Set consistent log and summary file names

[ElliottKasoar]

Resolves #132

As mentioned in the issue, sharing the summary is relatively straightforward, but extra changes were needed to use the FileNameMixin to set the log filename to be consistent with other output files.

Since the default filename moves into the Python, I added an additional flag that controls the logging, so a filename isn't required.

Loosely depends on fixing #279, for correct documentation, and tests will then require updating following a fix.

[ElliottKasoar]

I suggest #283 is reviewed before this, as it also address the logging suggestion, and this will need various conflicts resolving.

[alinelena]

if keeps logic simple I am fine with keeping md