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I had a pretty broken GRUB set up where booting required the enter key to be pressed. However today I ran sudo reboot and it powered off and came back up without a hitch. I doubt I fixed my GRUB issue (unless apt-get upgrade/update would affect it) so I thought that maybe the reboot doesn't go down as far as GRUB?

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    apt-get upgrade can regenerate grub configs, depending on which packages are upgraded. – jordanm Mar 30 '16 at 0:42
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reboot does a proper reboot, it won't bypass GRUB.

apt-get update would not affect it, but apt-get upgrade may have upgraded GRUB or installed a new kernel, and as a result regenerated GRUB's configuration.

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