Patches to add doxygen support to build and add some comments.

[Jef Driesen]

On 09-11-16 00:06, Ryan McLean wrote:
> Depends on previous patches as I'm not sure how to just create a single patch
> for that one file with Git.

I applied part of your patches with the build infrastructure. I made a few 
changes to move the makefile bits to their own directory, and fixed a few issues 
as well. I left out the actual documentation changes, because I prefer the 
existing javadoc style.

So the build infrastructure is in place now. Thanks for your work!

Jef