Simple examples (as integration tests)

[paulflang]

This PR deprecates #1 and #2 .

I could not implement the test cases

• toy_model_species_granularity_1
• toy_model_species_granularity_2
• toy_model_emergent_agent()
• toy_model_directionality()

from #2 as these require bond reactions with nontrivial domain (i.e. other than []). However, IIUC this would require handling of type mismatch between LHS and RHS, as two fully restricted agents on the LHS would create an agent with a new "emergent" site on the RHS.

[paulflang]

Network generation for the organic-chemistry example results in the error Species should already be added: "let bond_i [] in (Halo_dot [0.1, F []], Na [0.0])". Perhaps the first de Brujn index should be 0.0 and the second 0.1.