commonprefix doesn't work on relative paths and doesn't return directories so
so for the g-i build case it returned an empty string resulting in paths
relative to the working directory, making the build not reproducible.

To somehwat improve this make sure the paths are absolute, use commonpath
and if no common dir can be found just fall back to passing all directories
so we only write the basenames.

I guess we should look into passing --sources-top-dirs in the g-i build.