Thread: Filing Projects
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If you want to move a project into a folder, tap on the project's header to get the editor window. Tap the Info button if that section wasn't previously selected. Tap the Move button, and you'll get a list of folders. Tap the folder where you want it to go.

If, once you have it in the proper folder, you want to reorder the contents of the folder, go to the Project view in the sidebar, and drill down into that folder. Then tap the gear menu and choose Edit Sidebar (need to have the iPad in landscape orientation for this to be present). Drag the projects into the order you want using the three parallel lines at the right hand end, then tap Done.