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I have GPT, EFI (or UEFI?).

I've installed Windows 7, then Kali Linux (in opposite order too), but Kali doesn't want to boot -- Windows wants.

I tried to use update-grub, tried to switch the bootable flag of Windows loading partition off, but Kali boots only after deleting that partition. The problem is -- I can't boot Windows in this case.

Also my update-grub doesn't see Windows 7 (I've installed grub-efi-amd64 using LiveUSB and chroot), so I'll have to resolve this problem too.

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You can try looking into using rEFInd's boot manager: rodsbooks.com/refind. I'm not sure how good GRUB's support of EFI is right now but rEFInd's site explains a lot of EFI's boot process. – MSumulong Jul 7 '14 at 12:59
Thanks, refind's found Windows either Kali, but can't boot the Linux. It says, that everything's okay, but nothing more -- I was waiting for five minutes looking at the black screen with white and yellow static text of refind. – Charlie Jul 7 '14 at 18:55
Did you add an entry into your refind.conf to point to Kali Linux? Otherwise you can add a grub.cfg in the EFI partition which points to Kali Linux (ie. same location as the EFI/Microsoft folder, make an EFI/Kali folder and I believe rEFInd will find it automatically). – MSumulong Jul 7 '14 at 20:24
It didn't want to recognize initrd and vmlinuz of my Kali Linux (automatic search and refind.conf didn't help), but when I've put grub.efi and grub.cfg from the /boot/grub/ to my EFI/Kali, it became working! Thank you! Although grub still not seeing Windows, but it's not critical now: I can boot them using refind :) – Charlie Jul 7 '14 at 22:54
Yea, there's no point in using grub to boot Windows anymore since rEFInd takes care of choosing which OS to boot. – MSumulong Jul 8 '14 at 15:10

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