Improve model abstractions

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 (#517 / https://github.com/PEtab-dev/libpetab-python/pull/517#issuecomment-5566488336)
• 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.

Start by reading petab.v1.models.model.Model and the discussion in #517, including the linked pull request comment. Map how derived parameters and is_state_variable are used across the package before proposing changes. Done means the model abstraction reflects the constant, differential, and algebraic taxonomy without conflating simulator decisions.