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My handwritten TestCases are not executed in the TestSuite.

If you create a TestCase by writing everything yourself (which is good for more functional tests) just insert the call for that TestCase in the TestSuite you want. That's what the markers in the suite method are for.

public static TestSuite suite() {
  TestSuite suite;
  suite = new TestSuite("org.junitdoclet.demo");
  // JUnitDoclet begin method suite
  // JUnitDoclet end method suite
  return suite;