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.
remove dead code from fix colvars
fully case-insensitive test for .xyz extension
moved file reader functions from inline to regular object
small changes to silence harmless warnings with g++ -Wall
disable fit gradients when they are being handled by the auxiliary ref group
Refactored colvarbias_harmonic to colvarbias_restraint and colvarbias_harmonic and added
colvarbias_alb

I've refactored colvarbias_harmonic to be a colvarbias_restraint so
that there may be code re-use between a linear and harmonic
restraint. This also allows me to place the colvarbias_alb, the
adaptive linear bias, into the class hierarchy. This commit also
includes the initial version of the colvarbias_alb implementation.
added missing word in a doc sentence
Added an equilibration period, changed variable names for coupling
constant, and simplified algorithm

Added a correlation time to allow equilibration when bias is added and
when statistics are gathered. Also modified README with fork
notes. Decided to go with simpler/correct method since that's what I'm
going for in the paper.
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
Updated README.md with license