Have you tried using iCleaner and enabling the option for cydia sources? It's off by default. You can turn that on and try that. Turn everything else off that you don't want cleaned because if you've never run iCleaner, it'll delete a ton of junk and prolly will save close to a gig.
Can I still use this method on Cydia in 2015?
I do have iCleaner Pro 7.5 as well on iOS 9.0.2.
Does the Sources option do exactly what was manually outlined above?