Thanks, @rkaplan, for the description. From your description it sounds as if a PKM solution (such as the great Obsidian kit by @ryanjamurphy mentioned above) could be made to work for such a workflow as well.
I’d also be interested to eventually make my own app work for such a workflow. It sounds as if the basic pieces are already there, such as built-in support for citations, and linking to citations & annotations, as well as link types to describe the nature of a link (“refutes”, “supports”, etc) – and a graph visualizing these links / relationships. Better support for the creation of summary notes / outlines and comprehensive export options would still be missing, though. Anyways, I’ll keep this in mind, thank you!