If the warnings can be differentiated by a simple pattern then these warnings could be excluded from the MsBuildParser.

But wouldn't it be simpler to just remove the StyleCop parser from your job configuration? Or does the parser produce better results? Or is there an option to disable the duplicated output in msbuild?

All of the StyleCop error #'s begin with SA. They should be easy to separate. We would like them separate so that we can treat the MSBuild warnings with greater severity (possibly fail the build).

Then either the regular expression needs to be adapted or in the createWarning method should return FALSE_POSITIVE for these warnings. Interested in providng a pull request? The changes should be straight forward to MsBuildParser and the test case.

I don't think that the behavior of the MSBuild parser should be changed hard coded to filter warnings from StyleCop, because this is not a problem with the MSBuild parser. StyleCop just produces output that is conform to the MSBuild warning/error system which I assume is intended by the StyleCop delevopers.
Maybe a configureable regular expression would make sense to filter unwanted warnings/errors in certain situations.

You can exclude certain warnings by a regexp (based on the message).