atomize

name	atomize
description	Use when the user wants to atomize a source document into draft Cortex notes — "atomize this doc", "turn this into atomic notes", or /atomize <source.md>. Distills each section into one-idea-per-note drafts (type, folder, tags, wikilinks) and writes them safely into _inbox/ via the cortex toolkit.

Atomize a source into AI-distilled draft notes

You are the AI layer of the N1X Cortex atomize pipeline. The cortex toolkit is the deterministic engine; you do the distillation. Every file write goes through the toolkit — you only produce data.

Procedure

1. Resolve the source. Confirm the source markdown path (under the vault's Markdown/). Build the CLI path to toolkit/dist/cli.js (run npm run build in toolkit/ first if dist/ is missing).

2. Emit the plan. Run node <cli> atomize "<source.md>" --emit-json from the vault dir. Parse the JSON: segments, knownTypes, knownFolders, existing, statusFirst, lang, fields.

3. Distill each segment into one or more atomic notes, following the instructions field emitted by the toolkit. The emit output now carries the full distillation methodology (atomic notes, type/folder routing, the phantom-wikilink prohibition, update-vs-create-vs-skip, cold-vault taxonomy, citations) — treat that instructions text as authoritative. Produce the note specs it describes.

4. Write the distilled specs to a temp file distilled.json. The notes array holds two possible shapes — mix them freely:

   {
     "source": "<emit.source>",
     "notes": [
       { "title": "...", "type": "...", "folder": "...", "tags": ["..."], "body": "...", "fromHeading": "..." },
       { "action": "update", "targetPath": "<existing note path>", "title": "...", "body": "<full merged body>" }
     ]
   }
   

   Create notes (first shape, no action/targetPath) become new _inbox/ drafts. Update notes (second shape) merge into the existing note at targetPath in place.

5. Apply autonomously. Write distilled.json, then run node <cli> atomize --apply distilled.json --write. The toolkit creates new drafts under _inbox/ and merges update notes in place. Print a compact summary (creates, updates with their targets, any skips) — this is information, not a checkpoint.

6. Reassure + reversibility. Tell the user what changed and that every edited note was backed up — any update is undoable with cortex atomize --undo (or via git). Updates skipped by the shrink guard are reported; re-run with --force only if the shrink is intended.

7. Graduate ready notes (optional, autonomous). For each note you created or updated that you judge complete and correct, advance its status and promote it into the curated graph:

   • node <cli> set-status "<_inbox path>" documented --write — your confidence is the trust signal; leave notes you are unsure about as draft in _inbox/.
   • then node <cli> promote --write — graduates every note whose status is now beyond draft into its curated folder (_inbox/03-Rules/x.md → 03-Rules/x.md). It never overwrites an existing curated note.
   • Report what was promoted. The whole run is reversible: node <cli> undo reverses the most recent action (a promotion returns the note to _inbox/; an edit or status change is rolled back).

Safety (enforced by the toolkit, but respect them)

• Dry-run is the default; only --write writes. Always preview before writing.
• New notes (creates) land only in _inbox/<folder>/ as status: draft — they are never written as brand-new files into curated folders directly.
• Source files under Markdown/ are never modified. Existing curated notes are only ever changed through the update path, which backs up each note before editing. Every change — an edit, a set-status advance, or a promote move — is reversible: cortex undo reverses the most recent run.
• Citations are mandatory (the toolkit adds them); keep the source correct.