This look interesting https://unigraph.dev/. Still in beta though but you can sign up for the waiting list. I just did it today.
Ooh, this looks like it might check all the boxes for me. FOSS, local-first, aggregates things from other apps without replacing them, allows linking between different file formats, etc.
Unigraph looks promising. I’ve developed a home-grown personal search engine that has some of these features and it’s super useful.
BTW, it’s open source, so if you’re adventurous, you can build and run it from source.
And another one - Appflowy https://www.appflowy.io
Billed as a Notion alternative