Thought I had it all sorted out but got stuck on this detail:

From a user stand point, is it better to encode the whole zip file which then is unpacked in correct places or is it better encoding only the obj file? 
How do either way work with Mac and PC?
What is your user/provider experience of this?

The file has to work for both Mac and PC users, I'll be using RTeJava.
Good and bad solutions, any suggestions will be appreciated.
Thank you guys for your patience.