Fix reaction equality in sets and add upconversion to ODESystems in convert

[isaacsas]

1. Adds hash on reactions so they work properly in dictionaries and sets, fixing issetequal for collections of them.
2. Uses convert_system for upconverting non-ReactionSystem subsystems when possible, throwing an error when an appropriate convert_system does not exist.
3. Added back exports of depreciated functions (we can keep them exported with warnings for one major release cycle).