[whpalmer4]

Unless you've changed your Flagged perspective from the factory default, the Inbox should not appear, because the Inbox doesn't appear in context-mode perspectives. If this change was unintentional or no longer desired, open the Perspectives window with Perspectives->Show Perspectives, select the Flagged perspective, and select Revert Perspective to Default Settings from the gear menu at the bottom left of the window.

If you want to continue with the Flagged perspective in a project mode view (why?), or wish to edit a project mode perspective to show only projects and not the Inbox, you can proceed mostly as wilsonng suggests, but you'll get better results if you skip the Focus step, and instead select the top-level Library folder in the sidebar, then check the Restore Selection box in the Perspectives window. Using Focus will work, but leaves you with a continuing maintenance issue in that every time your list of projects changes, you potentially have to rebuild any perspective like this to have the current list of projects.