Introduction
For a drive with PC partitions (which is what you'll find on most USB sticks), the bootloader consist in a tiny part at the very beginning of the drive (the stage 1 bootloader, in the boot sector of the drive) and a larger part elsewhere (the stage 2 bootloader, in a file). The stage 1 data contains the physical location of stage 2. If you copy the whole device (what you tried with dd), the stage 1 part is in the same physical location and the stick works, but the new stick has to be at least as large as the original. If you recreate the partitions and copy the files, you're missing the stage 1 since it's not a file.
I think (but I haven't checked) that the stage 2 is in the first (FAT32) partition. If so, you can copy that partition wholesale, and copy the boot sector as well, then edit the partition table so that the second partition occupies exactly the space that's left, and copy the files on the second partition. You might as well keep a raw image of the boot sector and of the first partition in a file on a hard disk (but you can clone them from a USB stick too).
Making a clone of a different size
Below I'll call the device containing the original stick /dev/sdb and the device containing the clone /dev/sdc; substitute names as needed. Create mount points if needed. I assume that the FAT32 partition (at the beginning of the disk) is numbered 1 and the ext3 partition is numbered 2; substitute different numbers if needed.
First part, if cloning from a stick:
head -c 512 </dev/sdb >/dev/sdc
partprobe /dev/sdc
cat </dev/sdb1 >/dev/sdc1
First part, if cloning from image files:
cat boot_sector.img >/dev/sdc
partprobe /dev/sdc
cat first_partition.img >/dev/sdc1
The call to partprobe is needed so that the kernel reloads the partition table from the disk (it's in the boot sector, and the first command in either scenario above modifies the boot sector). If you omit it, either you'll get errors or the kernel will silently write garbage to the stick.
To make the image files:
head -c 512 </dev/sdb >boot_sector.img
cat /dev/sdb1 >first_partition.img
Now after you've got the boot sector and the first partition, you need to edit the partition table again, to resize the second partition. You can do this automatically by feeding the right input to fdisk. Warning, this is extremely error-prone, and I haven't tested it. If you don't feel completely comfortable with this part, do it by hand.
sed -e 's/ *#.*//' <<EOF | tr -s ' ' '\n' | tr -d _ | fdisk /dev/sdc
d 2 # delete partition 2
n p 2 # new primary partition 2...
_ _ # ... using all available space
w q # write and quit
EOF
Finally reload the partition table again, create an ext3 filesystem, and copy the files there.
partprobe /dev/sdc
mke2fs -j /dev/sdc2
mount /dev/sdc2 /media/sdc2
cp -a /media/sdb2/ /media/sdc2/
umount /media/sdc2
Simplified method to make a larger clone
If you prefer, you can store an image of the whole stick. You'll be able to use that image directly on any stick that's at least as large: just copy that image onto the new stick with cat <whole.img >/dev/sdc, then run partprobe /dev/sdc (or unplug the stick and put it back in) to re-read the partition table.
Then, if you like, you can enlarge the clone. In this order:
- Enlarge the partition. Unfortunately, I don't know how to do this in a simple way.
parted can do it with the move command (not resize, which resizes the filesystem), but you need to figure out the right arguments — switch to sectors (unit s) to avoid rounding errors.
- Enlarge the filesystem. That part is easy: just run
resize2fs /dev/sdc2 to make the filesystem use the whole partition size.
If you're starting from a larger stick than necessary, you can shrink it by following the steps above in the reverse order (first shrink the filesystem with resize2fs, then shrink the partition with parted).
Alternatively, you can first copy the stick to an image file, then work on that image file. To access the partitions, use a loop device, specifically associating a portion of the file to a disk. Here's a sketch of the steps if you want to shrink the image (warning, untested, proceed carefully and double-check the math).
fdisk -lu whole.img # note starting sector of partition 2: $S
losetup -fs -o $(($S * 512)) whole.img
# Let $D be the desired size of partition 2, in kB
resize2fs /dev/loop0 $ # replace /dev/loop0 by whatever losetup prints
losetup -d /dev/loop0
parted whole.img
# Use parted to resize the second partition
dd if=/dev/null of=/file/to/truncate seek=1 bs=$(($S/2+$D+1))k
