Compare window should be open in new window.
Today I integrated this tool with the VS2010. But before Check-in if compare files then compare window should open in new window. Else its not possible to see actual comparison.

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AdminDevart (_, Devart) commented
You can use the '/blocked' command line argument in your VCS diff tool settings to prevent such situation or open comparison only in a standalone application by another command line argument: '/environment=standalone'
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Gabe Halsmer commented
That's awesome! Thanks for asking the question, and thanks for the answer.
To the dev team, you may want to make this a formal option in the settings, because at least in my case I like to divide my documents in Studio using panes. So that my wide monitor can see two code files side by side. When Code Compare opened inside of Studio, it would be just one pane. And of course Code Compare is a side by side view, so essentially each document being compared was only 1/4th of my monitor's width, which really didn't work.
Launching as a separate application resolved this issue.
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Etienne Poirier commented
It is possible to open the comparison in CodeCompare instead of VisualStudio, by adding this argument in Visual Studio Compare Arguments : /environment=standalone
So whole arguments would be /SC=TFS /W /T1=%6 /T2=%7 %1 %2 /environment=standalone