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If existing source code that was added manually doesn't have merge markers, the code gen process will ignore it. But an option should be added to the code gen dialog (and the project customizer for Code Generation) that forces all source elements to have a merge marker added to it. Default for this option is "false" (disabled).
Added a new check box with the label "Add Merge Markers to Existing Source Elements". Also passed in the value as a property to the code gen task class. Just needs to be implemented to produced the desired result.
verified in build netbeans-hudson-trunk-1546-full.zip