Clean up the Makefile and reorganize source files and directories

[sseyler]

Create a cleaner Makefile with proper recipes and more efficient building. Also, reorganize the directory structure so that build files will be separated from the source files. Probably will want to reorganize the top-level directories as well to accommodate the Python code that will be used for wrapping.

[sseyler]

The include statements and use statements can be conditionally included/excluded using a preprocessor. This might be useful for toggling some modules (e.g., random.f90). To manually turn on this feature in:

• gfortran: use the -cpp flag
• ifort: use the -fpp flag

Here's a good example of how this could be done in fortran: https://github.com/szaghi/OFF/blob/master/src/OFF.f90