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* Switch breathe to stable releases. It was previously pulling directly
  from master because a required bugfix was not in a stable release yet.

* Force update sphinx and RTD theme. When using conda, readthedocs pins
  sphinx==1.3.5 and sphinx_rtd_theme==0.1.7, which is a bit older than
  the ones used in the RTD regular (non-conda) build. The newer theme
  has nicer sidebar navigation (4-level depth vs. only 2-level on the
  older version). Note that the python==3.5 requirement must stay
  because RTD still installs the older sphinx at one point which isn't
  available with Python 3.6.

[skip ci]

Fixes #667

The sphinx version is pinned by readthedocs, but sphinx 1.3.5 is not
available with conda python 3.6. The workaround is to pin the python
version to 3.5 (it doesn't really matter for the docs build).

* Make 'any' the default markup role for Sphinx docs

* Automate generation of reference docs with doxygen and breathe

* Improve reference docs coverage