Obsidian Topic Atlas

Obsidian Topic Atlas

When to Use

• The user wants a cluster map of the vault or a subtree such as Knowledge/ or Personal/
• Future agents need a fast entry point into a dense note area
• You need to identify hub notes, thin hubs, and under-linked regions
• You want a derived atlas under _codex/ without touching canonical notes

When Not to Use

• Do not use for rewriting or reorganizing canonical notes
• Do not use for generic note summaries when no cluster map is needed
• Do not use for a whole-machine discovery pass outside the vault
• Do not use when the real need is a project-specific operational map; prefer obsidian-project-normalizer

Inputs

• Vault root, usually ~/Documents/Obsidian_base/learn
• Optional subtree such as Knowledge/, Personal/, or Journal/
• Safe write area, usually learn/_codex/
• Existing local guides:
  • learn/AGENTS.md
  • learn/_codex/write_policy.md if it exists

Output Files

• Primary: _codex/topic_atlas.md
• Variant for bounded runs: _codex/<scope_slug>_topic_atlas.md

Constraints

• Do not edit, rename, move, or delete existing notes
• Treat canonical notes as read-only unless the user explicitly asks otherwise
• Ignore Cache/ and .obsidian/ for semantic analysis
• Prefer high-confidence clustering over exhaustive coverage
• Mark uncertain boundaries explicitly

Procedure

1. Read the nearest AGENTS.md files before scanning the vault.
2. Confirm the safe output area. Default to learn/_codex/.
3. Inventory folders and note counts for the target scope.
4. Identify candidate hubs from:
   • dashboard notes
   • atlas/index notes
   • backlog/planning notes
   • repeated wiki-link targets
5. Sample a small set of representative notes from each suspected cluster.
6. Group notes into thematic clusters that predict future navigation value, not just naming similarity.
7. For each cluster, record:
   • short summary
   • core notes
   • hub notes
   • whether the cluster is strong, thin, or weakly linked
8. Add a short uncertainty section for ambiguous overlaps or missing nodes.
9. Write the atlas as a derived note under _codex/.
10. Verify the atlas does not claim certainty where only filenames or sparse samples were available.

Definition of Done

• The output identifies a bounded set of thematic clusters rather than listing folders mechanically
• Each cluster includes anchor notes or hub notes that improve future navigation
• Weakly linked or thin areas are called out explicitly
• Uncertainty is visible wherever the cluster boundary depends on sparse evidence
• The note links back to canonical sources and does not impersonate them

Vault-Specific Guidance

• For learn, expect high-value clusters around:
  • vault control and planning
  • AiStats / football analytics
  • VLM / CV / detection
  • RL / theory
  • math / university
  • personal operating notes
  • prompt libraries
• Use Home.md, Backlog.md, Knowledge/Knowledge.md, Personal/Personal.md, and Journal/Journal.md as initial anchors.
• Use references/atlas_note_template.md when you want a stable output shape without rethinking the section layout from scratch.