Allow for Make to recover from a previous failure better

Migrated from #594 (closed)

1. The port file had invalid data: it had something like 3000 echo 3001>port. This caused make to fail right out of the box, and nothing was set up properly. Perhaps earlier validation should be done here with a better warning message.
2. Even after fixing the port file, make didn't check out all the dependencies (e.g. gitlab-shell, gitaly, etc.). I had to run make gitlab-shell-setup and make gitaly-shell-setup etc. to get this working.