[FEATURE] Reserve 'skills/' for user-managed skills, relocate internal skills to 'system/'

Problem

Users may symlink ~/.claude/skills to a shared location like ~/.agents/skills/ to maintain a unified skills directory across multiple AI agents (as encouraged by Vercel's skills ecosystem).

If Claude Code stores internal functionality in ~/.claude/skills/.system/, this breaks when skills/ is symlinked:

1. Symlink target pollution - Claude Code's internal .system/ directory ends up in the shared ~/.agents/skills/ location
2. Cross-agent leakage - other agents see Claude Code's internal files
3. Unexpected behavior - the symlink target may be read-only, versioned, or managed by external tools

Proposed solution

Relocate internal/system skills from ~/.claude/skills/.system/ to a separate directory:

Option A (preferred): ~/.claude/system/ - clean separation at the top level
Option B: ~/.claude/.internal/ - hidden directory for internal resources

This allows ~/.claude/skills/ to be safely symlinked without dragging internal resources along.

Alternatives considered

• Keep .system/ inside skills/ - breaks symlink scenarios
• Document "don't symlink skills/" - fights the emerging ecosystem convention

Priority

Medium

Category

Configuration and settings

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References:

• Skills.sh - The Agent Skills Directory
• vercel-labs/add-skill - CLI tool for cross-agent skill installation