Add changes from the 'modulated-development' branch. #455
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This PR includes all changes from the 'modulated-development' branch for the files that are still in this repository. It is unlikely that the branch will be merged in the conventional way due to the repository being split into multiple smaller repositories, so I wanted to highlight the changes that still apply to this repository. Note that some of the changes might no longer be relevant (e.g. the default values are now quite discouraged by the IUCr).