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I have a Macbook Pro and almost always use it with an external, larger monitor, which I have set up so that it is right above the MBP's built in screen. I have this same setup at home and at work. This is my arrangement:

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with the Dock at the bottom of the lower (built-in MBP) screen. Usually I have most of my important windows positioned in the upper (external monitor) screen. This provides the best ergonomics for me because I can look straight ahead instead of down.

When I leave one of these locations the MBP goes to sleep. Then when I plug in at the other location, there is usually a moment (maybe 5 seconds) where the external monitor is not plugged in. If that moment is too long, then all my windows reposition into the lower, built-in MBP screen. Sometimes the windows end up shrunk in height to be very short as well. So then, if I want to get back to where I was I have to drag all my windows (for umpteen apps) back up into the upper screen and expand the shrunken ones.

Is there any way to avoid this? For example, can I cause the windows to have a preferred location that they could snap back to when possible?

I'm on OSX Lion (10.7.5). This is a 15-inch MBP, new in spring 2011.

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Stay should solve this for you. It's not free, but it's not expensive either.

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Looks intriguing!! – jlarson Dec 12 '12 at 18:58

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