Added trivial const qualifiers

Added trivial const qualifiers

Const qualifiers were added to function arguments. No changes were
made inside function bodies, except for adding const qualifiers to
convenience references within functions. These changes help the
development of a MD state object, as they reflect more clearly where
write access to data is _really_ needed.

Refs #2616

Change-Id: I779b4dfed2fbd0ad129e226c9b535ed97a8bb01f