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3.1.0 Update

Mike Koch requested to merge 3-1-0 into master

Closes #535, #428, #397, #565, #549, #561, #562, #560, #531, #395, #405, #456, #353, #551, #559, #557, #556, #524, #523, #527, #528, #525, #339, #522

Edited by Mike Koch

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