make_analysis needs redesigning+cleaning up to utilise plug-ins

[christuart]

At the moment, the make_analysis method contains things which should go into plug-ins. This will make the code more clear, and also allow the user to stop them from happening from the UI, meaning that other plug-ins can augment all elements of the simulation.

E.g.
if (settings.contamination_mode_time == "constant" && settings.contamination_mode_space == "constant") { ...

This in fact isn't the only method that needs this - initialise manually checks for source sections rather than allowing interrupt_element_link_creation(...) or interrupt_pre_simulation() methods to vary the behaviour

[christuart]

Simulation timing is another aspect that should be moved into a plug-in. The plug-in may need to make sure that it is the last item in the 'pre-simulation' and 'post-simulation' vectors, or it may do something like checking for the 0th and (steps()-1)th steps and using those to time things?