It's early days yet but this is exactly what I'm trying to achieve with stash[0], plus the ability to browse notebooks over HTTP and run/embed dynamic queries into documents. It's essentially a specification of a directory structure for plain-text files and a bunch of tools for doing bulk manipulation. I began migrating all of my notes from Evernote a few months ago and it seems to be handling it well.

[0] https://github.com/no-silo/stash-design, https://github.com/no-silo/stash-server