Safari 13 update sets negative com.apple.quarantine -1 making multiple directories inaccessible Updated to Safari 13 today on Mojave 10.14.6 and suddenly a bunch of my ~/Library/ directories are inaccessible via terminal and other apps (even with sudo).  Checking the xattr I see:

com.apple.quarantine -1


Directories affected:

~/Library/Calendars (previously 28)
~/Library/Cookies (previously 15)
~/Library/Mail (previously 19)
~/Library/Safari (previously 15)


Two other changes in ~/Library/ I found are with:

com.apple.metadata:com_apple_backup_excludeItem -1


Directories affected:

~/Library/PersonalizationPortrait (previously 61)
~/Library/Saved Application State (previously 61)


Now I can't access these directories via terminal or some other apps.  Interestingly I can navigate to the directory with Finder.  e.g. Navigate to ~/Library/Safari/Extensions/  But when I click on Extensions.plist, Xcode does not have permission to open it.

I can't seem to find documentation on what the negative values mean and how to change it because sudo doesn't even have permission to change it.

Something more weird is my High Sierra machine doesn't have these com.apple.quarantine changes.

Update:  It's very possible that multiple directories outside ~/Library/ are also affected because my next Time Machine backup was over 1 GB and the only thing that changed is the install of Safari 13.

Update 2: My High Sierra machine's next Time Machine was over 11 GB after this one Safari 13 install.  Something weird is definitely happening with this update.
Ok, after wasting lots of time chasing this issue, I found one possible solution but it has raised more questions.

If I give Terminal Full Disk Access, the quarantine value shows the original values.  Which means either the Safari 13 update also contains Gatekeeper system updates or Apple pushed an independent silent Gatekeeper data update around the same time.

More questions:


Why was this working fine before?  Terminal never had Full Disk Access permission.
Note that Xcode still doesn't have permissions.  That means I need to give Xcode Full Disk Access too.
Why the huge difference in Time Machine backups post update?