Improve speed of large models initialization (e.g. plastic forces)

Large models were initialized really slowly due to deserialization
process. Each time a new atom, radial bond or angular bond was added,
invalidation change hooks were called. That was causing large number
of unnecessary recalculations of the model state. So, while adding 250
atoms, state was recalculated 250 times.

Now add functions are configurable, so they can skip triggering change
hooks. They are instead managed by the deserialization functions.
Rm duplicated actions from makefile rule

$(MAKE) convert-mml does exactly the same thing.