GitHub Desktop 3.6 Adds Worktrees and Deeper Copilot Integration for Commits and Conflicts

GitHub Desktop 3.6 is out today, and it has two things worth paying attention to: native worktree support and Copilot features that actually know your codebase’s conventions.

Worktrees

Git worktrees let you check out multiple branches at the same time in separate directories, running off a single repository. Desktop now surfaces this with a “Current Worktree” button in the toolbar, so you can switch between them without stashing or cloning.

The feature is especially relevant if you’re running coding agents. Both Claude Code and GitHub Copilot’s agent mode spin up worktrees to run isolated sessions in parallel. Being able to see and manage those from the desktop app closes a gap that previously required dropping into the terminal.

Copilot Commit Authoring

Commit message generation was already in Desktop. The 3.6 version is more aware of where it’s running. It now reads .github/copilot-instructions.md and AGENTS.md for custom instructions, and it respects commit metadata rules defined for the repository, things like conventional commits format, required issue references, or character limits.

That means the same commit style enforcement that Copilot follows in VS Code should now carry over to Desktop. If your team has rules, they apply here too.

Every Copilot feature in Desktop also gets a model picker in this release. You can use any model available through your Copilot plan, or bring your own key from a third-party provider or a locally running model.

AI Merge Conflict Resolution

The merge conflict view now includes a Copilot panel that explains what changed in each side of the conflict and suggests a resolution. You review it, accept or edit, and complete the merge.

The explanation piece is the more useful part. Conflicts in long-lived feature branches can be hard to reason about when you weren’t the one who wrote the conflicting code. Having the model narrate what each side was trying to do gives you something to work from.

One SDK Under Everything

All Copilot features in Desktop share the same Copilot SDK that GitHub has been rolling out across their tools. Commit authoring, conflict resolution, model selection, and BYOK all run through a common foundation rather than being independent experiments bolted on separately.

GitHub Desktop 3.6 is free to download for macOS and Windows. The Copilot features require an active GitHub Copilot subscription.

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Source: GitHub Changelog: GitHub Desktop 3.6