Write out `.sh` file for reproducing command

[dennisbrookner]

All three MatchMaps utilities now write out a shell script which can be used to re-run the utility with the same parameters.

• At present, this feature cannot be turned off
• By default, the file is called run_matchmaps.sh and will overwrite any other file with the same name. A different filename can be provided using the --script flag.
• Unlike all other matchmaps functionality, the shell script is written out in the current working directory. This is done to ensure that the supplied input/output paths remain correct. Personally, I recommend the following file architecture:

  .
  ├── input_files
  │   ├── file.pdb
  │   ├── file1.mtz
  │   └── file2.mtz
  ├── mmrun1
  │   └── manyfiles
  ├── mmrun2
  │   └── manyfile
  ├── mmrun3
  │   └── manyfiles
  ├── run_matchmaps_run1.sh
  ├── run_matchmaps_run2.sh
  └── run_matchmaps_run3.sh

  but of course there are many good options.