Switch remaining main() functions and copyrite.c to C++.

Switch remaining main() functions and copyrite.c to C++.

Required to be able to use gmx::ProgramInfo from these (done in
separate commit), and simplifies the compilation of mdrun as well.

Resolved compiler/cppcheck/clang warnings that were present in these
files.  Some include file clean-up, motivated by the fact that force.h
causes warnings when included in C++ files, and fixing that requires
fixing #1294, where the solution is not yet decided on.

Change-Id: I69f4200c1c1783340d88381a6aca82151d1230cb