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A frequent problem of JaCoCo users are classes showing 0% coverage while the classes are expected to be executed. In most cases this is caused by the fact that different classes are used at report generation time and at runtime.
Therefore the report and check tasks/goals should issue warnings, if the execution data does not contain a class with the same id but with the same name.
Also the core API should allow to provide such warning also in other tools see jacoco/eclemma#74