IO Robustness

[ptheywood]

Increase the robustness of input and output classes/methods.

The initial implementation(s) are lax in checking for existing files, producing sensible error messages, race conditions with multiple simulations attempting to write to the same paths etc.

This should be drastically improved (and ideally tests implemented)

Additionally, output files are emitted at the end of the simulation, requiring an ever growing volume of host memory during the simulation and on output. This is probably OK for planned model scales and simulation durations for some/most output files. Per infection event may be problematic if implemnented and there are many infection events.