I thought about it too - the "apps" would be modules in a standard format, and for example calibre could have an option of (un)installing given modules(which would mean rebuildng autorun.xml and adding/removing support files). It's actually fairly easy since it's xml and we could use standard libraries - the only thing to care about are overlapping names. I'm working on it - as soon as I figure out, how to put multiple "windows" into autorun.xml and switch between them, I'll post it here.
greetz
Martin
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