Remove deleted local repositories from the preferences

Currently, a local repository that is not (or no longer) associated with a project in the workspace remains in the Mercurial Repository Exploring view, even after being deleted. Upon deletion, the repository is removed, but it shows up again upon restarting the workbench.

I suspect this is because not all references to the deleted repository were removed from the preferences stored on disk, which causes the repository to be resurrected when the preferences file is read at the next startup.