need to resize per atom arrays after we know whether extended flags are used
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12637 f3b2605a-c512-4ea7-a41b-209d697bcdaa
update some custom makefiles for recent changes in build system
update Makefile.shlib to be in sync with the standard makefile
disallow using fixes from the QEQ package with newton pair off
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

Resolved Conflicts:
	src/pair_hybrid.cpp
update C++ headers with emacs mode cookies
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12638 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12639 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12640 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12642 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12643 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12644 f3b2605a-c512-4ea7-a41b-209d697bcdaa
update colvars to state of 2014-10-21 with some additional refactoring
add basic multi-replica support for colvars
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

Resolved Conflicts:
	doc/Manual.html
	doc/Manual.txt
	src/USER-CUDA/fix_set_force_cuda.h
	src/USER-CUDA/pair_lj_sdk_cuda.h
	src/USER-FEP/compute_fep.cpp
synchronize with the colvars git repo again
update colvars library to version 2014-10-23
gpu library updates from trung