How do I clean my MacBook Pro and upgrade to latest macOS version?

Are you backing up to Time Machine? My suggestion is to back up your computer, then go into Recovery Mode, erase your computer's hard drive, then reinstall the operating system software in Recovery Mode. Once that is finished, open up Migration Assistant in your Utilities folder, and transfer your files to your computer. I've done this with a few computers and it has cleared up a number of issues.

+1

And I'll add that before reinstalling user files, go ahead and update/upgrade the OS to the level you want it.

When that is done, then go ahead and recover the user files from the TM backup drive.