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As seen below in output of parted, Windows 8/8.1 seems to use flags in GUID partition entries:

GPT disk

I guess that for example partition with hidden flag is not shown in Windows Explorer. However, does Linux also use GPT flags?

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Does it use GPT flags? Define use :)

The only "important" flag to Linux is the boot flag, and that's not directly handled by Linux per se: your system's firmware at boot time will select the filesystem with this flag and search therein for an EFI bootloader, boot that, and then the bootloader will use the filesystem in which it lives to configure itself and do all that it needs.

Linux probably wouldn't modify filesystem flags without your knowledge or consent, and I can't think of a way that it would rely on them as they're not too useful to a booted OS. If you were to also install a BIOS-based bootloader on a GPT volume, there's a flag for that and Linux might use that to determine where it should, say, update that BIOS bootloader.

Typically, you're on your own when it comes to filesystem layout and Linux won't make decisions for you. If you want your EFI volume mounted, you need to shove a line into /etc/fstab. If you have a separate /boot partition, you're going to need to shove that into /etc/fstab too. The only thing I can think of which might look at flags would be bootloader code/installation code, so possibly GRUB or rEFInd. (rEFInd probably just uses EFI variables, though, which are something else)

To answer your question about Windows, it maintains a "secret" partition and uses these flags to hide the partition from the operating system. It's still there and you can access it if you want, but it's made to be difficult. Linux couldn't care less if you call it secret or not, and if you plug in a hard drive with one of these partitions installed, it will show up and be displayed and may be automounted if your machine is configured for that.

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