Organize the vault

Read the note format and vault layout reference first — organize reuses its folder-placement rule, index maintenance, and linking pass.

This skill never runs as a side effect of capture or anything else — only when the user explicitly asks (e.g. "organize the inbox", "sort my notes", "tidy the vault", "any orphan notes?", "what's not connected?").

Filing mode

Trigger: "organize the inbox", "sort my notes", "tidy the vault", or similar.

1. Resolve the vault per Resolving the vault. List everything in inbox/. If it's empty, say so and stop.
2. Normalize anything that isn't already in the template's shape. A file the user dropped into inbox/ themselves (not via capture) may have no frontmatter and no source/content/connections structure. Before deciding its destination, wrap it into templates/note-template.md's current shape: derive a title/slug if it doesn't already look like one, set the source role (the original filename, or "pasted" if there's no clue), and place its existing text verbatim under the content role. This is structural normalization, not a rewrite — the wording stays exactly as given; it's not turned into a summary in anyone's "own words" the way a fresh capture would.
3. For each inbox note, decide its destination — projects/<slug>/ or notes/<topic>/ — using the same folder placement rule and fallback question as capture, but with the benefit of whatever's been captured since. Before moving, re-check the uniqueness rule against the destination: if the target folder already has a same-named file, ask the user whether to update it or rename the incoming note — never overwrite. Move the note (a plain move; delete-and-rewrite only if the host has no move primitive), creating the destination folder if a clear new grouping emerges. If it lands in notes/<topic>/, update the index for that topic. A note that's still not a confident fit for either stays in inbox/ — organize doesn't force placement just to empty the folder.
4. Regenerate the master index, once, if anything moved in step 3. Regenerate indexes/README.md per Master index — a moved note always changed inbox/ and one of projects/<slug>/ or notes/<topic>/, so one regeneration after the whole pass covers every change from step 3.
5. After moving a note, re-run the linking pass against the fuller vault — a note captured before a related one existed may not have had anything to link to yet.
6. Report what moved where, what got newly linked, what got normalized from a raw drop, and what's still sitting in inbox/ unplaced.

Link audit mode

Trigger: "any orphan notes?", "what's not connected?", or a similar request to find unlinked/isolated notes.

1. Scan every note's outgoing [[wikilinks]]. Build the reverse (incoming) map from that.
2. Report every note with neither incoming nor outgoing links.
3. This is a report only. Don't force-link an orphan — a genuinely standalone note is a valid outcome, not a defect. The user decides whether to connect it (via a follow-up capture or edit) or leave it as is.

Out of scope

Doesn't rewrite a note's wording or summarize on its own initiative — step 2's normalization only wraps already-existing text into the template's structure, it never rephrases it. Doesn't run automatically after every capture; only on an explicit request.

Error handling

• Move collision (destination folder already has a same-named file): ask, don't overwrite — same rule as capture's collision handling.
• Vault directory not writable: report the error and stop.