Make inputrec const at simulator level (leaves some TODOs)

Make inputrec const at simulator level (leaves some TODOs)

This does not resolve the last few instances that change inputrec, but it
makes sure that the intent of inputrec being const is clear, and that future
code changes don't easily introduce additional non-const uses of inputrec.
See !46 for a similar change targetting the global topology.

Refs #3854.