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For some reason I am unable to pinpoint, the Mono TODO setting in Text Editor -> Source Analysis -> C# is not saving properly between cases of running MonoDevelop. Every other setting is being saved as expected but quitting MonoDevelop and starting it again will for some reason or another revert Mono TODO back to the default state (Enabled).
Works for me correctly in 6.0.
(However the code analyzation got rewritten)