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3.9.1 How do I make the active window follow the mouse?

Customize the variables focus-follows-mouse and mouse-autoselect-window. The former can be used to mislead Emacs into giving focus to other frames when the mouse is over them, even though Windows has a click to focus policy by default (there is software available to change that though). The latter can be used to make Emacs use a focus-follow-mouse policy within its own frames.

You can also change the Windows click-to-focus policy by changing settings in the Registry. The details vary according to your Windows version; look on the Internet for instructions to enable “active window tracking” for your version of Windows.