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Updated docs for sphinx 1.6

Duncan Macleod requested to merge github/fork/duncanmmacleod/sphinx-1.6 into develop

This PR updates the docs infrastructure, and generally improves the docs a bunch, so that they run under (minimally) sphinx 1.6.

The missing dependency is still doxylink, which has been updated to python3-only. We should revisit this when we can generate the docs on python3.

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