Have we discussed physfs before? Googling against "site:glest.org" didn't turn up much, but maybe it was lost in the big crash last year.
http://icculus.org/physfs/Physfs is an API that provides, among other things, some platform abstraction and the ability to easily work with archives (like .zip, .wad, etc.) which would give us the ability to distribute mods in a single zip file that you don't have to extract. Anyway, I was meaning to mention it at some point. It would indeed add "one more thing we link against and bloat the code with", but it will also allow us to nuke some code that I think is a bit ugly in our own project and have some unified interfaces for doing stuff. Since it's a C library, I do think we should make a C++ interface to it, however. I also think it can facilitate allowing Lua scripts to safely write data to directories where it's specifically allowed (as I was discussing in the 'Age-of-mythology-like "speech" in glest?' thread.
Anyway, I'm working on the 0.2.12 saved game issue right now and noticed that file access was one of the issues where confusion (and inconsistency) was an issue.