To restore the Java refactor key combo (and deactivate the key combo for PyDev):
- Eclipse -> Preferences... -> General -> Keys
- Sort by Binding by clicking the Binding column header
- Select the row: Command: Set Next Statement and Category: Python - Run
- Click "Unbind Command" button
- Select the row: Command: Rename - Refactoring and Category: Refactor - Java
- Click to select Binding field
- Type Command+Option+R
- Click Apply button then OK button to save.
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