Update Vault Dependencies

Finds what still references vault paths that moved or were deleted. Report first. The only vault edit this skill makes is a wikilink rewrite, and only after the user confirms. Files outside the vault are never edited.

1. Find what moved and what points at it

python3 -B -I ~/.claude/skills/update-dependencies/scripts/find_moved_refs.py [options]

Show the report as printed. The script is read-only (git plumbing only, it never touches the index) and compares the vault's git history plus the working tree, so a move is seen whether or not it was committed. Always run it as python3 -B -I (stdlib only, system Python 3.9, no __pycache__).

• The default base is the last commit older than 2 days, because the vault auto-commits every 6 hours and a move is soon buried under later commits. If it is unclear when the restructure began, ask the user, then pass --since <date> (or --ref <rev>) to start before it. The report header prints the commit range.
• --ref <rev> sets the base commit (--ref HEAD = uncommitted changes only).
• --move OLD NEW adds a move git cannot see (repeatable). NEW of - means deleted. An absolute OLD covers a relocated vault root.
• --all lifts the 60-line cap on long lists. --vault <dir> points at another checkout.

Sections: What moved; External references (file:line in AGENTS/CLAUDE files, hooks, settings.json, other skills, agent-config/bin, LaunchAgent plists, memory); Wikilinks to update (including bare [[name]] links that now silently resolve to a different note); Duplicate-basename risks; Standing checks (informational, shown on every run: leftover paths of the old iCloud vault). All clear ignores the standing checks.

2. Run the existing audits

Do not re-implement them:

bash ~/.claude/skills/audit-vault/scripts/audit_all.sh links
bash ~/.claude/skills/audit-paths/scripts/audit_paths.sh all

links reports broken wikilinks and duplicate basenames across the whole vault. audit-paths reports dead paths in CLAUDE.md, memory and LaunchAgent plists.

3. Rewrite wikilinks (only after explicit confirmation)

Show the "Wikilinks to update" list and ask first. Proposals marked [ambiguous] need the user's pick. Then:

1. Run the checkpoint: bash ~/.claude/skills/update-dependencies/scripts/checkpoint_vault.sh. It refuses to run from 10 minutes before to 20 minutes after 00:00, 06:00, 12:00 or 18:00 (auto-sync can start late and would commit a half-edited tree), then stages everything and tags checkpoint-<timestamp> on a snapshot (or on HEAD if the tree is clean). Finish all rewrites before the next window; it prints the minutes left.
2. Rewrite each link with the Edit tool, keeping !, #heading and |alias.
3. Re-run find_moved_refs.py and audit_all.sh links. The wikilink list should be empty.
4. Roll back one file with git -C ~/Documents/obsidian checkout <tag> -- <path>.

Rules

• Never auto-fix external files. Report file:line with the proposed edit and let the user decide.
• A hit tagged [line also mentions the new path] usually narrates the move (a memory note). It is history, not a stale reference.
• The vault's 10_journal/ (alias ~/Documents/journal/) is read-only: never rewrite links or move files in it.
• Ask before deleting a note. Private files listed by exact path in the vault .gitignore (such as mac_disaster_recovery.md) stay where they are: a moved copy is no longer ignored and the next auto-sync pushes it.
• This skill sits in a public repo: keep secrets and personal data out of it.

Troubleshooting

• error: unknown revision or not a git repository: the --ref commit does not exist, or --vault is not a repo root.
• A moved file is missing from "What moved": git cannot see moves of gitignored files, and the move may predate the base. A heavy edit during a move can show as delete plus add. Pass the pair with --move OLD NEW, or an earlier --since.
• Too many hits: narrow the base (--ref HEAD). Basename-only matches are skipped when the old filename still exists elsewhere.
• skipped or missing lines under Notes: that source was not checked (absent, binary or over 1 MB). Add its new path to SOURCE_PATTERNS in the script.