How do you effectively compare 15000 files multiple times?

Question

I am comparing two almost identical folders which include hidden .svn folders which should be ignored and I want to continually quickly compare the folders as some files are patched to compared the difference without checking the unchanged matching files again.

edit: Because there are so many options I'm interested in a solution that clearly exploits the knowledge from the previous compare because any other solution is not really feasable when doing repeated comparisons.

Answer 1

If you are willing to spend a bit of money, Beyond Compare is a pretty powerful diffing tool that can do folder based diffing.

Beyond Compare

Answer 2

I personally use WinMerge and find it very useful. It has filters that exclude svn file. Under linux i prefer Meld.