Improve model abstractions

[dweindl]

The current model abstraction in petab.v1.models.model.Model isn't great. Non-exhaustive list of problems:

• We don't have proper handling of derived parameters (Evaluate BNGL parameter expressions instead of dropping them #517 / Evaluate BNGL parameter expressions instead of dropping them #517 (comment))
• is_state_variable conflates different questions. The simulator decides what's treated as a state variable - that's none of PEtab's business.
• Ideally, the library would more closely adopt the specs' taxonomy regarding constant, differential, and algebraic entities.

Improve that. This will probably impact quite a number of places and needs to be addressed carefully.