Adding command line options to the application class.
Merge branch 'use' of https://github.com/furious-luke/libhpc into use

Conflicts:
	src/main/application.cc
	src/main/application.hh
Some additions and bug fixes to the application layer,
the hdf5 layer, the debug layer and also adding an
algrithm to calculate displacements from counts.
Removing the use submodule so I can replace it, and
updating the usescript.
Trying to recover from removing a module.