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I've been running strace to see if I could spot some file opening patterns here. Here's what I've found for now. (note, running FW 4.8.11073)
Opening and closing an epub is pretty glaringly obvious, as Qt spawns some ipc files in /tmp/. More specifically, "/tmp/qipc_sharedmemory_comkoboadobepixmapsurface<hash?> and "/tmp/qipc_systemsem_comkoboadobepixmapsurface<hash?> only exist when an epub is open. Note, <hash?> is a long string of hex that doesn't change between reboots, but could differ between devices/firmwares).
Opening a kepub seems to trigger Nickel to search for mime/packages in a few directories such as /usr/<local>/share.
Opening the home screen (not the book-list) seems to trigger Nickel to look for /mnt/onboard/.kobo/guide and /mnt/sd/koboExtStorage/guide. In my poking around, I haven't got it to try accessing the guide dir anywhere else.
That's was just a few of my findings after a bit of poking around. Don't know if anyone will find them of any use.
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