This is my understanding. rooting your system opens the abilty
for apps to access the main system files.this would make it very easy for apps with viruses or malicious intebt to gain hold of your system. say maybe through a website or some other way you recieved an unwanted app or script. so super user takes charge. nothing is alliwed to perforn a root function untill suoeruser says so. so everytime you open an app that requires root superuser asks you if its ok for it to have root access..super user will remember an allow the app to run without asking after initial permission
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