Another double post, but I seem to be the only one trying to keep this thread up to date. As of 30 December 2015, this is what you need to do to build the latest source using the latest devkitpro (r45). I'm sure this will be resolved soon.
1) Install r45
2) git clone --recursive
https://github.com/smealum/ctrulib -> make -> make install
(this is because there have been a couple of commits since r45 was released, and those commits look important to me, like reversed registers and such)
3) git clone --recursive
https://github.com/mid-kid/CakeHax -> make (while in the Cakehax directory)
4) git clone --recursive
https://github.com/mid-kid/CakeBrah -> make (while in the Cakebrah directory)
5) git clone --recursive
https://github.com/roxas75/rxTools.git
6) delete the Cakehax and Cakebrah folders from the rxtools source
7) Copy the Cakehax and Cakebrah folders that you cloned into the rxtools folder
8) make release (in rxtools folder)
Edit: as of this moment (1 Jan, 1345 JST)(until the changes get reverted) after cloning the rxtools repo, you should also do "git checkout a08cfdd" from inside of the main rxtools folder. Changes after that the last few days severely broke the build.