Need to add documentation

[bremerm31]

I would preferably use doxygen.

[bremerm31]

The files in the following directorires need to be documented

• [x] source/basis
• [x] source/basis/polynomials
• [ ] source/communication
• [ ] source/geometry
• [x] source/master/
• [x] source/master/elements_2D
• [ ] source/problem/SWE
• [ ] source/simulation
• [x] source/integration
• [ ] source/preprocessor
• [ ] source/preprocessor/ADCIRC_reader
• [ ] source/shape
• [x] source/utilities
• [ ] partitioner
• [ ] mesh_generators