Let me add my humble opinion.

1. This confusing matter is definitely turning people away from ubuntu.
I also think the user should have some knowledge to make a difference
between a partition and a disk, or where grub2 is installed at all, but
we simply can not blame only the user. You simply can not offer a list
of all disks and partitions, and add to it "if in doubt select all".
Period...

2. The more important thing, and I think this deserves URGENT BUG REPORT
ON ITS OWN, IMMEDIATELY!!!! Have you noticed that if you do this upgrade
in wubi, it will actually write to the real hdd MBR and partitions???

I am relatively new to ubuntu and I don't know the correct terminology,
but: wubi is sort of virtual install of ubuntu inside windows. It places
a file and everything is inside that file, allowing the user not to
partition before installing and keeping his partitions safe. That was
the point if I understand it, right?

Well, has anyone noticed that this upgrade in wubi is writing grub2 to
the hdd MBR and the partitions (depending which boxes you select when it
asks you where to install grub2)? And, while selecting wrongly all
partitions in a dual boot allows you to at least continue booting
ubuntu, because only booting windows will suffer, with wubi you are
almost certain to lose booting capability completely. Because grub2 was
never on the MBR, windows bootloader is there. So even if you select
grub2 to be installed only to the MBR, it will write to the real MBR of
the disk, not to the virtual one.

How did you allow a virtual system to write on the real partitions? For
example, if you have a test OS in Virtual Box, you expect it to stay
there, right? And even if you trash it completely, who cares. Now
imagine your test OS writing and messing up your real partitions, not
only the virtual hdd. What is that if not complete disaster???

Anyone familiar with meierfra's boot info script will notice it right
away, others may need to look little closer. Take a look at the results
in post #13 here:
http://ubuntuforums.org/showthread.php?t=1500321&page=2

The user never had a full dual boot, only wubi installed inside windows.
After upgrading the wubi to 10.04 and unfortunately selecting all boxes
when asked what to do, the MBR and all partitions ended up with grub2,
regardless that wubi should be virtual only. Thus, the computer is
completely unbootable because it was using windows bootloader on the MBR
to boot, with an ubuntu entry in it. And even if the user had selected
only /dev/sda when asked, that would still mess up everything because it
would overwrite the windows bootloader with a grub2 install which has no
/boot/grub files to turn to, because full ubuntu is not even installed
on the machine.

-- 
Ubuntu Lucid grub2 dist-upgrades result in confusion
https://bugs.launchpad.net/bugs/576724
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