Using Disk Utility to make a bootable clone on external firewire hard drive

I was just experimenting with making a bootable clone of my Mac HD (OS X 10.5.2) on an external firewire drive. The external drive booted up and all programs worked. However, there were 3 extra folders on the clone: Dev, Net, Home. The folders were empty so I deleted Dev and Net, just to see what would happen. When I restarted the computer, it simply shut down upon reboot. So, I held the option key and rebooted back into my Mac HD.
My (5) questions are:
What are those folders?
Why were they put there?
Can I get rid of them, or hide them?
Once the bootable clone works as a boot drive, can I delete the data from my internal Mac HD or,
Does the bootable clone somehow rely on the internal drive for additional startup information?
Thank you so much for any information.
Dave

These are system folders that the OS needs to operate. DO NOT delete them.
They are normally invisible which is why you don't see them.
You should simply leave them alone. If they bother you visually and you want to hide them, open terminal and run the following command
*sudo chflags hidden /Volumes/"Nameoftheexternaldrive"/dev /Volumes/"Nameoftheexternaldrive"/home /Volumes/"Nameoftheexternaldrive"/net*
Put the name of your external in the above.
You'll be prompted for your admin password which you won't see. That's normal.
To answer your last question, a bootable clone does not rely on the internal drive in any way. You can boot from the clone and do whatever you like to the internal. However, it's not recommended to run your computer from an external for everyday use. Bootable clones should be mainly used for backups. If you hose your system on an internal, boot from the clone and clone it back to the HD.

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