Patcher
Simply take one version and a higher version of the same programs, run this, and it'll make a patch to update the orginal file to whatever version the higher version was. (Basicly you take a V .02 and a V.5 of the same program. The patch will equal the diffrence between their sizes and can be applied to and version >.2 and <.5 to update it to V.5)
Not really sure how diffrent versions of this file would work though. It could be 2 diffrent programs though. (One to create the patch, one to apply it)
Archiver/Compressor
Basicly it compresses a file into a smaller size. Like encryption, the file would be unusable until decompressed. Two diffrent programs, one to compress, the other to decompress.
Don't like the patcher idea. It ruins research in a sense, the same way Steal Research File missions do now.
I like the compressor however, I have suggested it before.