Generally, when I have to do this, I go for low tech:
cd ~/a
find . -type f | sort > ~/fooa
cd ~/b
find . -type f | sort > ~/foob
vimdiff ~/fooa ~/foob
This allows me to refine the results. "Oh screams, I wanted to exclude the .svn directories from ~ / a," so restart the ~ / fooa file without the .svn directories, and then reinstall.
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