PSA for people running FW 4.12 (and more generally, I'd say anything > 4.8):
If you're developping stuff that tries to restart Nickel on its own when it exits, make sure you reset PWD to a sane value first (say, /), because having a PWD located in onboard leads to wonderfully sneaky breakage of USBMS handling in Nickel, which leads to massively twisty issues that are hard to make sense of, and may wreak havoc on your filesystem.
I've fixed this in today's KOReader nightly, and Plato was also fixed in v0.6.3

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TL;DR: As usual, I'd recommend making sure your custom software is *always* up to date

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In the mean time, when in doubt, reboot

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