For good measure I added another commandline option to the techtree and faction validators so now you can see a list of files that are NOT used by your techtree or faction using:
./glest.bin -validate-techtrees=megapack
To automatically delete this files you add this option:
./glest.bin -validate-techtrees=megapack=purgeunused
Please send your feedback and let me know if there are bugs.