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Andrew medlin/update docs jun2020 (#197)

Completed updating readthedocs documentation by improving automation and fixing coding and reStructuredText problems that were blocking documentation generation.
* Revising readthedocs files to cover missing modules
* Removing reference code that should be stored external to HiPerSeis
* Fixed code design and rst documentation issues that were blocking complete generation of documentation
* Ignoring plotting files for code coverage metrics
* Upgraded minimum sphinx version

Co-authored-by: Fei Zhang <fei.zhang@ga.gov.au>

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