Removing iteration + constraints framework

Getting rid of iteration + constraints required by the use of MTTK +
constraints, in order to simplify the main loop.

Eliminated related variables and arguments that are now unused.

Left some otherwise useless brace pairs in do_md(), so that
uncrustify-friendly formatting was preserved, so we can more easily
review this for correctness. Left TODOs to remove those braces later.

Implemented mdrun check so that an old .tpr with MTTK + any form of
constraints cannot be run.

Refs #1137

Change-Id: I22816de7db4420a66341fa8bf35d967a71ad6568