Replace individual dataframe arguments by Problem objects

Currently, have a number of functions that take several individual dataframes. It would be more convenient and future-proof to change them accept Problem instances. I'd suggest doing that in a 1.0 release instead of adding dozens of deprecation warnings. Most of those functions are probably anyways not really used outside PEtab.

Start by inventorying the functions that accept several individual dataframes and inspect the existing Problem API. Determine the migration scope and confirm that all affected PEtab-facing functions consistently accept Problem instances as part of the 1.0 release plan.