Desktop "local agent mode" plugin snapshot goes stale and never refreshes (retired skills persist, new skills missing) — survives full app restart

Environment

• Claude Desktop 1.24012.9 (Code tab / "local agent mode")
• macOS 26.5.2
• Plugin installed from a Git-backed marketplace with autoUpdate: true (SHA-versioned, no explicit version in plugin.json)

Summary

The Desktop app stages a per-session copy of each marketplace plugin's skills. That staged copy can get stuck on an old revision and is then never refreshed — not by the marketplace auto-update, not by the installed_plugins.json version bump, and not by fully quitting and relaunching the app. As a result, the Code tab keeps offering slash-commands for skills that have been renamed/removed at the source, and does not surface skills that were added.

The on-disk marketplace cache and pin are correct throughout — only the Desktop app's staged snapshot is stale.

Steps to reproduce

1. Install a plugin from a Git-backed marketplace and use it in the Desktop Code tab.
2. At the source, change the plugin's skill set (e.g. rename a skill skill-old → skill-new, and add another skill). Push; let the marketplace auto-update pull the new commit.
3. Observe that the underlying cache is updated (see "Evidence" — cache pin now points at the new commit and contains the new skills).
4. In the Desktop Code tab, the old slash-command /skill-old is still offered and /skill-new is unknown.
5. Fully quit the app (Cmd-Q) and relaunch. The stale commands persist.

Expected

After the marketplace cache updates (or at the latest on app relaunch), the Code tab should offer the current skill set: renamed/removed skills gone, added skills present.

Actual

The Code tab indefinitely reflects an old plugin revision. In my case the staged snapshot was ~24 days behind and had survived many restarts.

Evidence / apparent root cause

The app stages plugin content per session at:

~/Library/Application Support/Claude/local-agent-mode-sessions/<session-uuid>/<session-uuid>/rpm/plugin_<id>/skills/

tracked by a sibling rpm/manifest.json. Each plugin entry has an updatedAt, and some also carry updatedAtVerified: true.

• The affected plugin's entry had an old updatedAt (~24 days prior) and no updatedAtVerified flag.
• A different plugin in the same manifest had updatedAtVerified: true with a recent updatedAt and was correctly up to date.

So the refresh/verification path runs for some plugins but silently skips others, and relaunch resumes the same session directory and replays the stale snapshot rather than re-verifying it against the cache.

Meanwhile the sources of truth were all current and mutually consistent:

• marketplace clone HEAD = <new-sha> (contains the new skills)
• ~/.claude/plugins/installed_plugins.json pin = <new-sha>, and the corresponding cache/.../<new-sha>/skills/ contains the new skills
• The stale rpm/plugin_<id>/skills/ copy contained the old skill set matching a much older commit.

A plain claude CLI session (which reads ~/.claude/plugins/cache/ directly) showed the correct, current skills the whole time — the discrepancy is specific to the Desktop staged snapshot.

Workaround

With the app fully quit, rename/remove the staging directory so it is rebuilt from the cache on next launch:

mv ~/Library/Application\ Support/Claude/local-agent-mode-sessions{,.bak}

Relaunch and open a new chat — the plugin re-stages from the current cache and the correct skills appear. (Removing just the affected rpm/plugin_<id>/ snapshot also works.)

Suggested fix

On app launch (and when the marketplace cache pin changes), re-verify each staged plugin snapshot against the current cache revision and re-stage if they differ — and ensure updatedAtVerified is set consistently for all plugins, not just some. Resuming a session should not blindly replay a stale snapshot.