As a long time user of vimwiki with an awful lot of hacks and plugins to work for doing something like this, margin seems like the kind of thing I was originally looking for. Vimwiki is great but suffers from having almost no machine readability, which makes integrating it with things like time tracking difficult without large, complex plugins.

However, margin doesn't really seem to have any equivalent of links between files, which I find essential for organising thoughts in anything beyond small notes. This seems like something that's contrary to the philosophy in a sense, but what would be the margin-ish equivalent of something like that, and (following from that) things like file tags? Would those be done with annotations?