- 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. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>