Bond/react custom group support

update reference for SPIN package

enables consistent syntax when using custom groups

Update Colvars library to version 2018-10-16

thanks to Sagar Patil for report

rebase

Various small fixes

Bond/react: update edges option

option to update all atomic charges, even when edge atoms are defined

rebase

Reduce namespace pollution for VORONOI package

Bug fix for merge sort by Jeffrey Frey

Updates to contributing guidelines

rework some of the pull request instructions to be realigned with the recent changes in the workflow.

reorder operations in init() to fix a bug with compute chunk/atom del…

Patch release 24 October 2018

Bug fix for Kspace refactoring in USER-INTEL package

More Documentation consistency improvements

Enable use of fix halt for minimizations

Refactor kspace base class to have a settings() method

Implement dummy classes for deprecated and removed styles