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Enable "Hide Empty Folders" in Make Target view. Notice that the view becomes completely empty and the "New Make Target" command is disabled. Either "Hide Empty Folders" should not hide projects. or "New Make Target" should not be disabled in this scenario.
I think it was working that way before and bug 313232 complains about that. I am unaware what caused the change in behavior. We may need a preference to accommodate the opposite requirements.
The most important requirement is to avoid user confusion. Adding a preference doesn't achieve this goal since the user may not be aware of the preference. One possibility is to hide empty projects only when there is at least a single target, so that the view doesn't become completely empty. Another option is to enable "New Make Target" without selection and prompt for project if there is more than one to choose from.