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It is just a drag of the pop up window to the main window. Key is to drag by tab title not by main window. In your case, start dragging at tab titled console!
Under Window > Preferences , go to the Run/Debug > Console section, then you should see an option "Limit console output." You can uncheck this or change the number in the "Console buffer size (characters)" text box below.
Reopen console form Window -> Show View -> Console and voilà, it will appear.
There are two buttons on the console toolbar at the bottom that allow you to take focus (or not)...one for stdout, one for stderr. I have an image with the buttons circled.
There are two icons - "Show Console When X changes" in the console view. Unselect those.
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