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We also have this problem. We run the additional tests from a shell buildstep. If the buildstep runs after the maven execution the extra tests are not reported, but if we move the step to pre-build stage, they get properly shown.
The main drawback of this workaround is that 'clean' target cannot be used in the list of maven goals, because it removes the target/surefire-reports directory where the junit reports are copied to.
Update:
If the execution of the extra tests can be binded to the maven test phase, the produced junit does appear in jenkins along standard surefire reports if the resulting junit xml is copied there. At least for us and for now, this is an acceptable workaround.