Plugin skills duplicated in /context report and system prompt

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?

Every installed plugin's skills appear twice in the /context output and twice in the system-level skills list injected into the session prompt.

Example from /context output:

| claude-md-management:revise-claude-md | Plugin | 22 |
| claude-md-management:revise-claude-md | Plugin | 22 |
| using-git-worktrees                   | Plugin | 59 |
| using-git-worktrees                   | Plugin | 59 |
| systematic-debugging                  | Plugin | 31 |
| systematic-debugging                  | Plugin | 31 |

This affects all installed plugins. The superpowers plugin (installed from a GitHub URL, exists only in ~/.claude/plugins/cache/ and NOT in the marketplace directory) is also duplicated — which rules out "scanning two different directories" as the cause. The bug must be in session prompt construction itself.

What Should Happen?

Each skill should appear exactly once in the /context skills table and once in the session system prompt.

Error Messages/Logs

Steps to Reproduce

1. Install one or more plugins via claude plugin install
2. 2. Start a new Claude Code session
3. 3. Run /context
4. 4. Observe the Skills table — every skill is listed twice

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.50 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Enabled plugins from ~/.claude/settings.json:

{
  "enabledPlugins": {
    "claude-md-management@claude-plugins-official": true,
    "playground@claude-plugins-official": true,
    "claude-code-setup@claude-plugins-official": true,
    "skill-creator@claude-plugins-official": true,
    "superpowers@claude-plugins-official": true
  }
}

The superpowers plugin was installed from a GitHub URL (https://github.com/obra/superpowers.git) and exists only in ~/.claude/plugins/cache/claude-plugins-official/superpowers/4.3.1/ — not in the marketplace directory at ~/.claude/plugins/marketplaces/claude-plugins-official/plugins/. Despite having only one copy on disk, its skills still appear twice in /context.