Make QM/MM code always compile
Brought all the old interfaces back to a state where they can always
compile regardless of the build configuration, and give fatal errors
if used from a configuration that didn't support the method.
When configured, this should work as before, but we have no ability to
test that in Jenkins.
Added some necessary const correctness.
Did QM/MM preparation all in the same place, to simplify runner.cpp
Added deprecation status to release notes.
Refs #2706, #2569
Change-Id: I4a6566c60bfbf27a7b1916be1874b36987fb7da5
12 files changed: