Account skills sync moves locally-installed skills out of ~/.claude/skills/ into skills/.trash, though the docs scope the sweep to skills/synced/

Summary

Across seven separate events, Claude Code moved 83 skill directories that live flat at ~/.claude/skills/<name>/ into ~/.claude/skills/.trash/. 69 of them are a third-party skill pack installed locally two months ago by copying directories into ~/.claude/skills/ — they were never uploaded to, or enabled on, claude.ai.

~/.claude/skills/synced/ has never existed on this machine — not on disk, and not in any commit of the git repository that versions ~/.claude (checked with git log --diff-filter=A -- 'skills/synced*' → 0 commits).

The docs scope this mechanism to synced/ only, so the observed behaviour appears to be a bug rather than the documented opt-out.

Environment

• Claude Code 2.1.276 (the waves also occurred under 2.1.273 and 2.1.274)
• macOS 24.6.0, arm64
• ~/.claude/settings.json: "syncClaudeAiSkills": false, "syncClaudeAiPlugins": false
• No settings.local.json, no managed settings file present
• ~/.claude is a git repository, so every moved file is provably tracked and restorable — which is how the loss was measured precisely

What happened

Each wave creates one ~/.claude/skills/.trash/<epoch-ms>-<pid>-<rand>/<skill-name>/ entry per skill, all sharing one timestamp, each wave under a different pid.

| # | UTC | entries |
|---|---|---|
| 1 | 2026-09-16 18:30:27 | 69 |
| 2 | 2026-09-17 07:40:47 | 69 |
| 3 | 2026-09-17 15:30:30 | 69 |
| 4 | 2026-09-17 17:28:03 | 69 |
| 5 | 2026-09-17 17:33:18 | 84 |
| 6 | 2026-09-17 20:33:11 | 69 |
| 7 | 2026-09-18 13:03:19 | 69 |

Between waves the directories were restored from git, which is why the same skills were moved repeatedly. Wave 7 happened 48 minutes after a restore, with no session started in between that I could correlate — consistent with the documented background check "about every 10 minutes" rather than with "at the next launch".

~/.claude/plugins/synced/.bucket-<uuid>_<uuid> was created at 2026-09-16 18:30:25 UTC — two seconds before wave 1 — and is empty. No skills/synced was ever created.

What was moved

• 69 directories from a third-party skill pack, installed locally on 2026-08-10 by copying them into ~/.claude/skills/, committed to my own repo, never touched by claude.ai.
• 14 account-provisioned skills (xlsx, pptx, pdf, docx, docs, morning, theme-factory, slack-gif-creator, canvas-design, brand-guidelines, algorithmic-art, mcp-builder, internal-comms, import-memory) — these I would expect to be in scope.

Not moved: 62 other flat directories in the same parent (my own authored skills). So the selection is not "everything under skills/" — but it does include locally-installed directories that were never synced.

Why this looks like a bug

From the docs:

• en/skills: "Claude Code downloads your account's skills into ~/.claude/skills/synced/ in the background, then checks claude.ai for changes about every 10 minutes."
• en/skills: "To stop syncing on a machine, set syncClaudeAiSkills to false in your user settings. Claude Code stops downloading, and the next time it starts it moves the skills it already synced to ~/.claude/skills/.trash/ and no longer loads them."
• en/skills: personal skills live at ~/.claude/skills/<skill-name>/SKILL.md and are described as a separate location from claude.ai account skills.
• en/claude-directory: skills/.trash/ is "synced skills that Claude Code removed".

Nothing in the docs describes a path by which a flat ~/.claude/skills/<name>/ directory that was never synced is treated as synced or swept. On this machine, directories in exactly that location, with no synced/ present at all, are being moved.

Reproduction

I have not reproduced this on a clean machine — it is reproducing continuously on mine, and I can run any diagnostic you would like. The shape appears to be:

1. Sign in to a claude.ai account that has account skills enabled.
2. Install a skill pack locally by copying directories into ~/.claude/skills/<name>/ (no synced/ directory, no upload to claude.ai).
3. Set "syncClaudeAiSkills": false in ~/.claude/settings.json (the waves began before I set this, so it may not be required).
4. Leave a session running, or start one, and wait.

Expected: only skills under ~/.claude/skills/synced/ are ever moved to .trash. Actual: flat, never-synced directories under ~/.claude/skills/ are moved.

Impact

Every skill in the pack stops loading, silently. There is no message at the time of the move, and nothing in a session says why a skill vanished — the first wave went unnoticed for about 24 hours. Users whose ~/.claude is not version-controlled would be relying on .trash alone, which the retention sweep deletes after cleanupPeriodDays (default 30).

Questions

1. Is the sweep supposed to consider anything outside ~/.claude/skills/synced/?
2. When synced/ does not exist, does the sweep fall back to treating ~/.claude/skills/ as the synced root?
3. Is there a supported way to mark a locally-installed directory as out of scope? I could not find one in en/skills, en/claude-directory, or the settings reference.

Happy to attach the full list of moved directory names, the per-wave pids, or anything else useful.