Ask HN: Visual note taking

I'm about to start on a project that will attempt to create an elegant solution for taking notes, organizing them and managing them without mucking about with files and folders directly (my intention is to still store them in plaintext files and avoid any sort vendor lock-in). Current idea in my head is something like an intersection between mapping software, drawing software (diagram, not sketching, so like https://draw.io), and an editor.

What kinds of benefits have you noticed in current solutions? Is there something that's really bugging you with current approaches? What could applications do to avoid interrupting you while you're doing deep work or are in the zone with UI/UX annoyances?