Minor fixes to Colvars module

Update Kokkos library to v2.03.13

Implementing short neighbor lists for three-body gpu styles

Fixes for stable

More tweaks for stable release

The default compiler flags in voro++'s config.mk file do not include
-fPIC, which makes it incompatible with building the shared object for
the python wrapper.

This reverts commit 4e97b575.

when recomputing special bonds, make certain we do not shrink atom->maxspecial and add force->special_extra only once

Final tweaks and doc changes for stable release

correctly use the term CUDA (instead of Cuda) when not referring to the KOKKOS device flag (which is Cuda)

Final build system changes for stable release

remove attempts to use urllib and use curl for all downloading. restore printing help with no flags.

- remove cross compiler stuff
- make use of Install.py consistent
- provide options for Makefile.serial and Makefile.mpi that match those in src

Installation scripts and docs reviewed for release