Whether I'm just working with my own files or using Safari to browse the net, I keep getting these annoying user prompts that I never got with my previous OS. They keep asking me do I want to do this or that and they're totally unnecessary. Is there any way to turn them off?
What Mac OS are you using? If it is anything except El Capitan (OS 10.11.x), then you can Repair Permissions as oldscribe suggested. If it is OS 10.11.x, then that option is no longer available. However, you can download the excellent freeware program Onyx to Repair Permissions no matter which OS you are using (along with other useful tasks). You can get Onyx from here:
http://www.titanium.free.fr/onyx.html
Note that you'll need to download the correct version, which depends upon what OS you are using.
Also, as oldscribe stated, you'll need to run the Repair Permissions feature of Onyx at least twice, and maybe more times.
(Glad I went to that page, as I see where Titanium Software is working on a version that will be compatible with OS 10.12, Sierra. That also means I will not be installing OS 10.12 right away, as besides Onyx, 4 other critical apps I use will need to be compatible with Sierra before I upgrade).