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You should start Data Modeler by double clicking on OracleDataModeler.app.
Do not open the internal structure and launch datamodeler.sh.
Looks like it's also mandatory to set the directories in Tools .. Preferences .. Data Modeler before doing any file manipulation. That is, the defaults (blank) are unworkable, and no clue is given as to either best practices for setting them, or at the minimum the constraints on what they might be for the product to work. The lack of basic setup documentation makes the out-of-box experience (OBE) for this product on the Mac very poor.
Apparently, the Oracle documentation for a Mac install is either missing or incorrect. Disappointing.