Prepared documention for upcoming 3.0.0 release

* Renamed folder ``user`` to ``2.0.x``.
* Created folder ``3.0.x`` and merged documentation of ``2.0.x`` and ``helium``.
* Removed references (i.e., :ref: links) because they cause ambiguity when the same
  label is defined twice (not surprisingly). Use :doc: instead, and always use relative
  paths!

This PR changes will cause many dead links in the website. Hence, before merging I'll create a PR in the website git repo that will prevents the dead link (best effort here, some may still slip through). However, I'd like to get your thumb up before starting to do that.