Input files overwrite if they have the same suffix

[fusmatrs]

If the different input files to be modified / run have the extension (such as .i for MOOSE and NEML2) then they overwrite when modifying. Both get written as 'sim_0.i' for example. Possibly helpful to specify different input names for each of the modifiers to avoid this.

[ScepticalRabbit]

Should be an easy fix - I thought this would be a problem so the mooseherd class has a list of input file names called self._input_files. I just haven't written the functions to expose this. For a quick fix you could just access this variable in the mooseherd class and manually set it after creating the herd.

[fusmatrs]

I've done a quick and dirty fix for the mean time of retaining the original file names. It does mean that you can't run multiple files in the folder though. For what I'm doing currently that's not an issue, but will be for other applications.
The problem arises because the moose input needs to point at a NEML2 input relative path. If the NEML2 file changes name then the relative path needs to change, but then that needs to change something in the moose file.
It is also something to consider with Gmsh as well, when we're pointing to a mesh with the same relative path name in the folder

[fusmatrs]

I've made this change in my rs_merge branch. Default behaviour is to name input files sim_a, sim_b, ... and so on for each of the given modifiers. I have also had to do a change to the _mod_input method to check if file_number exists in the moose variables block and if so, pass it the worker number. Seemed the easiest (if a bit bodgy) way to get the file number to moose so it can read the correct neml2 .i file.