Eclipse: How do I refresh an entire workspace? F5 doesn't do it

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.

If you want to refresh all Projects, ignoring closed projects, then the easiest way is to:

• ctrl-click and item in the Project Explorer (to ensure the P. Explorer has focus)
• ctrl-click the item again so that it's no longer highlighted (but the P. Explorer still has focus)
• F5 will now Refresh the entire workspace

Effectively F5 refreshes the Workspace when a navigation view has focus and nothing is selected.

Ctrl-A, then F5.

You can set up the workspace to automatically refresh when it detects changes in the preferences. (Window > Preferences > General > Workspace > Refresh Automatically)