For the structure I "solved" that problem by creating folders with three main files:
Websites/foo.com/username
Websites/foo.com/password
Websites/foo.com/email
Sometimes I add "/notes" with unstructured text contents, and for a few special cases I created a file "/json" with some machine-readable things in JSON format.It's not perfect, and I do dislike the way that the metadata isn't encrypted, but on the whole I'm happy with the solution.