feat: Allow signing git commits; fix: Delete exact path instead of parent when source is missing

[klaidliadon]

Summary

• Bug: In git-commit, when a listed path doesn't exist in the source repo, the else branch used dirname to compute the deletion target — deleting the entire parent directory instead of just the missing path
• Impact: e.g. api/client/ missing caused rm -rf on api/, nuking all sibling directories
• Fix: Delete only the exact path in the destination, or skip with a log message if it doesn't exist there either

Test plan

• Path exists as directory → syncs normally (no change in behavior)
• Path exists as file → syncs normally (no change in behavior)
• Path doesn't exist, exists in destination → deletes only that exact path, not its parent
• Path doesn't exist, doesn't exist in destination → skips with log message, no deletion