I think it's a cool idea, but you'd need some pretty hefty tests to make sure you still have a stable environment when it's done removing code. I hate to say it, but, despite using Linux 5 days a week and OS X for home use (and using Linux off and on for almost 20 years), I'm not familiar enough with GNU/Autotools, makefiles, etc. to figure out everything that's going on there without spending some time pouring over documentation.
One thing I did want to point out, though, is that the only real benefits to joining the files are for distribution (and most modern methods of distribution would minimize the benefit there) and obfuscation. On most sites, the difference in speed between loading 1 file vs. multiple files will be negligible, and you'd have to modify the loader (and a few other classes/functions) to deal with the change in location when loading the classes in the combined file(s).
