Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into remote

Conflicts:
	includes/Resolver/PdbPreprocessor/pdbpreprocessor.hpp
	src/Resolver/PdbPreprocessor/pdbpreprocessor.cc
Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into remote

Conflicts:
	src/Resolver/PdbPreprocessor/pdbpreprocessor.cc
Merge branch 'remote' of /clients1/delaram/Projects/gems/gmml into remote

Conflicts:
	includes/Resolver/PdbPreprocessor/pdbpreprocessor.hpp
TopologyFile export
pdbpreprocessor final changes
Merge branch 'remote' of /clients1/delaram/Projects/gems/gmml into refactoring
Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into refactoring
TER card removal for atom cards without atom
Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into remote
lib_files parameter has changed to amino_lib_files, glycam_lib_files, other_lib_files
Amino acid chain - glycam residues
Pdb reader
Merge branch 'remote' of /clients1/delaram/Projects/gems/gmml into refactoring
Pdb preprocessor bug fix