If you use git worktree to add additional worktrees and try to use the plugin there, it fails to find the Git repository. The reason is, that JGit even in 4.6 does not yet support linked worktrees, but there is work done. See https://bugs.eclipse.org/bugs/show_bug.cgi?id=477475 for further status information regarding the feature in JGit.
If you use
git worktreeto add additional worktrees and try to use the plugin there, it fails to find the Git repository. The reason is, that JGit even in 4.6 does not yet support linked worktrees, but there is work done. See https://bugs.eclipse.org/bugs/show_bug.cgi?id=477475 for further status information regarding the feature in JGit.