Rename the patches directory or improve the documentation

[ojcchar]

From the conversation I had with René (via email), "the naming of the directory (patches) in the framework is ambiguous and probably confusing".

Here there are some details from René:

"Each patch provided by Defects4J (such as defects4j/framework/projects/Closure/patches/1.src.patch) is a bug-inducing rather than a bug-fixing diff. In other words, applying such a patch to the fixed program version reinserts the bug. This is exactly what Defects4J does to checkout a buggy program version. If you want to view or use the bug-fixing diff instead, you can use a tool such as interdiff to invert the diff."

[Greg4cr]

I think that renaming the directory would introduce more trouble than it is worth (breaking scripting both internal to D4J and using the framework). However, this is something that could be clarified with better documentation.

I am adding the "tutorial" tag to this so that we do not forget about it when adding new documentation in 2.0.