Claude Code Is The Best Worktree Manager
Built-in worktree managers are guaranteed to be limited. They usually assume one repo, Git, a blessed branch flow, and a product team's idea of what setup should mean. Real codebases do not stay inside those lines.
The Zen of cmux is that developers should build their own tools and explore the search space of ways to work with code. Worktrees are one useful primitive, but so are multiple checkouts, backend/frontend repos in different folders, remote machines, no-git projects, local scripts, and occasionally just coding on main because it is the fastest thing for that task.
The super repo pattern
A super repo is one control checkout that knows where all the real repos live, how worktrees are created, how related repos are paired, which scripts prepare each workspace, and how PRs get reviewed and merged. cmuxterm-hq is a super repo: it contains the primary cmux checkout, per-task cmux worktrees, Zed checkouts, hq scripts, reusable skills, and the rules agents follow to avoid stepping on each other.
The point is not that everyone should copy this exact directory tree. The point is that one local control repo can describe your whole engineering operating system. A backend repo and frontend repo can be opened together. A mobile app and web API can be reloaded together. A branch can be created in one repo and a matching branch in another. That shape belongs to your team, not to a generic worktree button.
Let the agent manage the worktrees
Claude Code and Codex are better worktree managers than most built-in worktree managers because they can read your repo rules, run your scripts, create worktrees across multiple repos, clean up their own worktrees, fix conflicts, push branches, open PRs, and merge after CI and review gates pass.
Our most-used flows are task-worktree-pr and autoreview. They work because agents can read files, write files, run commands, inspect GitHub, wait for CI, respond to review comments, and operate across repositories. If a task needs cloud and desktop changes together, you can tell the agent to look in both places and let the super repo encode the rest.
Why built-in worktree support loses
A product-level worktree feature can be polished for the common case, but the edge cases arrive immediately: no Git, several repos, generated clients, private setup scripts, paired backend/frontend branches, unusual merge policy, or a team that intentionally pushes to main for small internal changes.
A programmable workflow can adapt. Ask Claude Code to create a worktree, start Codex beside it, run the setup command, open the right browser pane, watch tests, and remove the worktree when the PR merges. Then change that workflow tomorrow.
cmux gives the workflow a surface
cmux does not need a built-in universal worktree manager. It gives you custom commands, a programmable CLI and socket API, and reusable skills. The plus button can launch your own worktree command, multi-repo setup, no-git sandbox, or remote environment.
That is why cmux home matters. The best worktree manager is the one your agents can change when your workflow changes, and the best terminal for that loop keeps notifications, Cmd+Shift+U, and Cmd+Control+U wired into the surface.