Make setup_links.py handle non-link directories during cleanup

The trybots ended up in a state that could not be cleaned up
when other tryjobs were altering the checkout with different
variations of dependencies.

TBR=pbos@webrtc.org

Review URL: https://webrtc-codereview.appspot.com/46139004

Cr-Commit-Position: refs/heads/master@{#9110}