Improve functionality to write new in.dat from an mfile

[clmould]

This functionality currently requires 3 arguments:
[-f path/to/MFILE.DAT] [-i path/to/IN.DAT] [-o path/to/new_IN.DAT]

This needs changing to be shorter and easier to use:

-f path/to/MFILE.DAT -o new_IN.DAT

The new IN.DAT would by default be created in the same directory as the specified MFILE, but the user could specify a different directory if they wished.

[clmould]

Once data structure done, we can write the whole data structure to the output file and then can do as suggested above, as currently there's no way to read the copy of the in.dat from the end of the mfile.dat.