Reorganization of the code and new program.

A lot of changes in this commit:

   1. Added the spectrum calculation to the spectral module.
   2. Added a program to investigate nonlinear aliasing.
   3. Reorganized files into core and executables folder. Adjusted CMake for
      these changes.
   4. Added aliasing analysis folder and plots.
   5. Added more options to the IO module for file output. This is mainly to
      accomodate outputting spectra.