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I have recently bought an SSD and I am getting ready to clone my windows partition and such.

The partition I wish to clone is smaller than the size of the SSD, So if I expand the partition will I screw anything up like the partition alignment or allocation size?

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Use something like dd or dd_rescue from the Linux command line to clone the partition (or drive) bit for bit. It will not screw any of the structure up since it is essentially making a mirror image of the drive. The only other advice I can give is to be careful when you clone the drive so you don't destroy any of your data.

Once the disk is cloned just use something like gparted to expand the drive to use the maximum amount of space.

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