To fix this issue To answer my own question: Specifying the rules explicitly as I outlined above is the correct way to customise the rules list, the reason I was getting a different number of results back was because the "default" rule set in Gendarme leaves out scanning for Code Smells, once I added this scan to the default list, the defect totals matched.
How to suppress specific Gendarme rules at project or assembly level
hop of those help? The easiest way is to create an .ignore file for your project. E.g. to ignore a specific rule for all assemblies (e.g. a project) you can add the following lines in your ignore file:
it should still fix some issue I was missing another dependency Mono.Cecil.dll. I got it from here and copied it to /mono/lib/gendarme along with Mono.Cecil.Mdb.dll from the installation of MonoDevelop as mentioned in the question.
C#, Gendarme, Sonar and Jenkins : Exclude generated files from Gendarme