Skills from plugins registered twice in system prompt, doubling context usage

Description

Every skill from every enabled plugin appears twice in the system-reminder skill list injected into the conversation context. This doubles the token cost of the skill registry and can push sessions over the prompt limit at initialization.

Steps to Reproduce

1. Enable multiple plugins in ~/.claude/settings.json, for example:

``json
{
"enabledPlugins": {
"claude-md-management@claude-plugins-official": true,
"ralph-loop@claude-plugins-official": true,
"claude-code-setup@claude-plugins-official": true,
"superpowers@claude-plugins-official": true,
"agent-sdk-dev@claude-plugins-official": true
}
}
``

1. Start a new Claude Code session in a project that also has local skills (e.g. .claude/skills/)
2. Observe the <system-reminder> block listing available skills — every skill appears twice

Observed Behavior

The skill list in <system-reminder> contains duplicate entries for every registered skill. Example (truncated):

- utf16-char-matcher-design: Use this skill when designing...
- simd-charclass-jdk26-valhalla: Use this skill whenever generating...
...
- claude-md-management:revise-claude-md: Update CLAUDE.md...
- ralph-loop:help: Explain Ralph Loop plugin...
...
- claude-md-management:revise-claude-md: Update CLAUDE.md...  (DUPLICATE)
- ralph-loop:help: Explain Ralph Loop plugin...  (DUPLICATE)
...

With 8 plugins enabled (~30 skills total), this results in ~60 skill description entries in the system prompt.

Expected Behavior

Each skill should appear exactly once in the skill list.

Impact

• "Prompt is too long" errors at session start — With enough plugins + project CLAUDE.md + MEMORY.md + MCP server context, the accumulated system prompt exceeds the limit before the user even sends their first message.
• Wasted context tokens — The duplicated skill descriptions consume context budget on every single message in the conversation, reducing available space for actual work.

Environment

• Claude Code version: latest (as of 2026-02-22)
• OS: macOS Darwin 25.2.0
• Number of enabled plugins: 8
• Local project skills: 2

Workaround

Reducing the number of enabled plugins alleviates the issue, but users shouldn't need to disable useful plugins to stay within prompt limits.