Combined fixes and updates to gen_multimap.py

Allow different deformation amplitude between leaflets, small fixes

Fix reading input from --deformation-map-mask option

Issue identified by @1004parky, mask map was initialized to 1 in all cases.

Silence NumPy warnings

Small fixes

Fix handling of PDB files in generated VMD input

Make single-map CVs optional

Allow customizing selection for COM and orientation restraints

Make generated NAMD and VMD scripts more uniform

Unify writing of Colvars input between NAMD and VMD

Add support for mapFile keyword