Eclipse will change the border color
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I think this is based on the "Window Color and Appearance" (ie name if you are under windows) of your desktop personalization, just like the top bar maximizes / minimizes / closes.
So, you can always go there and change it in "3D Objects", but keep in mind that this change will affect all of your desktop / window visuals.
Altho, that was said, I know there are ways to customize it. This might give you a hand: http://marketplace.eclipse.org/content/eclipse-4-chrome-theme#.UYrzEkAW1J0
Also the css spy tool helps you find what you want to edit faster: http://marketplace.eclipse.org/content/eclipse-4-tools-css-spy#.UYrzSkAW1J0
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