Give MDModules responsibility for option handling
Centralized responsibility for option handling to avoid repetitious
code. This includes the (temporary) need to convert old-style mdp
options to key-value paths during the transition period, and the
ongoing need to integrate the default values declared by modules for
their options with the user's input (which will eventually be given in
key-value form).
Eliminated init_ir, after one of its responsibilities disappeared.
Noted TODOs for future changes.
Change-Id: Ifd763e050944055c1d51a416fa0f9f3a7682ec5d