What are some good file comparison utilities other than Beyond Compare, which I use but find rather clunky and not as accurate as I'd like (for programming)?

I'd recommend Guiffy 8.0 - it is extremely efficient and provides for three-way comparison and conflict reconciliation as well-).
There is a comparison chart of most popular comparison tools designed for developers: http://www.diffutils.com/our-recommendations/for-developers/

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