[Feature request] - tidy output files

[alexvalentine94]

Is your feature request related to a problem? Please describe.

There are multiple output files from geouned in a single conversion -this is likely to grow.

Describe the solution you'd like

It may be better to organise outputs by a minimal set of folders. Something like:

other small improvements related to output:
For the log files, only the status file should be created if there is a input filename error - fuzzy_log.log and solids_log.log should not be created.

The phits output is currently named, csg.inp, this is not consistent with the naming for other transport code outputs.

Describe alternatives you've considered

Keeping as present

Additional context

[alexvalentine94]

something like this afe5dbd

[alexvalentine94]

related to #150