[BUG] Custom cowork plugin commands wiped by Claude Desktop update without warning

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

All custom cowork plugin commands were silently deleted after a Claude Desktop update.
Commands created via cowork-plugin-customizer (e.g. custom legal, sales, marketing
commands) no longer exist. The cowork_settings.json was also reset, disabling all
plugins except cowork-plugin-management.

What Should Happen?

Custom plugin commands should persist across Claude Desktop updates. Either:

• Store custom commands outside the marketplace git repo (in a separate user directory)
• Warn the user before overwriting local customizations
• Auto-backup before any marketplace sync/reset

Error Messages/Logs

No visible error. Silent data loss.

From ~/Library/Logs/Claude/main.log (2026-02-26):
"plugin:enterprise-search:notion" status: "needs-auth"
"plugin:finance:stripe" error: "Streamable HTTP error..."
"plugin:customer-support:slack" error: "Incompatible auth server: does not support dynamic client registration"

Steps to Reproduce

1. Open Claude Desktop cowork mode
2. Use cowork-plugin-customizer to add custom commands to existing plugins (e.g. legal, sales)
3. Let Claude Desktop auto-update
4. Reopen cowork mode → all custom commands are gone, cowork_settings.json is reset

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Before 1.1.4498 (last working: ~February 26, 2026)

Claude Code Version

1.1.4498

Platform

Other

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Root cause (self-diagnosed): custom commands are stored as .md files inside the local
clone of anthropics/knowledge-work-plugins. On update, Claude Desktop does a git reset
on this repo, wiping all local modifications with no warning or backup.

Location of affected files:
~/Library/Application Support/Claude/local-agent-mode-sessions/{device-id}/{org-id}/cowork_plugins/marketplaces/knowledge-work-plugins/

Workaround applied: manually restored cowork_settings.json to re-enable standard plugins.
Custom commands are permanently lost.