It will indeed only refresh the current project (or, more specifically, the current selection in the project explorer). I just click somewhere in the project explorer, do Ctrl+A to select all projects and then press F5 to achieve a complete refresh.
You can set up the workspace to automatically refresh when it detects changes in the preferences. (Window > Preferences > General > Workspace > Refresh Automatically)
This answer led me to an even simpler solution, no configuration necessary.
Cmd-3 build all (control-3 on windows)
Edit: Correction -- I need to both refresh and build. Build does not automatically refresh. I'm currently using two actions, "echo" from my comment in the linked answer I just referred to (an External Tool configuration with a hook to refresh all), followed by cmd-3 "build all"