This look interesting https://unigraph.dev/. Still in beta though but you can sign up for the waiting list. I just did it today.
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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.