Git Worktrees Management

Running multiple autonomous AI coding agents in the same working directory creates write collisions, dirty git indexes, and accidental merge conflicts.

Quay 2 solves this by integrating native Git Worktree management directly into your workspace workflow.

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Why Git Worktrees for AI Agents?

E:\Projects\Quay2\                <-- Main Repository (master branch)
├── .git/
├── src/
└── .worktrees\
    ├── feat-auth\                <-- Isolated Worktree (Branch: feat/auth)
    │   └── (clean working tree)
    └── fix-conpty\               <-- Isolated Worktree (Branch: fix/conpty)
        └── (clean working tree)

Quay 2 creates each worktree in a .worktrees folder inside the project, in a folder named after the branch.

By assigning each autonomous agent to its own dedicated worktree:

• Zero Collision Risk: Multiple agents edit, compile, test, and commit concurrently without clobbering each other's unstaged files.
• Instant Branch Switching: No waiting for git checkout or git stash to clean your directory.
• Shared Git History: All worktrees share the same underlying .git object store, saving disk space and eliminating redundant fetches.

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1-Click Worktree Creation (Ctrl+B W)

Pressing Ctrl+B W opens the New Git Worktree dialog for the active project. The dialog's footer shows the project folder it will use.

1. Branch Name: Enter a branch name (e.g. feat/oauth2), or click a prefix button (+feat/issue-, +fix/issue-, +wayfinder/issue-) to start one. The label beside the field shows the folder the worktree will get, .worktrees/<branch>, with each / or \ in the branch name replaced by -. For example, feat/oauth2 goes in .worktrees/feat-oauth2.
2. Create as new branch: Checked by default. Quay creates the branch from the base branch in the from field, which defaults to main. Uncheck it to check out an existing branch instead.
3. Launch Claude Code terminal immediately: Checked by default. Quay opens a Claude Code terminal inside the new worktree as soon as it is created.
4. Click Create Worktree.

Quay always creates the worktree from the project's root repository. Pressing Ctrl+B W while a worktree is selected adds another worktree of the project, never one nested inside the selected worktree.

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Collapsible Navigation Rail Hierarchy

To preserve vertical real estate in your sidebar when managing repositories with dozens of worktrees:

• Secondary worktrees under each project start collapsed by default.
• Click the chevron next to Worktrees (N) to expand or collapse the worktree list.
• Smart Focus Dot: If your active terminal belongs to a worktree that is currently collapsed, Quay 2 displays a distinct blue dot on the worktree header, alerting you that the active session lives inside.
• 1-click New Terminal in Worktree (+) and Remove Worktree (trash icon) buttons appear when hovering over any worktree row.
• Safe removal: before closing any terminal, Quay checks the worktree for modified or untracked files. If it finds any, Quay shows the refusal git worktree remove would give, with the changed files, and leaves the worktree and its terminals untouched. If removal fails for another reason, Quay shows git's error in the same dialog. Remove anyway closes the worktree's terminals and runs git worktree remove --force, which discards those changes.