Makefile Improvements

[zdevito]

Track headers correctly. Build dependency for making libOpt.a on API/o.t

[Algomorph]

Would you be interested in switching the build system to CMake? I've been having problems with the existing Makefiles and already have a working CMake skeleton around the code, please see #130 for details.

[Mx7f]

I would not mind a parallel build system committed in the tree; but it is unlikely to be the main build system in the near future.

[fabiencastan]

@Algomorph It would be great to have a cmake build system. Could you share it?

[Algomorph]

@fabiencastan, you can check out the skeleton code at my fork here.

The CMake skeleton is only for examples and the mLib library they all use, since that's what I had trouble building with the included Makefiles. Specifically, I made the full tree for volumetric_mesh_deformation example, but adding CMake for the rest of the examples should be trivial.

I haven't done CMake to build the Opt static library itself, and you might need to fiddle a little with the paths in Makefile.inc to get that to work. The biggest obstacles are the incompatibilities between multiple versions of Clang / Terra / CUDA (you'll find a ton of issues about this here), which sort of led me to abandon Opt, at least for the time being. When CUDA 9 / 10 are supported in Terra I'll give it another try.