Output file names inconsistent between MPI and non-MPI runs

[MatthieuSchaller]

A bit of a mix between bug and feature request.

When compiling the code with MPI all the output files have an .0 appended at the end of their name whilst the version of the code compiled without MPI does not. I think this is a left-over from the pre-parallel-hdf5 era where there were many files in the output.

Maybe the difference is intended behaviour though.

Another useful thing maybe would be to append a .hdf5 and .txt to the files to make humans (and hdf5 tools!) more happy when looking at files in a directory.

[rtobar]

I looked at this yesterday and indeed there are many inconsistencies as output filename generation is duplicated across many places in the code. I'm working on first unifying the generation of output filenames, then it will be relatively easy to address any required changes.