Shared Git State in Parallel Worktrees Can Cause Ref Corruption for AI Agents

AI coding agents deployed across separate Git worktrees can encounter unexpected failures despite operating in isolated directories. While each worktree has its own files and staging index, they all share a single underlying .git directory containing the object database and branch references. Concurrent destructive Git commands, like force resets or branch deletions by one agent, can immediately invalidate references for sibling agents. This shared architecture can lead to broken operations such as diffing or rebasing if not properly managed. To prevent these issues, experts recommend restricting agents to non-destructive commands and having an orchestrator assign unique branch names.