Sphinx API: OmeroPy links review

This PR:

- reviews and updates all Epydoc-style links (`L{}`, `U{}`, `C{}`) under `components/tools/OmeroPy` to use the Sphinx markup (`:class:`, `:meth:`) instead
- exposes all private members in the Sphinx API generation (check esp. the `omero.gateway` package which defines classes/methods starting with `_`)
- fix miscellaneous warnings related to the private members exposition

To review this PR, review the auto-generated content under http://ci.openmicroscopy.org/job/OMERO-5.1-merge-build/ICE=3.5,label=ome-c6100-3/javadoc/python/ and check all the modified markup create proper links to the relevant classes/methods