You would have to modify Geany to use that distributed copy as the default when it creates a new config directory. IIUC currently it writes out defaults stored in the code.

Unless Geany is broken, it won't clobber the user's custom keybindings.conf file with hard-coded defaults, so if the MacOS launcher script puts some platform-specific keybindings.conf file in the user's config directory if it doesn't yet exist, Geany won't clobber it and instead use it as the defaults.

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