>>git difftool branch1 branch2 opens my difftool (Beyond Compare:BC) with every file that has a diff between the branches. I have to close BC after each file
>>git difftool branch1 branch2
Starting with git v1.7.11, you can use git difftool --dir-diff to perform a directory diff.
The answer that follows applies to git installations older than v1.7.11.
This issue is not related to BC, but to the way git works. Fortunately, there is a solution at this URL - git-diffall