Hmm, the baselibc and libfixmath are defined using svn:externals. It should automatically fetch them when you do a svn checkout:
Fetching external item into 'logic/baselibc'
...
Fetching external item into 'logic/libfixmath'
...
You will have to cd to the baselibc directory and type make to build it first.
I have used CodeSourcery 2011.09 for building the logic app. It’s GCC 4.6.1. Apparently my code has some stuff that newer GCC versions complain about, I’ll fix those when I get around to working more on the logic app.
I just did a fresh checkout of logic and it built correctly, so all the files should be there.
Currently the QuadPawn code is the newest and cleanest. It also prints some debug to serial port at 115200 bauds, so you can use it to check that your serial connection works.