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This builds on things like the tabbed editor suggestion, but essentially I'm talking about a scenario where you'd have your one (editor) window open working on your program, you click 'run...' or 'debug...' from the menu, and a shell and debugger area open up at the bottom of that one window, and you can resize that area.
This is analogous to what happens if you click 'inspect element' in most web browsers nowadays.
Getting rid of the *need* for multiple windows would help simplify a lot of things.

Many of us want to reorganize Idle from multiple windows, some with menus, to one window with multiple frame or panes. The initial steps: 
a) create a new application window with an application menu. (I believe OSX partially forces this on Macs anyway.) The menu should have items added or deleted, or just activated or not, according to the active window and other conditions. Adjust the menu construction functions, including the ones used in extension files, accordingly.
b) remove the menu and Toplevel from the base editor window used for editor, shell, and output. Leave frame that can be added to other containers, whether Toplevel, Frame, Paned Window, or Notebook.
c) remove the Toplevel from dialogs that we think should be non-modal and insertable into containers. I think the debugger, as you say, aumented config dialog, and improved search/replace dialog, are all candidates for this treatment.
I think users, or at least class instructors, should have some control over placement. There definitely should not be a single, locked down design.

Yes that's exactly what I was thinking. If everything is a frame rather than a toplevel it'll be much easier to reconfigure things.

Is this a duplicate of https://bugs.python.org/issue9262 Either way, there's some good discussion there and also on https://bugs.python.org/issue24750 (ctrl-f for "tabbed")

#9262 is step b) above, and therefore a dependency for this issue.

#24760 - config dialog not modal, is part of c)

https://www.youtube.com/watch?v=nO78ECRighw shows IDLE on Mac with a shell and editor window. Because Mac pulls the menu off of each window and puts one above both, which are side by side, it looks like an example of what we want to have on all systems.