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docs: knowledge-graph (TheBrain-style note linking) design proposal - #212

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@davior

@davior davior commented Oct 20, 2026

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Adds docs/knowledge-graph-design.md, a design proposal for linking notes into a graph you can navigate, in the style of TheBrain. This PR is documentation only; there are no code changes.

The proposal covers:

  • TheBrain's model: thoughts, parent, child, jump and sibling links, the Plex view, mentions and backlinks, mapped onto the existing gecko-notes model: parent_note_id, childNote and noteReference blocks, diagram note-links, and extract_linked_note_ids().
  • A NoteLink index table: rebuilt from note content on every save by one SQLAlchemy flush hook, so links stay correct through renames, moves, archives, deletes and version restores.
  • Inline note links: a new noteLink inline content type with a [[-style picker that can also create a new note.
  • API: neighbourhood, backlinks and graph endpoints, plus a UI plan: a linked-notes panel, a deterministic Plex view, a past-notes trail and a global graph.
  • Link discovery: unlinked mentions through SQLite FTS5, entity notes, and AI-suggested links that only change content after review.
  • Converting existing notes: a non-destructive backfill of existing links, then opt-in suggested-link passes.
  • A phased rollout plan and open questions.

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