Copy entire file system hierarchy from one drive to another

What you want is rsync.

This command can be used to synchronize a folder, and also resume copying when it's aborted half way. The command to copy one disk is:

rsync -avxHAX --progress / /new-disk/

The options are:

-a  : all files, with permissions, etc..
-v  : verbose, mention files
-x  : stay on one file system
-H  : preserve hard links (not included with -a)
-A  : preserve ACLs/permissions (not included with -a)
-X  : preserve extended attributes (not included with -a)

To improve the copy speed, add -W (--whole-file), to avoid calculating deltas/diffs of the files. This is the default when both the source and destination are specified as local paths, since the real benefit of rsync's delta-transfer algorithm is reducing network usage.

Also consider adding --numeric-ids to avoid mapping uid/gid values by user/group name.

Michael Aaron Safyan's answer doesn't account for sparse files. -S option fixes that.

Also this variant doesn't spam with the each file progressing and doesn't do delta syncing which kills performance in non-network cases.

Perfect for copying filesystem from one local drive to another local drive.

rsync -axHAWXS --numeric-ids --info=progress2

I often use

> cp -ax / /mnt

Presuming /mnt is the new disk mounted on /mnt and there are no other mounts on /.

the -x keeps it on the one filesystem.

This of course needs to be done as root or using sudo.

This link has some alternatives, including the one above

http://linuxdocs.org/HOWTOs/mini/Hard-Disk-Upgrade/copy.html