Ignore repositories deleted during a file walk

When starting a file walk, a directory listing is first taken and then each of the directories are walked in lexicographical order. If a directory not yet walked is deleted after the file walk was started, WalkFunc receives a 'not exists' error. This commit ignores those errors/directories instead of aborting the walk.

Includes changes to test helpers in order to clone test repos in a test specific storage rather than the shared test storage.

Closes #2611 (closed)