added missing word in a doc sentence
read and parse index file in binary mode

seek on text files is not reliable on windows due to the
automatic CR-LF conversion. the file stream will not be
repositioned correctly. since the parser itself can handle
files with LF and CR-LF conventions equally well, opening
in binary mode should work, even when reading LF terminated
files on windows and CR-LF files on linux
Add colvarvalue and colvarfreq for NAMD Tcl

From Mikolai Fajer. Add the internals for the two Tcl routines that
are useful for swarms of trajectories.
fixed doc error for enableForces; agnostic energy units
edited warning message to be consistent with Usage Case 6
Add XYZ parser

Transparently replaces the PDB parser when file extension is xyz or XYZ.
Remove unused variable
added LGPL version 3 text file
Update README.md
Small text fixes
Initial import of abf_integrate
Add data consistency checks in abf_integrate
More consistent extended DOF force trajectory

Extended Lagrangian colvars now output applied and system forces
that are more consistent with non-extended ones, and more clearly
documented. Only affects the content of the colvar trajectory.
update LAMMPS code to match the current LAMMPS distribution
added simple makefile for colvartools
Update colvars ref paper
Improve documentation of ABF fullSamples
reorder colvaratoms initializer to silence GCC
fix bug due to uninitialized variable in LAMMPS proxy class

This fixes the bug report by Michalis Palaiokostas-Avramidis
from 2014-04-16 on the lammps-users mailing list. When reading
a restart the colvarsRestartFrequency is initialized to the value
of the restart_every member variable. however, this one is only
set, when either a restart command is included in LAMMPS, or
colvarsRestartFrequency is set explicitly.
update LAMMPS sources to be compatible with current LAMMPS versions.

NOTE: this will break compatibility with older LAMMPS versions, but
there is not simple way to have it both ways.