I would like to compare a complete folder with another folder and see all changes between them. But changes that are only comments (with #) should be ignored as well as any whitespace or newline changes.
With diff -r I get nearly all files back cause in my case in every fiele there was the version number added in the head.
The best would be a graphical diff-tool like Kompare
I haven't tried it myself, but I would check out Meld for a nice, graphical tool. It supports comparison of directories (among other things) and is designed for software projects possibly under version control.
It runs on Linux, Windows and Mac OS.