How I would structure the code

This is how I would build, structure and code the website.

pros:
 * All express-related configuration occurs in app.js instead of spread in many files
 * All express-middlewares and helpers are kept inside the helper library in /doc
 * All request handlers are aptly put in a folder called request handlers to better group handlers together
  - Due to each request handler being exposed, makes it easier to unit test them.
 * All code is kept inside /lib as is almost per-standard for node libraries.
   - This separates the code from the other stuff
 * All repository-related functionality are kept in a folder called repositories.
   - This allows for better unit testing as well as grouping everything that uses external resources into single folder

cons:
 * todo <_<

WARNING: This is completely untested and stuff moved around blindly.