ref: use new prepare code and remove some old #2876
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The following actions uses node12 which is deprecated and will be forced to run on node16: ResearchSoftwareActions/EnsureCleanNotebooksAction@1.1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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