Is there a way to natively compare files and folders for content, perhaps in command prompt? If not, is there a good program for that?
I've heard of WinMerge, is it any good?
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As mentioned before, WinMerge is a good program - as are a handful of other options.
I recommend Beyond Compare.
I know the question has long been answered, but thought this might still be helpful for later readers.
SourceGear DiffMerge compares files and folders, and is free to use.