Optimized OFile

Removed many scans of the output buffer by keeping trace of buffer length.
Time needed to write a long line with a sequence of file.printf() is
now linear with line length. Before it was quatradic, causing problems
especially when logging huge atom lists at startup.
Fix

cmd("useNaturalUnits") was erroneously crashing
Fix

Running a LJ in LAMMPS (no charges) was crashing
Small optimizations

Relevant when using a huge number of restraints
Fixed bibliography
Fixed links in doc
Merge branch 'v2.0'
Merge branch 'master' into walkers-mpi