- Remove silent="true" which caused step to be skipped
- Make setup step explicit with MANDATORY instruction
- Check for both .git directory AND .git file (worktrees/submodules)
- Add explicit "You MUST run using Bash tool" instruction
Prevents commits going to parent repo when initializing
projects in subdirectories.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>