Hi all,
This is a known limitation in the Agents Window (Glass layout). The sidebar currently groups chats by repository (based on the git remote URL), so worktrees and multiple clones of the same repo appear under a single section rather than separately.
Per-worktree sidebar grouping in Glass is being worked on. In the meantime, worktrees are still available via the /worktree slash command in agent chat, which creates an isolated checkout for the agent to work in. More details here: Worktrees
A few related threads for context:
For per-worktree sidebar separation right now, your best options are:
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Switch to the Editor layout (Cursor Settings > General > Layout) – the Editor layout preserves per-folder scoping, so each worktree gets its own sidebar context
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Multiple Cursor instances per worktree (as Dmitrijs mentioned)
I understand this is a blocker for adopting Glass, especially for monorepo workflows. Your feedback here helps with prioritization.