Editing TODO files
Commiting changes to FileMaster, and consequences.
Changing command line to use -p and -c options.
Merge branch 'devel' of github.com:/dmorse/simpatico into devel
Small corrections to user manual.
Adding -p & -c options to mdPp.
Fixing bug in Processor.cpp, cleaning examples
Cleaning examples
Merge branch 'devel' of github.com:/dmorse/simpatico into devel

Conflicts:
	examples/dihedral/N8/mc/AtomDisp/clean
	examples/dihedral/N8/mc/HybridMd/clean
	examples/dihedral/N8/md/param.nve
	examples/dihedral/N8/md/param.nvt
	examples/worm/dd/clean
	examples/worm/mc/AtomDisp/param
	examples/worm/mc/HybridMd/param
	examples/worm/mc/Reptation/param
	examples/worm/md/clean
	examples/worm/md/job
	examples/worm/md/nve/clean
	examples/worm/md/nvt/clean
	examples/worm/md/param.nve
	examples/worm/md/param.nvt
Cleaning examples
Cleaning up & documenting examples.
Removing explicit output with append from FileMaster.
Cleaning up FileMaster
Fixing documentation of FileMaster.
Cleaning doxygen documentation.