I had a look at the first commit (CDVFile.m file) and it's using a now deprecated method to set the 'do not backup' attribute according to:
"Warning The code that follows has been deprecated and should only be used on iOS 5.0.1 or earlier. When running in iOS 5.1, apps should use the NSURL and CFURL keys described above."
I guess you want to keep backward compatibility with ios 5.0.1 and earlier, but, in the case of iOS, forward compatibility looks more important as most devices are up to date. with iOS 6 coming soon, this fix looks already obsolete.
Wouldn't that be possible to use the new methods when available, and fallback to the old method if necessary?