Doctor reports stale plugins from removed marketplaces

Description

/doctor reports 5 plugins as "not found in marketplace" for marketplaces (ruflo, understand-anything) that are no longer in the user's configuration:

Plugin (ruflo-federation@ruflo): Plugin ruflo-federation not found in marketplace ruflo
Plugin (understand-anything@understand-anything): Plugin understand-anything not found in marketplace understand-anything
Plugin (ruflo-autopilot@ruflo): Plugin ruflo-autopilot not found in marketplace ruflo
Plugin (ruflo-swarm@ruflo): Plugin ruflo-swarm not found in marketplace ruflo
Plugin (ruflo-core@ruflo): Plugin ruflo-core not found in marketplace ruflo

Investigation

These plugins do not appear in any user-accessible configuration:

• enabledPlugins in settings.json — only valid plugins listed
• known_marketplaces.json — only claude-plugins-official and claude-code-warp
• extraKnownMarketplaces in settings.json — only claude-code-warp
• installed_plugins.json — only 4 valid installed plugins
• claude plugins list — same 4 plugins, none of the 5 stale ones
• claude plugins uninstall — all 5 fail with "not found in installed plugins"
• claude plugins prune --dry-run — "Nothing to prune"
• claude plugins marketplace list — only 2 valid marketplaces

Steps attempted to fix

1. Deleted stale empty data dirs (~/.claude/plugins/data/ruflo-core-ruflo/, ~/.claude/plugins/data/understand-anything-understand-anything/)
2. Ran claude plugins marketplace update
3. Tried claude plugins uninstall for each plugin (all fail)
4. Ran claude plugins prune --dry-run (nothing found)

None resolved the issue.

Hypothesis

The plugin registry maintains internal state that persists stale references to plugins from marketplaces that were registered and later removed. The cleanup path for marketplace removal doesn't cascade to the plugin index.

Environment

• Claude Code v2.1.142
• macOS (darwin)
• Shell: zsh