Doxygen fixes #154
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Doxygen fixes #154
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…This will hopefully fix the readthedocs issues of calling docs/conf.py rather than cd into docs and calling conf.
* Changed Threader to use more references and less full pass by value in strings and knowledge bases
* Added .bak to .gitignore * Updated docs/conf.py to target build/html, which is supposedly what readthedocs targets now
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