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I have noticed that since the declaration of the patchs are not directly in the same location as the verification (one being with the plugin configuration and the other in the assert clauses) that it is very easy to get them mixed up. And if you are validating that the file doesn't exist at the end of the operation as with the clean plugin, if you are not testing the absolute right thing then your assert will be working when the test itself might have failed. So make sure you check these conditions, perhaps even asserting something is there before the mojo execution and then asserting it isn't there at the end.
this might actually be made easier with the addition of the ability to set and get variables in the instantiated mojo from the java side of the fence