When I first was dealing with this back when the GM released, I found some sandboxing activity monitor process I could quit that would temporarily alleviate the issue, but I seem unable to locate it now. Are all my files from time machine damaged in some way? The data all seems to be there and works well if I can get it to open, but something about using sandboxed applications with the files does not work. I've been dealing with this problem for months and nothing I try solves it. Quitting and reopening the app seems to be the only way to open a new file from those directories. It seems to be a sandboxing issue, as it only effects things like Preview, Pages, and Sketch (apps I know to be sandboxed). I've tried repairing ACLs on the folders and files. I've tried removing extended attributes on the files. I have checked, double checked, and triple checked for permissions problems and I can't find any. It's not until I try to open a second document of any type: "The file “Messages.pdf" couldn’t be opened because you don’t have permission to view it." If I open an image or pdf in Preview while the app is closed, it works fine and opens the document.
I OFTEN (not always) cannot save to folders that I brought in from time machine. New documents created on my machine work perfectly as long as I avoid any folders brought in from time machine.
I even tried many clean installs and dragged my documents from time machine manually. Ever since I updated to El Capitan (the GM candidate when I first updated, now on the most recent version) many of my documents will not open in sandboxed apps.
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