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"If I try setting the security attributes manually I get a warning "The permissions on Restricted are incorrectly ordered, which may cause some entries to be ineffective."" First this warning is normal for directories that have emulated UNIX-style permissions. If you try to manipulate it manually without knowing what you're doing you can mess it up worse (though I'm not sure how it would have gotten messed up in the first place).

A fix that's worked for me in the past is to do something like the following. In the Sage shell run:

$ setfacl -b -k /dot_sage

This strips all ACL (access control list--how Windows manages file permissions) entries from the /dot_sage directory. Then reset it so that you own the directory, and so that it has safe permissions:

$ chown -R $(whoami):$(whoami) /dot_sage
$ chmod -R u+rwX /dot_sage