https://triliumnotes.org/ is my clear recommendation. It's quite more powerful than the usual contenders and it may take a while to explore its depths, but it's also not pushing its complexity in your face like Logseq and some others do.
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.