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You could use my WebPortal mod to do JS / CGI apps using Kobo's webbrowser (some sample apps included), only problem is by default the browser refuses to start when wifi is not available. (And if wifi is available you could use actual webapps if you're not doing anything that specifically has to run on the kobo itself locally).
Apart from that it's all about writing a program that somehow manages to talk to the eink framebuffer / touchscreen directly and using strange ways (inotify and such) to put them into the Kobo menu...
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