Next step is to give up on files/filesystem. As long as it's opensource, there's no lock-in. As long as the storage backend is clean and structured (SQLite or comparable), you actually get so much more (full text indexing, standard querying, ...)

I initially was cautious when going from "bunch of .MD files" to https://triliumnotes.org/ , since it's been pretty great.

Hmmm, it has been years since I last tried it, perhaps it is time for another chance indeed. Thanx.