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
Added support for multidimensional centers and tweaked the running lipschitze estimate.

Changed initial lipschitz estimate (coupling_accum) from 1 to 0, since
it was heavily influening small step sizes
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
Some varaible name changes to be more succinct and consistent. Added new max coupling rate change that will temper some of the aggresive first steps in the program. May be initially set or are guessed from updateFreq