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I want to make some programmatic changes to the edited file. How can I do it so one Undo undoes it all?

Create a Runnable that will do all of the code generation/munging you want to do. Pass it to org.openide.text.NbDocument.runAtomic(doc, runnable). Or BaseDocument.runAtomic() can be used (the Document in the editor should be an instance of BaseDocument - it will be for Java files and most other things).

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