you might wanna have a look at pubs [0]. It is a command line bibliography manager.

The folder structure looks like this:

  ~/.pubs/
      bib/
      doc/
      meta/
      notes/

The bibkey is the filename for the different files in those folders, and for notes you can use markdown. You can then keep your pubs folder under version control (or symlink the (sub)folder(s) to wherever).

[0] https://github.com/pubs/pubs