bootstrap: Only override base cfg files if they are git tracked

When bootstrap is run once, all files are updated
properly. However, as it runs on subsequent times,
modifications in the base cfg file will be ignored,
since the files were already populated. So, add the
additional criteria that the base cfg files can only
be overriden if the test specific file is git tracked.

This way, */update_config.py will always produce the
desired effect (actually replacing the local test
cfg files with the new, modified files).
Signed-off-by: NLucas Meneghel Rodrigues <lmr@redhat.com>