`java.lang.AssertionError: Can't get .git directory from repo root path when git root removed`

[PawelLipski]

To repro, add a new git root in the project, open Git Machete tab (make sure that there are git root to select from the dropdown), and then remove .git folder from the newly-added git root. Git Machete won't reload the git roots, and will try to operate on the non-existent git root. As a remedy, add some extra check + issue a warning about removed git root.