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mdrun appends when checkpoint specified by -cpi is not found - Redmine #2829

If I invoke mdrun with all paths correctly specified:

gmx mdrun -s md.part0001.tpr -cpi md.part0001.cpt -noappend

I get the expected behavior of creating a bunch of files named md.part0002*. However, if I have a typo I will get unexpected behavior:

gmx mdrun -s md.part0001.tpr -cpi md.part001.cpt -noappend

In this case, md.part0001* files will be backed up and the simulation will just start from the tpr as if the simulation has not started yet.

There is a note which seems to be about this in the mdrun help text

There are three scenarios with
-cpi:

* no files with matching names are present: new output files are written

but this seems like unexpected behavior if I have explicitly specified -noappend. If I have no cpt file and I give the -append flag to mdrun it will throw an error, so it seems like the reverse case of saying -noappend while not giving an actual file to -cpi should also throw an error.

(from redmine: issue id 2829, created on 2019-01-12 by ejjordan, closed on 2019-04-09)

More tests for how mdrun -cpi restarts handle files

These tests clarify the behaviour of mdrun -cpi -noappend. It should
append ".partNNNN" to output files, but it is currently possible to
produce output files named like md.part0001.part0002.log

Added some unit tests around the string-handling behaviour that needs
fixing and left TODO comments to show what issues need fixing.

Reduced use of the deprecated mdrun -nsteps option

Refs #2804, #2829

Change-Id: I7e370b835d6fd3512fcaac575d0ff627b33c6e47