Plugins from project enabledPlugins shown under 'User' scope and cannot be uninstalled

Description

Plugins referenced in a project's .claude/settings.json enabledPlugins that were never actually installed (no entry in ~/.claude/plugins/installed_plugins.json) are displayed under the User scope in the /plugin UI instead of Project. They also cannot be uninstalled via /plugin uninstall since they're not in the installed plugins registry.

Steps to Reproduce

1. Have a project .claude/settings.json with enabledPlugins referencing plugins that were never installed:

``json
{
"enabledPlugins": {
"some-plugin@some-marketplace": true
},
"extraKnownMarketplaces": {
"some-marketplace": {
"source": { "source": "github", "repo": "org/repo" }
}
}
}
``

1. Open Claude Code in that project
2. Run /plugin and go to the Installed tab

Expected Behavior

• These plugins should appear under Project scope (since they come from project settings)
• There should be a way to manage/remove them from the UI (or at minimum a clear indication they need to be installed)

Actual Behavior

• Plugins appear under User scope
• They show as "failed to load · 1 error"
• Running /plugin uninstall plugin-name or claude plugin uninstall plugin-name fails with Plugin "plugin-name" not found in installed plugins
• The only way to remove them is manually editing .claude/settings.json

Screenshots

Plugins from project enabledPlugins showing under "User" instead of "Project":

  Project
❯ anvil2 Plugin · ServiceTitan · ✔ enabled    <-- this one is actually installed

  User
  code-review Plugin · Anthropic · ✘ failed to load · 1 error     <-- from project settings
  feature-dev Plugin · Anthropic · ✘ failed to load · 1 error     <-- from project settings
  ralph-skills Plugin · ralph-marketplace · ✘ failed to load · 1 error  <-- from project settings
  stdocs Plugin · ST-ToolbeltExtensions · ✘ failed to load · 1 error    <-- from project settings

Environment

• Claude Code v2.1.41
• macOS (Darwin 25.2.0)