fix: Add complete bash permissions for all project tools
- Replace git submodule:* with git:* for full git access
- Add mkdir:* for directory creation
- Add jq:* and yq:* for data processing
- Reorganize permissions list for clarity
Covers all tools used by commands, skills, and agents.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>