Why Git Worktrees Fail as Isolation Boundaries for AI Coding Agents

Git worktrees are not an isolation boundary for coding agents

I discovered that Git worktrees do not provide true isolation for AI coding agents because they share critical repository state like hooks and configuration. An agent in a worktree can execute code on your host or rewrite your commit identity. My benchmarks show that using a fully isolated clone costs the same in time and disk space, making it the only safe option for running agents in parallel.