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Question:

Our latest game, built in Clickteam Fusion 2.5, is having trouble launching from the itch app. The setup file we're distributing is built with the in-engine Install Creator, which I guess isn't recognized by the itch app yet. Is there a way to make the itch app extract certain files contained in a ZIP to other directories, say, a subdirectory in AppData, or am I looking at changing my setup file into an InnoSetup executable?

ClickTeam's Install Creator is not supported (and won't be) because it doesn't allow silent installs.

I heavily recommend using butler to upload your game - the itch docs have everything you need to get started: