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netbeans works fine for debugging with Unix/lf, DOS/cr/lf line endings withing editor or when debugging. But for Mac/cr only line endings things are messed up. I have to dos2unix modify the source code to be able to edit the original files without extra line breaks or for the debugger to properly match up lines with source code. This issue been around for many nettbeans editions.
This is IMHO an editor issue.