I run CCleaner every so often and it does a great job of clearing out the junk. Specifically, I clear Temp Internet Files, History, Typed URLs, Recent Documents, and System Temp files. None of these have caused me any problems. When I have accumulated a lot of cookies then I will also select the option to clear them. That does cause some issues. Namely, auto logins like Netflix and Citizens First no longer recognizes my computer. These are minor since a manual login to Netflix restores that and Citizens First calls me with a code to prove I am who I say I am. I also used Options, Cookies to protect cookies from some sites I knew would cause a problem.
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