Fix repos with checked-in .gitmodules

Some repos have checked-in .gitmodules files from repositories that
are checked directly into repos, rather than being submodules. For
repos that leave the git configurations around, trebuchet breaks
during the fetch phase. This change checks to see if the .gitmodules
location is a valid top level repo by checking the status of
'git submodule status --quiet'.

Bug: 63029
Change-Id: I8b1fe930452a811d50fe3b0c8319f46d2faa318b
Merge "Fix repos with checked-in .gitmodules" into production