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Yes they could, just like Microsoft could just patch all those vulnerabilities to completely eliminate viruses in Windows, but they choose not to, for the lolz.
 
if there are no security flaws, then jail breaking would not be possible. does apple actively fix the flaws because of jail breaking? no. they fix them because they're security vulnerabilities. could they eliminate jail breaking totally? only if there are no flaws to be exploited in the OS, which is highly unlikely.
 
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