Maybe reinstalling macOS repaired the permissions or whatever was wrong. I think I saw reinstalling as a possible solution somewhere.
For restoring from a backup, I was vague because there are more than one option. Such as…
If your system is working normally now, and all your files are present, I would declare victory, and move on to my next adventure.
I would be a little surprised if that were true, though. My understanding of reinstalling macOS from Recovery without erasing the drive was that it did not change permissions on user directories, but perhaps I was mistaken.
Is your system behaving normally now?
Thanks @mschmitt , I went ahead with the Apple steps to erase, then when it started up again, chose to migrate from a CCC backup. I migrated everything but one unused account and once up and running again, some oddities were there, like Little Snitch not working right although I flipped the appropriate Settings switches, which did not hold, and then I tried to restart twice, confirmed and nothing happened. Chose shut down and nothing appeared to happen, and as I was clicking elsewhere the Mac shut down.
I took a break and have just now re-erased it and am migrating all but the System Settings in case something odd was in there. It will be time consuming to configure again but at least I feel like this time the Macs permissions and all will be fresh and provide a good point from which to resume.
Thanks @josehill , you are correct! see my reply above to @mschmitt … I’m usually not this stupid but the Mac has worked so well last few years I haven’t gone thru this process in a while and am anxious and worried so maybe not properly concentrated…
The next Big Adventure will be getting this MBAir setup with admin and standard accounts then learning all I can about Sharing so I can set up the Mini properly, which is what I was doing when this started.
First thing I notice to correct is that although I gave a location the time is set to Cupertino.
Yes it seems to be working now. Spent about an hour going through System Settings checking everything, opened some key apps, checked email and so on. Seems to be working ok now though I’m not educated enough to know if the permissions and behind the scenes things are working right, but the weird behaviors and lack of permissions seems to be gone.
Oddly enough, after the second erase, I chose to migrate from the same CCC backup as the first one, and I deselected System Settings to migrate, yet most of the settings were as I had left them before, I only had to change a few of them. Similar to erasing some iPads last winter. It was supposed to erase everything but didn’t.
Little Snitch was initially indicating it was damaged and could not repair itself, needed an Extension permission switched on. Did that and came back to it some minutes later and it repaired itself and is working again.
Orion browser indiated it was damaged and offered a button to remove it so I did. VueScan same, with a note that its download date could not be determined. Anyway, looking usable but I will stay on guard before fully trusting it and resuming backup and normal usage.
I’ve hit the “damaged application” problem after doing a restore from a clone, both when truly recovering from a hard drive failure, and when testing a bootable clone. I’m not sure if the application is truly damaged, or if it is just that the Gatekeeper database is out of sync.
I don’t know of any way to get it to re-scan the application once it has decided it is damaged. It doesn’t work to move it. Nor to zip it, delete the application, unzip it. The only solution I’ve found is to reinstall the application from the original source.
And that’s one reason I save downloads.
I think system settings are distinct from per-user settings. The former affect all users and are stored in /Library/Preferences. The latter affect only one account and are stored in ~/Library/Preferences.
If you restore your full user account (not just its documents), then it should end up restoring all your user settings, even if you aren’t restoring system settings.
If it’s a Gatekeeper thing, you can see if you can open it by popping up the app’s context menu (right-click or ctrl-click it) and select Open from there. This sometimes gives you the option to override it with a password.
Also, after Gatekeeper blocks an app, there should be a button you can click in System Settings (under “Privacy & Security”, if I remember correctly) to grant permission to run the blocked app.
If neither of the above fail, you can use the xattr command from a Terminal window to manually remove the Quarantine flag:
xattr -d com.apple.quarantine /Applications/QuarantinedApp.app
If none of those work then yeah, a reinstall may be necessary.
Aha, ok that would make sense, I didn’t know about that. The migration option had no Info button or anything to explain it and the tick box was for System Settings iirc, which to an average user would mean every setting in System Settings. There was a separate tick box for Privacy and Security, which I left ticked for restoration.
Probably too late by now, but when I have discovered something very recently gone bad like this mis-step of applying to enclosed items, I have rolled the whole machine back from a TM snapshot on the local drive, You can pick any time from the previous 24 hrs. It is much quicker than EACAS and restore from backup.
Howard Oakley has had a recent article about this little known method.
Wow, yeah rolling back to a snapshot would have been something to try. Ah well. At least now I feel like I have a fresh setup with proper settings, though it took quite a few hours to do. Thanks!
I feel really dumb asking this …. when you refer to the “home folder”, what is exactly is that?
I’m referring to your user folder in /Users. In theory macOS is multi-user and everything used by a user is in the user’s user folder.
Apple calls it the Home folder; see Finder > Go > Home.
Not just theory. In reality. Just like all Unix-based operating systems.
My Mac has four accounts - an administrator, my normal login, one for my wife and one for my daughter.
Although only one of us can be logged in to its console (display, keyboard and mouse) at a time, all can be logged in at once via SSH and other kinds of remote-access tools.