I had noticed that worktrees that were created by my AI agent in the .worktree subdirectory of my top level project were not showing up in the list of worktrees to be opened. When I went to try to create one using worktree manager, it showed the location it was going to create them in was in /.git/modules/s3/nginx/.worktrees rather than /.worktrees, which is where I guess it is also looking for them. s3/nginx is a subtree attached to the main repo.

I had noticed that worktrees that were created by my AI agent in the .worktree subdirectory of my top level project were not showing up in the list of worktrees to be opened. When I went to try to create one using worktree manager, it showed the location it was going to create them in was in /.git/modules/s3/nginx/.worktrees rather than /.worktrees, which is where I guess it is also looking for them. s3/nginx is a subtree attached to the main repo.