Header File Issues

[jehicken]

Remove redundant header includes from .cpp files.

Also, header files should be included as follows:

1. System (C++ libraries) level headers
2. Other dependencies (e.g. mfem, Adept,...)
3. Our own (mach) headers

There should be a space between each of these groups. Here is an example:

#ifndef MACH_SOLVER
#define MACH_SOLVER

#include <fstream>
#include <iostream>

#include "mfem.hpp"
#include "adept.h"
#ifdef MFEM_USE_SIMMETRIX
#include <SimUtil.h>
#include <gmi_sim.h>
#endif
#ifdef MFEM_USE_PUMI
#include <apfMDS.h>
#include <gmi_null.h>
#include <PCU.h>
#include <apfConvert.h>
#include <gmi_mesh.h>
#include <crv.h>
#endif

#include "mach_types.hpp"
#include "utils.hpp"
#include "json.hpp"

[tuckerbabcock]

Also, header files should only include other header files if absolutely necessary, we should prefer to have the .cpp files do the including they need for implementation, and use forward declarations in headers where possible.