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Root question about temp root and running certain programs.

haven't done all the necessary research so that i feel comfortable doing a full on root yet, but i have done the visionary temp root. my question is can i run programs like setcpu with only the temp root? i've got it set the way that i want, but i'm pretty sure i need to reboot the phone for it to take effect. will it work if i have visionary set to temp root at each boot, or will the changes not take effect?
 
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