Update wave solver and improved dev documentation

This version is close to what the first public release will be. The solver for the Wave equation has been updated and we now have a specific reference and a one to one match between implementation and analytic derivation. For more details about the differences between the previous and current implementation, have a look at pull request #95.

Also, the code is now commented, Doxygen generated documentation is more readable for both dev and nondev types.