Just a couple of minor convenience suggestions (as I'm getting back into AppGameKit from discovering an old never-finished project):
A "Rename" function for included project files could be handy (on right-click on an editor tab and / or left-hand panel project overview list)
A "Save Project As" function (which if saved in a new folder then also do a "Save All" into this folder, including media folder(s) and contents etc.).
( Perhaps a "Project" menu for project related functions as well, to separate these from the "File" menu stuff? )
Granted these might not be overly important (no hit for AppGameKit in a search), especially as the "Windows Explorer method" works good enough. At least for copy and rename of the project folder and the AppGameKit project file.
But it's a bit cumbersome with additional project source files (with the duplicating, renaming, open file then adding said file to project, then removing the old named files from project, then deleting said old named files in explorer... maybe I'm doing it wrong though?) Changing any #include directive probably should be as-is; manual editing. Or should it?
EDIT: Minor edit for clarification.
Apologies for any typos and strange grammar.