Fix issues with data in `niva-tidy`

[JamesSample]

Some issues need fixing with the data in niva-tidy. Some of this can be handled by a script.

I have already written code (here) to "flatten" files within the images directory.

In addition, I suggest the following for each mission folder:

1. Read the config. file.
2. If the grouping attribute is set to Mapping, update it to {organisation}-{project} (see e-mail discussion with Hege, Medyan and Kim on 02.04.2024).
3. If spectrum is msi, set it to MS.
4. Count the files in the images subfolder and update the nfiles attribute.
5. Save the updated config. file locally and check whether it validates using sb.ortho.check_config_valid(dir_path, verbose=True).
6. If the new file is valid, replace the config. in the mission folder with the new one; if it's still invalid, print the reason and fix.