I use Onyx as well, but Cleanmymac helps me with hidden rubbish , itunes stuff and a fast way to login and start daemons.
Why do you guys think it could screw the OS?
Just do a quick web search and you will know why. Developers of programs like CleanMyMac are a bit pretentious and often claim that they can give you back some space or make your Mac run faster. However, what they mostly do is remove small preference files that hardly consume any space and don’t affect your system, remove substantial amounts of caches and logs that will be rebuilt in no-time and remove parts of applications that they don’t control and can lead to actual problems.
As you’ve seen for yourself, CleanMyMac suggests disabling LaunchAgents or LaunchDaemons which can lead to problems in other applications. When a developer puts them there it is likely for a good reason, namely that a part of a program you installed needs to be started upon login. Programs like CleanMyMac encourage irresponsible behaviour and discourage people from getting to know their system and maintaining it properly. You hand out root access to your entire system and don’t know whether what the app tells you is good or bad. There is absolutely no need for this software when you observe a few ground rules.
The same is true for Onyx. It is certainly a powerful tool that you can use for particular tasks, but it also encourages you to do scheduled maintenance for which there is no need. What really gets me in the wrong way about Onyx is that they use a non-standard prompt to obtain root access. I don’t touch that program for that reason alone.
If you indeed feel that your system is getting heavy on disk usage or becoming a big slow or sluggish, you can always ask here for some guidance. Ultimately, Macs are super easy to maintain, you don’t need to know much.
By the way, better to waste an 8GB usb just for repair permissions is to do it by console, correct me if I'm wrong...
http://osxdaily.com/2015/11/04/verify-repair-permissions-mac-os-x/
I agree, it’s likely better than using a hacked version of Disk Utility. But you should use it for specific troubleshooting, not as a regular maintenance tool. Having ‘wrong’ file permissions is normal, it is not a reason for concern. It just means that the permissions have been altered at some point and deviate from the installer package. That doesn’t mean that the files can’t be accessed, modified or executed by the process that needs to do that.