MERGE OpenMD development 1783:1878 into trunk

MERGE OpenMD development branch 1465:1781 into trunk

removing cruft (atom numbers, do_pot, do_stress) from many modules and
force managers

Updating visitor architecture to something a bit more modern

Almost all of the changes necessary to create OpenMD out of our old
project (OOPSE-4)

fixed a spurious visitor deletion

Added a few visitors

Changing utility programs to use the new file format

adding a gay-berne switch to Dump2XYZ

adding AtomNameVisitor to convert atom name to its base name; wrappingvisitor
now wrap back to the center of the mass; adding P2OrderParameter into StaticProps

xemacs has been drafted to perform our indentation services

avoid building parallel executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps

adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into
ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;

adding LipidTransVisitor, GofXyz is working now

update help info

remove SelectionVisitor

(1) complete section parser's error message
(2) add GhostTorsion
(3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor

minor fix

Added the linear visitor

change Makefile to relative path