Parallel Work Without Conflicts: Worktree Isolation for Agents

Start with the problem

The most common accident when running agents in parallel is conflict from sharing one working tree. While one agent edits files, another switches branches or overwrites the same file — and uncommitted work silently disappears.

The fix: git worktree

git worktree lets one repository have multiple working directories, each checked out to a different branch. Give each agent its own worktree, and they can work in parallel without stepping on each other's files.

git worktree add ../agent-a feature/agent-a
git worktree add ../agent-b feature/agent-b

Each worktree has its own branch and file state, so A's unfinished changes are invisible to B.

When to isolate

• When two agents might touch the same file or module.
• When trialing a risky refactor apart from the main line.
• When a failure must not pollute the main workspace.

Conversely, if agents only touch different files, isolation can be overkill — it carries a disk and setup cost.

When you merge

Commit often in each worktree, and integrate finished work via a PR. Clean up worktrees that weren't changed.

In Marblo

Marblo can spawn an agent in an isolated worktree when needed, so parallel work doesn't collide. Controllable parallelism — isolation is its foundation.