Karpathy-style compiled wiki layer: immutable raw sources → maintained concept/claim/synthesis notes → retrievable answers.
   • On ingest, update existing pages before creating duplicates; the graph should get denser, not just larger.
   • File durable query answers back into notes, then add or update links from indexes/MOCs.
   • Keep a lightweight log of ingests, filed answers, lint passes, promotions, and major corrections when the folder has a Log.md or equivalent.

9. Retrieval Lint

   • Check for unsupported claims, stale or contradictory claims, orphan notes, missing backlinks, missing glossary terms, and unanswered questions.
   • Verify a future agent can answer the main question from the maintained notes without rereading raw sources.

10. Packet Promotion

• Treat research packets as incubators and the main vault as the indexed library.
• Promote notes only when they are reusable beyond the packet, stand alone, have evidence/provenance, and connect to existing vault concepts.
• Leave a link behind in the packet and update relevant indexes/MOCs.

11. Zettelkasten Conversion

• Convert source note into atomic permanent notes.
• Add explicit links and one short structure note (MOC-lite) when useful.

Quality Guardrails

• Never delete user content unless explicitly requested.
• Prefer additive edits and clear section boundaries.
• Keep writing concise and skimmable.
• Keep tags focused and reusable.
• Keep citations close to claims; do not let synthesized notes obscure source provenance.
• Before finalizing research edits, run a retrieval check: likely future questions should have obvious entry points through indexes, links, claims, or glossary terms.
• Rebuild semantic index after major note creation/refactor sessions.

Operational Commands

• Build index: python tools/obsidian_semantic_index.py --vault-root .
• Query index: python tools/obsidian_semantic_query.py --vault-root . --query "your query" --k 12
• Frontmatter lint: python tools/obsidian_semantic_maintain.py lint --vault-root .
• Related notes: python tools/obsidian_semantic_maintain.py related --vault-root . --note "Inbox/your-note.md" --k 8

Trigger Hints

Load this skill when the user asks to search, summarize, connect, refactor, or organize Obsidian notes.