Connect a notes store (Obsidian)

A notes store turns a folder of markdown — an Obsidian vault, a wiki, any notes app — into a knowledge base your agent reads and writes. Add it at init or later:

polydomain init --references obsidian   # core + Obsidian conventions
polydomain init --references notes       # generic core only
polydomain add reference obsidian        # add to an existing center

The index hierarchy (near-infinite context)

The store is navigable in three reads per question: a root _index.md lists topics, each topic’s _index.md lists its notes, and the note holds the content. The agent reads root index → topic index → note, instead of loading everything. This is what lets a store of thousands of notes fit in context.

Frontmatter

Every note carries type, created, updated, tags, source, and confidence. The confidence and updated fields let the agent judge staleness — a fact true today can be wrong tomorrow.

The four operations

• CAPTURE — drop a raw source into _inbox/, unchanged.
• COMPILE — turn it into a structured note, cross-link it, update the indexes.
• QUERY — navigate the indexes to answer; save valuable answers as notes.
• AUDIT — find contradictions, orphans, missing links, and stale notes.

Two ways to start

• Already have a vault? Ask your agent to audit it: it reflects your existing structure into an index and offers cleanups (nothing is imposed — every change goes through the review gate).
• New to notes? Ask it to generate a starter structure and teach you the operations.

Optional accelerators

Plain file reads work out of the box. For large vaults you may add a filesystem Obsidian MCP server (no plugin needed) or a local search CLI — none are required or bundled.

Promotion & privacy

When a note matures into a stable fact, promote it to its domain’s source-of-truth repo — reflect and link, don’t copy. Keep credentials out of the store; its content is sent to the model provider as context.