scanner: rework source root guessing code
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.
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