[BUG] Plugin marketplace UI shows plugins as disabled but their tools remain available

Preflight Checklist

• [x] I have searched existing issues
• [x] I am filing a single bug report
• [x] I am using the latest version of Claude Code

What's Wrong?

The /plugin command UI shows plugins as disabled (◯) but their tools and skills remain available in the session. Tools prefixed with mcp__plugin_<name>_ and skills prefixed with <plugin-name>: are accessible despite their parent plugins being shown as disabled in the /plugin interface.

Note: Claude Code was restarted after disabling these plugins, but their tools still remain available to the agent.

What Should Happen?

When a plugin is shown as disabled in the /plugin UI (◯), its associated tools and skills should not be available in the Claude Code session. Only enabled plugins (◉) should have their functionality accessible. Restarting Claude Code should respect the disabled state and remove those tools from the session context.

Steps to Reproduce

1. Install plugins from a marketplace
2. Enable some plugins via the /plugin UI
3. Restart Claude Code completely
4. Disable those same plugins via the plugin UI (they should show as ◯)
5. Restart Claude Code completely
6. Run /plugin command - verify plugins show as disabled (◯)
7. Ask Claude to list available tools or check which tools are available
8. Observe that tools prefixed with mcp__plugin_<disabled-plugin-name>_ are still available
9. These tools are functional despite their parent plugins being shown as disabled

Claude Model

Sonnet 4.5 (claude-sonnet-4-5-20250929)

Is This a Regression?

Unknown - not sure if this ever worked correctly

Claude Code Version

2.0.24 (Claude Code)

Platform

Anthropic API

Operating System

Linux (Fedora 41 - Linux 6.16.7-100.fc41.x86_64)

Terminal/Shell

bash (/usr/bin/bash)

Error Messages/Logs

N/A - No error messages, the tools simply remain available despite UI showing plugins as disabled.

Additional Information

This issue affects plugin marketplace installations. The plugin UI state (enabled ◉ vs disabled ◯) does not match the actual runtime availability of plugin tools and skills.

Tool naming confirms they come from the plugins (e.g., mcp__plugin_<name>_* pattern for MCP tools, <plugin-name>:<skill> pattern for skills).

This appears related to issue #6320 (Denied MCP tools have their tool prompt in the context) and #8888 (MCP server disabled config not being respected), but specifically affects the plugin marketplace UI state vs. runtime state.