Update API and docs for subsystems

[isaacsas]

Follow up to #404 to make as many API functions work with subsystems, and give an error message for those that don't support a ReactionSystem with subsystems.

Main changes:

1. species, reactionparams, and reactions now collect the states, parameters, and Reactions from only those subsystems that are ReactionSystems. This leaves the normal MT API (states, parameters, equations) to return larger sets that may include components from non-ReactionSystem subsystems. This seemed like a reasonable division to me, but we'll need further doc updates to make the distinction clear .
2. Depreciated with a warning params and numparms since we now have either parameters or reactionparams depending on what a user wants.
3. Depreciated merge since we now have MT.extend.

[isaacsas]

This should be good to go. Next would be adding @add_constraints.

[ChrisRackauckas]

lgtm. isequal_without_names is an odd name but it makes sense.

[isaacsas]

I’ll merge but change it if I come up with something better…