Restored from backup with Migration Assistant - now have many folders at root level?

[cmarcus]

My MacBook Air recently needed a hard drive replacement. I was able to make a full SuperDuper backup before it went in to the shop. When it came back I erased the new hard drive, did a clean install of OS X 10.5.7, then launched Migration Assistant and used it to migrate all my files from the SuperDuper backup to the hard drive.

That process all went smoothly (thanks SuperDuper!) but when it was over I had many more folders on the root level of my hard drive than I'd had before. Here are all the names of the folders:

Applications
bin
cores
etc
Library
private
sbin
System
tmp
Users
usr
var
Volumes

Some of these are familiar to me and I'd like them to stay (Applications, Library, System, Users) but the rest are unfamiliar. I'm guessing I shouldn't delete those folders, right? What should I do to get the root level of my new hard drive looking like the root level of my old hard drive?