I have a late 2011 MacBook Pro. It originally came with Lion and I upgraded to Mountain Lion on Release day. I did not do a clean install. I just let the upgrade run. I recently did a really stupid thing and played around with folder permissions. After realizing that I messed some things up I ran the disk utility to repair permissions. It did not solve my current problem. So I am thinking about formatting and doing a clean install. My question is this....I have a backup in time machine from this morning. I would very much like to use the migration assistant with time machine to restore all my programs and Itunes stuff. If I tell it to restore my whole system from the time machine am I going to be restoring my current problem back onto my system since my newest backup is from after I caused the permissions problem? Also since I have installed and uninstalled many programs since I got my mac will doing a full restore put all the stray files that were left behind when removing those old programs back too? Any help on this would be great.