You already have a rule set file, which I assume you figured out how to integrate into your projects and use through Visual Studio.
You can use the same rule set file in FxCopCmd.exe :
FxCopCmd.exe /out:Violations.xml /ruleset:=Custom.ruleset /file:MyAssembly.dll
I did this with Jenkins and everything works fine. Run FxCopCmd.exe with no arguments and you will see descriptions for all available command line switches.
Bernard
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