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My handwritten test methods get overwritten. How do I avoid this?

Put all your handwritten code between markers. Always! If you want to write a test method by yourself, write it between the marker at the class level. The marker is already there. (The instance under test is defined within this marker as well.)

// JUnitDoclet begin class
  org.junitdoclet.demo.SampleClass sampleclass = null;
  // and now a handwritten test method
  public void testHandwritten() {
    // ...
// JUnitDoclet end class