Make output files/folders readonly

It might make sense to make the output files that MUSE2 creates be readonly so that users don't accidentally modify them, which could be bad if the data files are being used for something important.

I think there are a few things to consider before doing this:

- Will making everything readonly make it annoying to delete output folders because of extra warnings etc.? This behaviour might be different between different OSes. If it is annoying, we may want to make this configurable in `settings.toml`.
- What are the implications of making a folder rather than individual files readonly? Should we do this as well given that the behaviour will be different between Windows and Unix? On Windows, it seemingly [has very little effect and you can still write files to the folder](https://superuser.com/questions/1247843/why-can-i-write-files-into-a-folder-that-is-read-only).