This project has not been tested with every contributed module, but this page will categorize ones that are known to have problems
- Views - Publicly accessible exposed forms, contextual filters (using query params), and AJAX does not work with Tome, since there is no Drupal site running to support them. Pagers on non-AJAX forms are supported, with some magic.
- Paragraphs - When a Paragraph is removed from a field, it is never actually deleted. This can lead to a lot of stale entities in your repository, which you would normally have to manually clean up. The "Paragraphs Clean" contributed module will delete Paragraphs when they are unreferenced. I use it on this site and it seems to work OK.