Sierra 10.12.6 Clear history/cookies

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Hi Folks,
First time poster. Communications hardware tech but not a software expert. Using an Mini 7.1 about 20 mos old after MacBook Pro suffered early demise. According to logs (Launchpad>Sys Info>Software>Logs) it had updated itself on 13 Jun 18 to Sierra 10.12.6 w/o my knowledge. Also saw in log that MRT (?) had updated or installed itself 27 Jun 18. Have habit before shutdown of clearing search history and cookies and will do so periodically during day if using computer a lot as it will run noticeably faster afterwards. Had always noticed that it usually takes 2 or 3 attempts at clearing before website data is empty. Do not use for gaming or any other streaming except occasional Youtube song or video, almost entirely text.
Last night 8 Jun 18 saw aberration: When I clicked Safari>Clear History> I got window that said "Clear Search History but keep website data" where it would normally say "All History". I backtracked and tried again and got same result. Opened inline ethernet switch and restarted. Now I get the normal sequence but on checking the actual website data list (Safari>preferences>privacy>manage website data) I have one site that will not clear and keeps coming back even with ethernet disconnected. It is variety.com/databases and I do not know if it is the problem or just happens to have been retained when the issue occurred. I visited the site to check out and it is just the normal magazine site but I had never actually visited it that day. Occasionally news sites I access have links to Variety stories along with others. I am astonished at how many cookies will be registered by visiting one or two news sites....I have seen 200+ at times. But they will always disappear when I clear history. Am usually very careful with malware attacks and is the reason ethernet switch is there as that is the first course of action if I click on a site and get a warning from the computer. Is also the reason for going from PC to Mac, although much of the software I use for my control system work is on a PC laptop that never goes online. PS Windows 10 is truly awful!!! But used to love XP except for vulnerabilities.
Any ideas what is going on?
Tnx, Jack D.
PPS Have not noticed any other unusual symptoms as of yet but I only use a very limited range of functions.
 
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OK, need to ask you some questions, along with making some observations/software recommendations (by the way, I own a Mac Mini 6.2 (late 2012 model, running High Sierra)):

1. Have you ever done any disk cleanup/maintenance/repairs, from a software perspective? You can actually do a good amount of disk cleanup on your own. One place to look is your downloads folder. Also, there are a number of excellent free and commercial products available that can help you with those tasks (I'll list some free ones below).

2. This is critical: are you making backups to an external device? If you are, what software are you using for that?

Regarding the automatic update of Sierra, I prefer to control the update process myself. There is a System Preference setting (via the App Store) that you can control this. This link describes how to do that:

http://www.businessinsider.com/apple-macos-sierra-how-to-turn-off-automatic-updates-2016-10

Not sure about MRT (I don't even know what that is).

Here are some excellent freeware products you can use:

Onyx - Available from here: https://www.titanium-software.fr/en/onyx.html

Rock Solid, has been around a long, long time, and has had many positive reviews. I use it religiously (along with a commercial program entitled Tech Tool Pro). I would not be without either of them. In fact, I will not upgrade to a new Mac OS until there are compatible versions of both of them for the new OS (along with 4 other critical programs that I have). Note that there are different versions of Onyx available, for each different Mac OS. You would need to get the correct version for the Mac OS you are using..

AppCleaner - Available from here: https://freemacsoft.net/appcleaner/

Another stellar performer! As you can see via that link, it will get rid of most stuff associated with an application that you wish to delete.

GrandPerspective - Available from here: http://grandperspectiv.sourceforge.net/

Nifty graphical way to see which files are on your drive. Good way to identify large ones that you might not need.

Malwarebytes - Available from here: https://www.malwarebytes.com/mac/

Good to use if you see adware and/or suspect you might have a virus. It also is good to run it every so often, even if nothing is wrong.

ClamXAv - Available from here: https://www.clamxav.com/

More extensive than Malwarebytes in terms of finding viruses. You can use it in demo mode, and it still has just about full functionality. (Recently two folks were able to resolve their issues using ClamXAv and AppCleaner).

Then of course you can use Disk Utility to check out your drive and/or do repairs. It's not as extensive as Tech Tool Pro (https://www.micromat.com/products/techtool-pro), Disk Warrior (https://www.alsoft.com/diskwarrior/?gclid=EAIaIQobChMI9qzeqcSF2gIViWp-Ch0NngwsEAAYASAAEgJg7_D_BwE), or Drive Genius (https://www.prosofteng.com/drive-genius-mac-protection-software/), but it gets the job "mostly" done. I use Tech Tool Pro, and in fact it is the only third party one so far that is fully compatible with High Sierra (that's the OS I use on both of my Macs)

However, 2 caveats with using Disk Utility:

1. A backup is mandatory.

2. You need to run it in "isolated" mode. For that, you would boot your Mac into the (Hidden) Recovery HD partition. This link explains how to do that, and what is on that partition:

https://support.apple.com/en-gb/ht201314
 
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