We've also issued new guidance to examiners to help ensure that patents cover only "new" and "non-obvious" inventions.
That's impossible in the field of software. There is simply too much activity and too many specialties for the patent office to have any hope of being able to reasonably evaluate whether a claimed invention is novel, or whether it's obvious to a skilled programmer in the relevant specialty.
This is one big reason (though not the only reason) why software is incompatible with the patent system. Patent law has a presumption of validity for issued patents, and that presumption is laughable if it's a software patent.
If millions of people carried machine shops around in their backpacks, mechanical engineering would be incompatible with the patent system too.