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By this I mean, this will only keep the window on top of all those windows which are part of the application, not all other windows related to other applications.

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By this I...

Setting always on top will only keep the windows on top of your application, not all of the applications running at particular time.

Plus, I didn't like that I couldn't modify/move some of the generated code
You can move.

Instead of being dependent on the IDE's, why don't you have a look at Swing Tutorials?
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