Does anybody have a suggestion for how to move the root partition to a new drive and set up grub2 to boot on that drive? I seem to have no luck instructing grub-mkconfig what it is I want to do (e.g. chroot'int into my new root just confuses all the scripts).

Background I am running Debian Squeeze on a headless low-power NAS. My current setup is / on sda0 and /boot on sde0 (a CF card): I needed the separate /boot because sd[a-d] need to do a delayed spin-up. Now I've found an old 2.5" IDE disk to use as / including /boot to allow me to spin all the big disks down.

What I've tried Basically I went

mount -o rw /dev/sdf5 /mnt/newroot
cp -ax / /mnt/newroot
cp -ax /boot /mnt/newroot/boot

Then I tried

chroot /mnt/newroot
update-grub

But that failed with grub asking if root was mounted. Then I did a half-hearted attempt at setting up /mnt/newroot/grub/grub.cfg to find the kernel image on sdf5, followed by a grub-install --root-directory=/mnt/newroot /dev/sdf. But this just landed me a grub rescue prompt when I tried booting from sdf.

My backup plan is to just reinstall, so a bonus question (no checkmarks for this one): What do I have to do to get my lvm2 and mdadm config across? Is it all stored in the filesystems (and will it be automatically discovered), or do I need to take of it myself?

Solution (thanks to Maciej Piechotka): As Maciej points out, I need to do a proper chroot for all the grub tools to work. For reference, this is how I did it:

janus@nasguld:/mnt/newroot$ sudo cp -ax / /mnt/newroot
janus@nasguld:/mnt/newroot$ sudo cp -ax /boot /mnt/newroot

All the files are now copied (see here for a discussion of copy strategies). Fix the new etc/fstab to point to new root:

janus@nasguld:/mnt/newroot$ diff -u etc/fstab.old  etc/fstab
    -UUID=399b6a6d-c067-4caf-bb3e-85317d66cf46 /     ext3 errors=remount-ro         0 1
    -UUID=b394b614-a977-4860-bbd5-7862d2b7e02a /boot ext3 defaults                  0 2
    +UUID=b9d62595-e95c-45b1-8a46-2c0b37fcf153 /     ext3 noatime,errors=remount-ro 0 1

Finally, mount dev,sys and proc to the new root and chroot:

janus@nasguld:/mnt/newroot$ sudo mount -o bind /dev /mnt/newroot/dev
janus@nasguld:/mnt/newroot$ sudo mount -t proc none  /mnt/newroot/proc
janus@nasguld:/mnt/newroot$ sudo mount -t sysfs none /mnt/newroot/sys
janus@nasguld:/mnt/newroot$ sudo parted /dev/sdb set 5 boot on 
janus@nasguld:/mnt/newroot$ sudo chroot .

We are now chrooted to the future root exactly as it will look. According to Maciej, it should be ok to just call grub-install, but I did an update-grub first to get a look at the generated /boot/grub/grub.cfg before installing the bootloader. I am not sure it will be automatically updated?

root@nasguld:/# update-grub
root@nasguld:/# grub-install /dev/sdb