ONYX changed file permissions

Running things like OnyX is not generally a good idea. OS X does a good job of keeping itself maintained without user intervention. If your Mac is having some sort of problem you are trying to diagnose, OnyX et al can be good troubleshooting tools. But if your Mac is not having any problems, running OnyX is a waste of time at best, and can cause problems at worst.

As far as file/folder ownership, Apple apps have their own specified permissions, and running the permission repair will set them back to what they are supposed to be. User-installed software may have differing file/folder permissions. It depends on whether or not the developer specified them in an installer script, or the app is installed by a simple drag and drop.

Permissions on applications are generally not something you need to worry about.

Disk Utility does a very good job at verifying and repairing corruption on hard drives. Tools like DiskWarrior can fix some serious corruption that Disk Utility cannot. But in my opinion, if corruption is so severe that Disk Utility cannot fix it, it is better to erase and reformat the hard drive and restore data from backups, than to rely on DiskWarrior to try and repair it.

That said, it has been many years (I believe I was running OS X 10.2 or 10.3) that I ran in to a disk corruption problem that Disk Utility could not fix.

Keep good, regular, and recent backups. That is the most important OS X recovery strategy if anything goes wrong. I have both a Time Machine hard drive, and a drive containing a SuperDuper clone that I update twice daily.

Onyx uses the same built-in utilities and scripts that things like Disk Utility use (which is why it really isn't needed), so there isn't anything new there. Repairing permissions will only have an effect on system files and things that were installed using an Apple installer - it will not change items in a user folder and those installed via drag-and-drop.

No files that you install will be affected by the built-in permission-repair routine, no matter where they are (unless you replace existing system files, which I hope you won't do.) As for Onyx, I don't know exactly what it does, but I agree with those who suggest getting rid of it.

Generally speaking, all public files -- those intended to be read or executed by all users -- should be readable by all, executable by all if applicable, and writable only by root or perhaps also by the admin group. That would include files installed in the local Library at the top level of the boot volume. If you choose to make public files writable by the admin group, then you should have an admin account that you use only for administrative tasks, and a standard account (not in the admin group) for all other tasks. Switch between accounts using Fast User Switching. That way, you minimize the risk of inadvertent modifications.

Just am concerned how much re-working is required to re-permission the software I have loaded for use by a non-admin account, as I have loaded exclusively with an admin-level (first, default account) from day one.

If you installed it in public directories with the permissions outlined above, no re-working is required.

As to "do not use Onyx", BGreg likes it. You do not. Not to suggest you are wrong, but, why?

I don't see a message from "BGreg" in this thread, and I don't know who that is. I do know that Onyx does things such as deleting system caches. There's rarely a reason to do that, and if it needs to be done you can do it by booting in safe mode. Onyx encourages people to regard cache "cleaning" as a routine maintenance task, which it is not. As for repairing permissions, that also needs to be done very rarely, if ever, and if it is needed, Disk Utility does it. If Onyx has functions that overlap what the system does, but aren't the same, I wouldn't trust it.

Overuse of third-party "utilities" and system modifications is the biggest cause of problems on the Mac platform, judging by what I've seen in these forums.

Disk Warrior is a recovery tool. It's useful in one situation only: you have an HFS volume with directory damage that Disk Utility can't repair, and no backups, or inadequate backups. In that case, Disk Warrior will sometimes be able to restore the damaged volume to a state in which it can be backed up. Some files may be lost.

Unfortunately, there's a tendency in these forums to tout Disk Warrior as a maintenance tool that all Mac users should have. That's a waste of $100 that could be better spent on backup devices. If a journaled HFS volume becomes damaged so that Disk Utility can't repair it, that's a drive failure. A drive that has failed once is not to be trusted again. You replace it and restore the data from one of your redundant backups. If the volume is itself a backup, you don't restore it; you just start a new backup on the replacement drive. Temporarily, the redundancy of your backups is decreased, something that will inevitably happen whenever one of your backup devices fails.

Sometimes the Disk Warrior advocates claim that it somehow makes HFS volumes perform better. The basis of that claim is a mystery, because the developer of Disk Warrior makes no such claim that I've ever been able to find, and there are no engineering data anywhere to support it as far as I know.