First thing - don't try to fix anything.
Check when your last back up was done. If you don't have a backup - stop and back up this Mac to a blank external drive (ideally) using time machine and be sure you have a good backup before proceeding.
Now write down some details:
- When did you start the update.
- What was the previous version (
softwareupdate --history should tell you all the recent updates on the Mac)
- What is the state of your storage (
diskutil list is a good indicator to share with someone technical )
Decide if you want to use Apple, someone local to work with, or trust us randos on the internet to know what your setup is and hopefully give good advice. The problem with us, is no matter how smart, honest and well intentioned we are - we only see your word and if you are mistaken, we may give you bad advice. Also, we could just be evil but hopefully if you are patient - votes will help see if we're all evil together or someone has good advice.
Finder now shows documents belonging to some sandboxed applications.
No other application shows these extra folders. In particular Terminal commands and Finder replacements, like Path Finder and ForkLift, do not show the folders.
The folders are only present in Finder when an application has put data in the ~/Library/Containers/app/Data/Documents folder.
The applications I see in ~/Documents all have content in iCloud Drive though the files in iCloud Drive are not the same as in Finder.
In my case, I see the pseudo-folders for 3rd party applications like BBEdit, iThoughtsX.
This behaviour seems to be designed to mimic the behaviour of the Files application in iOS.
There is no known way to turn off this behaviour. But I would be glad to shown wrong on this.
It is not a good idea to just delete the folders or the files in them. Deleting the files is likely to cause problems when using the applications because the content has been created by the application.
My solution is to create a new folder ~/MyDocuments and put all my documents in there. That leaves ~/Documents for Apple to manipulate.
If you dislike this behaviour, submit feedback to Apple.
Best Answer
Everything is correct. This is all due to the split of the system volume (Macintosh HD or whatever you called it) into a read-only volume and a read-write volume.
Start by looking at the disk with Disk Utility. Press Command-2 (or tick Menu -> View -> Show All Devices). You should see something like this (the names will be different):
Within the APFS container you can see two volumes. In myself case BethSSD and BethSSD - Data. In what follows replace these with your own system volume name.
BethSSD is the read-only (highly protected) volume created by the macOS install and has the same content same on every Mac with the same version of macOS.
BethSSD - Data is a read-write volume and contains everything not part of the read-only volume. As well as your files, it includes all the application you have installed.
So we have two volumes and both will have applications - so Finder does some trickery to show them as one.
Taking your three locations (but in a different order) and a fourth:
2 The applications on the read-only volume are the Apple macOS applications and can be seen in
/System/Applications.4 (what you have not seen): In Terminal do
ls /System/Volumes/Data/Applications. Here you will see all the applications you have installed - but none of the inbuilt macOS apps.1 and 3. macOS combines the two locations above into one using "firmlinks". These are what you are seeing as
/System/Volumes/<name>/Applicationsas well as/Applications.I hope that helps. To go much further requires much mind bending!