I recently purchased a new MacBook Pro, with Mavericks. I am using brew cask to install most of my applications, and it installs them into ~/Applications. I added this to my Alfred configuration, and I have reset my index a few times, but Alfred just refuses to index anything in ~/Applications.
I have tried repairing file permissions, re-indexing, deleting application cache, etc... The only thing I haven't tried is a full uninstall and reinstall.
Has anyone else experienced problems with Alfred 2 and Mavericks?