Auto-update to 2.1.87 wiped user-level settings, plugins, and MCP config

Description

Auto-update from native installation silently wiped ~/.claude/settings.json, ~/.claude/settings.local.json, and plugin activation state. No user action triggered this — the auto-updater ran on its own.

What was lost

• ~/.claude/settings.json — reset to only {"effortLevel": "high"} (had more settings before)
• ~/.claude/settings.local.json — completely gone (contained user-level MCP server config and permissions)
• Plugin activation state — claude plugins list reports "No plugins installed" despite marketplace data being fully cached in ~/.claude/plugins/marketplaces/

What survived

• ~/.claude.json (internal state file at home root) — intact
• ~/.claude/backups/ — contains .claude.json backups only (not settings files)
• Project-level .claude/ directory — intact (it's in git)
• Plugin marketplace cache (~/.claude/plugins/marketplaces/claude-plugins-official/) — downloaded but not activated

Timeline (from file timestamps)

• Mar 27 23:10 — claude.exe binary date
• Mar 29 22:01–22:04 — auto-updater downloaded v2.1.87 to ~/.local/share/claude/versions/
• Mar 29 22:13+ — everything in ~/.claude/ has fresh timestamps (directory was recreated)

Environment

• Windows 11 Pro 10.0.26200
• Native installation: v2.1.86 running, v2.1.87 downloaded
• Leftover npm-global installation also present (both had coexisted without issues previously)
• claude doctor output:

``
Currently running: native (2.1.86)
Path: C:\Users\info\.local\bin\claude.exe
Warning: Multiple installations found
npm-global at C:\Users\info\AppData\Roaming\npm\claude
native at C:\Users\info\.local\share\claude
Auto-updates: enabled
``

Expected behavior

Auto-update should preserve user-level settings, MCP configuration, and plugin activation state. If migration is needed, old settings should be backed up before being replaced.

Impact

User must manually reinstall all plugins and recreate settings.local.json from memory. No recovery path exists — settings.json and settings.local.json are not included in the backup mechanism (~/.claude/backups/ only backs up .claude.json).