myco_assimilate
Promote raw notes to integrated notes for stable knowledge. Assimilate bulk pending captures or a specific note for immediate visibility.
Instructions
Promote notes from notes/raw/ to notes/integrated/ — in bulk (all eligible raw notes) or for a single named note. Integrated notes are the substrate's stable knowledge layer; raw notes are the intake queue. A bulk promotion is typical during session-end or before a release: assimilate sweeps the raw queue, re-writes filenames to the n_.md convention, and leaves raw/ empty.
Use this when: raw_backlog reported by myco_hunger is > 0 and you want to integrate the pending captures. Use with note_id= when you want to promote exactly one specific note (e.g. a high-priority decision that needs immediate visibility); for that case myco_digest is the single-note equivalent. Do NOT assimilate before the note is ready (integration is supposed to represent stable knowledge, not half-thoughts).
Side effects: moves files from notes/raw/ to notes/integrated/ (delete + create; atomic). Updates frontmatter (status, promoted_at). R6 write_surface must cover both directories. Errors on a per-note basis are collected and returned; one failed note does not abort the whole batch.
Returns: { exit_code, promoted, already_integrated, errors, outcomes: [ { status, path, dry_run, note_id } ], synced_contract_version_updated }.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| note_id | No | Optional stem of a single raw note to promote (e.g. '20260423T054055Z_v0-5-22-migration-marker'). When null/omitted, assimilates ALL eligible notes in notes/raw/. Pass the stem (no extension, no directory prefix) as you'd read it from the filename. Nonexistent stems are returned as errors in the outcomes list, not raised. | |
| project_dir | No | Absolute path of the workspace / project whose Myco substrate this call targets. Overrides auto-discovery. When omitted, Myco resolves via MCP roots/list, then MYCO_PROJECT_DIR, then cwd — the substrate_pulse field in every response echoes which source answered. |