Have a coding agent work in a separate Git worktree when you want its edits kept out of your active checkout. A worktree gives the agent a distinct working directory, making independent or experimental tasks easier to review before you integrate them. It is code-workspace isolation, not a security barrier: it does not by itself restrict the agent’s commands, network access, or access to other files on your machine.
What a “copy” means in Git
A Git worktree is a separate working directory linked to the same repository. You can check out another branch there and let an agent modify that tree while your main checkout remains on its own branch and files. Git worktrees share most repository data; per-worktree details such as the current HEAD and index are kept separately. In other words, a worktree is not a full, independent clone, but it does separate the files the agent edits from those in your active checkout. See the Git worktree documentation.
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When to use a worktree—and when not to
| Situation | Better fit | Why |
|---|---|---|
| The task can start from committed code, and its edits should stay out of your current checkout. | A separate worktree | You can review the agent’s changes separately and integrate them after you are satisfied. |
| The agent needs your current uncommitted edits, untracked files, or other files in the active project folder. | The current folder | A new worktree starts from committed files on its selected base branch; it does not automatically bring over those local files. |
| You want several independent agent tasks to proceed in parallel. | Separate worktrees or isolated agent sessions, where supported | Each task can work in its own checkout rather than changing the same active directory. GitHub describes isolated sessions for parallel tasks in its GitHub Copilot app agent sessions documentation. |
| You need to limit filesystem, network, or credential access. | Sandboxing or other permission controls | A worktree separates code edits, but does not enforce those operating-system-level restrictions. |
VS Code recommends using the current folder for small interactive tasks that should use the files already in the workspace, and a new worktree when changes should be separated from that workspace. Its agent harness documentation explains the distinction.
What a new worktree does—and does not—bring along
A managed worktree in VS Code requires a Git repository with at least one commit. When created, it starts from committed files on the base branch you select. Do not assume it includes your primary checkout’s uncommitted tracked changes or untracked files.
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Ignored files are also absent by default. That can include a local .env file or installed dependencies. VS Code documents options to copy ignored files and an experimental option to symlink them. A symlink points back to the original file or directory, so edits made through it affect that original location rather than providing an isolated copy. Check the VS Code documentation for the available worktree settings and their current status.
If the task depends on local setup, decide how to provide it before starting: commit the necessary non-sensitive files, recreate dependencies in the new directory, or use a deliberate copy or sharing method. Avoid copying secrets into an agent workspace unless your permission model permits it.
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Create, review, and integrate the work
With Git, a straightforward approach is to create a branch and worktree for the task. For example, from the repository’s main working directory:
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git worktree add -b agent/task ../repo-agent-task mainThis creates a branch named agent/task in a sibling directory named repo-agent-task, starting from main. Replace main with the intended base branch. The command requires that the named branch and directory be available; if the branch already exists, use an existing-branch form or choose another branch name. Point the agent at the new directory, not the active checkout.
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- Confirm the starting point. Check that the chosen base branch contains the committed code the task needs. Bring over or recreate any required local setup separately.
- Let the agent work in the task directory. Keep the agent’s instructions and tools pointed at that worktree, and do not treat the separate directory as a restriction on what commands it may run.
- Inspect the changes before integration. Review the diff, run relevant tests, and resolve any issues. A separate checkout makes review easier; it does not make generated changes automatically safe or correct.
- Integrate deliberately. Merge or cherry-pick the task branch, or use your normal pull-request workflow. GitHub Copilot sessions and Cursor’s worktree documentation likewise frame isolated work as something to review and bring into the main project.
- Remove the worktree when finished. After retaining or integrating any needed work, remove the linked directory with
git worktree remove ../repo-agent-task. Git documents this command and other worktree management details at git-scm.com/docs/git-worktree.
Isolation is not sandboxing
A worktree keeps ordinary edits in a different working directory; it does not limit the agent’s command execution or network access. VS Code explicitly distinguishes worktree isolation from those controls. If you need to limit which files tools can access, whether they can use the network, or which credentials are available, configure sandboxing or appropriate permissions separately. GitHub’s agent sessions documentation describes local sandboxing as a way to restrict filesystem, network, and credential access available to agent-run tools.
Choose the control that matches the risk: use a worktree to keep task edits away from your active checkout, and use sandboxing or permission controls when the agent’s capabilities also need limits.
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