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
Merged license text