Recover jenkins test builds

Retyping parameters bugfix

rebase

Consistency tweaks to various package Install.sh files and related shell scripts

the qeq/fire style depends on pair style comb,
thus QEQ needs and explicit Install.sh file and
it has to depend on MANYBODY

Output individual energies in fix restrain

C++ style header includes and C++ standard conforming code changes in lib folder

Remove Kokkos deprecated code

rebase

cmake: remove obsolete BODY/POEMS conflict

More fixes to conform with C++ standards as indicated by Clang

Docs update and journal reference for USER-CGDNA package

Computation of forces/torques on rigid bodies moved to post_force