Add utility to detect duplicate anchors in docs

Library interface fixes, Python example fixes and better Python 3 compatibility

Added fix filter/corotate.

The interface of that function has changed and includes two additional
parameters, which haven't been added to the Python interface either.
This showed up by trying to run the simple.py example.

User cgdna

Add neigh/qeq option to Kokkos package

flow/gauss documentation update

Correct a typo in the fix_halt.txt documentation.

Colvars update 2017-03-10

Fix Kokkos issues

Add alloc flag to ev_setup

Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp

Fix spelling "correction" from 3a054d1a: iterations not interactions and imd_writen not imd_written