Well, from my point of view, the very first thing you'd want to do to get the repo ready is to rename master into some other branch and get the current 2.50.x branch as master. Since that should take all of 5 minutes ... I'm not really sure what exactly you guys are doing.
Anyway, as for building on linux - the only problem I had was the sound only working with oss, which I'm pretty sure I've narrowed down to how allegro was built. Since we're not interested in allegro 4.4 right now, and I won't be able to get ZC's frakenstein version of 4.2 to compile without tens of hours of work, I don't really have much more to contribute to the discussion. Take a look at my makefile if you want. It's considerably shorter, and halfway decently commented.
(The actual changes to ZC making it compatible with 4.4 amounted to around 15 lines of code. And that was all
undoing the changes that somebody decided to hack into ZC's allegro because having threadsafe file loading is vitally important.
)