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I'm not sure if this was intentional, or if this is a problem, but when I open the App Store or Messages, they don't show up at all in the dock, but they run just fine otherwise. Why is this and how can I change this behavior?

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Here are some steps to fix problems with the Dock:

  • Run killall Dock from a terminal
  • Log out and back in
  • Reboot the machine
  • Reinstall the apps affected
  • Try to create a new user profile
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