This is definitely a permissions issue, as I am experiencing the same thing. I do not know whether Apple has changed the authorization process/required permissions, but I'll add a pair of observations (which may or may not be obvious):
Alfred can still see all of my third-party, non App-Store-installed applications in my /Applications directory;
Running a `ls /Applications` command also shows only the aforementioned subset of the /Applications directory's contents, so my shell does not appear to have full permissions either!
Alfred does not appear in the Aut