All the stuff was an attempt to integrate most of the patches from TOSPATCH (https://www.markusheiden.de/atari/tospatch.html) already when compiling, and in a safer way in case there are also other changes. Most of this should actually work, except for the WINX patches which are incomplete.
But note that, if you set BINEXACT to 1 again, it will ignore the defines, and create an "official" 3.06 version again. So depending on what you've changed, you might as well take the previous source archive. Some of the patches might be useful however, and some fix some actual bugs (take a look at common/patchdef.h for explanation).
Note also the i've split the archive, there is now one with the actual sources (http://tho-otto.de/download/tos306de.tar.bz2) that can used to compile it eg. on Hatari, and another one with all the remaining stuff (http://tho-otto.de/download/alcyon.tar.bz2, sources of the alcyon compiler etc.) That second archive also contains the various makefiles to compile it on linux. That split was needed to make the sources fit on a 16MB harddisk image.
I hope i didn't miss anything again

