SO I proceeded with the dir. reorg. last night and I have the head compiling and all that. I still have some other little tweaks, but the largest chunk (excluding packaging) has been committed.
Please make sure that I did not break anything. The icons and extensions folders now are inside share. Also, I put the svg files that were in icons (about.svg, keys.svg, and tutorial.svg) and put them into share/screens and updated and created a variable INKSCAPE_SCREENDIR instead of INKSCAPE_PIXMAPDIR for these files where accessed in help.cpp (this is defined in src/Makefile.am).
ISHMAL, could you please look and see how a fresh cvs windows build works. I have a strong feeling that a I broke it, as I have no test box and tried to conceptually follow what I did on the linux side. The part that might not work I'm pretty sure is contained in config.h.mingw and Makefile.mingw I believe. I became slightly confused after staring at weird makefile syntax for a couple of hours.
I will delve further into cleaning up the makefiles now that I understand automake and makefiles much better. There is sooo much legacy architecture and cheap hacks where the same paths are called in different places in the makefiles. Also, would you all agree that I should migrate the current recursive makefiles to just one top-level makefile? You all might also email me/the list a wishlist of how to clean up the source tree and the makefile nasties as they currently exist.
If you want to refer to the dir. reorg plan: http://inkscape.org/cgi-bin/wiki.pl?DirectoryReorgProposal
Thank you,
Jon