Regression: .claude/skills/ writes prompt for confirmation in bypassPermissions mode since 2.1.78

Description

Since updating from 2.1.74 to 2.1.79, writes to .claude/skills/ prompt for confirmation even with bypassPermissions mode enabled. This worked correctly in 2.1.74.

Steps to reproduce

1. Set "defaultMode": "bypassPermissions" in ~/.claude/settings.json
2. Have Claude edit a file under .claude/skills/
3. Claude prompts for confirmation instead of auto-allowing

This happens both in the project root (.claude/skills/...) and in git worktrees (.worktrees/<name>/.claude/skills/...).

Expected behavior

Writes to .claude/skills/, .claude/commands/, and .claude/agents/ should be exempt from the protected-directory prompt, as documented and as it worked in 2.1.74.

Actual behavior

Edit prompts appear for .claude/skills/ files. Choosing "Yes, allow all edits during this session" downgrades the permission mode from bypassPermissions to acceptEdits, which is a further undesirable side effect.

Environment

• Claude Code version: 2.1.79 (regression since 2.1.78)
• Last working version: 2.1.74
• OS: macOS (Darwin 25.3.0)

Additional context

Adding explicit allow rules like Edit(**/.claude/**) in settings.json does not help — the hardcoded protected-directory logic appears to override allow rules.