CRITICAL: Fixed dependency resurrection bug that caused removed/orphaned
dependencies to keep coming back after sync.
Root cause: mergeDependencies() was doing a union (additive only) and
completely ignored the base parameter. This meant any dependency present
in either left or right would be included, even if it was intentionally
removed.
Fix: Proper 3-way merge where REMOVALS ARE AUTHORITATIVE:
- If dep was in base and removed by left OR right → stays removed
- If dep wasn't in base and added by left OR right → included
- If dep was in base and both still have it → included
This fixes months of issues with orphaned parent-child relationships
being resurrected during git sync operations.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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