Allow for full user defined filename
Description of work This permits the use of output filenames including '.' separators preceeding the .mda extension (i.e. 'PositionPowerSpectrum.result1.mda').
Fixes Closes #986
To test
I think that the new code works around the problem of . characters in the file name, but fails to recognise the cases where the extension is already at the end of the file name, and adds a second one. So, in some tests the output filename is given as output_filename.mda, but the code ends up writing output_filename.mda.mda.
When I run jobs from the GUI, the converter jobs are fine and the output trajectory names are handled correctly. The analysis jobs still have a conflict where .mda gets appended again to a name that already ends with .mda. Then the GUI protects the name output.mda and tries to load output.mda which fails, because the real output file name was output.mda.mda.