--dangerously-skip-permissions still prompts for .claude/ directory writes (including exempt paths)

When running with --dangerously-skip-permissions, edits and writes to files under .claude/ still trigger permission prompts. This includes paths that should be exempt from the protected-directory check, like .claude/skills/, .claude/commands/, and .claude/agents/.

Minimal repro

# Create a temp project with a repro settings file
mkdir -p /tmp/claude-repro/.claude/skills
cat > /tmp/claude-repro/.claude/settings.json << 'EOF'
{
  "permissions": {
    "allow": [
      "Edit(.claude/**)",
      "Write(.claude/**)"
    ]
  },
  "skipDangerousModePermissionPrompt": true
}
EOF

echo "# test skill" > /tmp/claude-repro/.claude/skills/test.md

# Launch with bypass and ask it to edit the skill file
cd /tmp/claude-repro
claude --dangerously-skip-permissions -p "Edit .claude/skills/test.md and add a line"

Despite bypass mode + explicit allow rules, a permission prompt appears.

Expected behavior

• .claude/skills/, .claude/commands/, .claude/agents/ — no prompt (documented as exempt)
• Other .claude/ paths (settings, CLAUDE.md, etc.) — prompt may be intentional, but explicit allow rules in settings should be respected

Actual behavior

All .claude/ paths prompt, including the exempt ones. The allow rules in settings.json don't override the hardcoded protected-path check.

Version

2.1.81