Allan Eckert wrote:
If you clone your system to another formated drive, the directory structure on that drive would not be corrupt so when you clone if corruption of the directory is causing the problem, the clone should not have that problem.
This is not necessarily true: a clone made by the +block copy+ method will preserve any directory corruption on the original, since it is just a block-by-block copy without regard for what those blocks contain. Several cloning utilities, including Disk Utility & Carbon Copy Cloner, will use block copying when possible because it is faster than the file copy method. The file copy method (the only one used by SuperDuper!) is not a workaround for this -- it will eventually fail if it can't resolve the bad links in the corrupted directory structures, the same as would a Finder copy (which is essentially what it is).
However, running Disk Utility's verify or repair disk step beforehand will generally at least detect if not repair the directory damage. So whatever cloning method you use, run this before making the clone. Most dedicated cloning applications, including Carbon Copy Cloner & SuperDuper!, have built-in options to run the verify disk step automatically, so use them.
IOW, cloning doesn't repair file or directory damage. A good cloner "blesses" the system & performs the other necessary chores to make the clone bootable that copying alone cannot do, & may do other things like skip copying temporary files that will just be created anew on each startup anyway, but these are not repair steps.