Everybody has a lot of junk on their computer. Sometimes a lot of the stuff is a copy of something else and it's been changed. To straighten out the mess you need to merge the files. Scooter Software has a great product for finding the differences between two files and a simple way to merge them, it's called Beyond Compare. It works on Mac, Windows and Linux. Programmers use it a lot to figure out what changes other programmers made to files.

It also shows the differences between two folders and the folders underneath them. This is very useful. The tool is reasonably priced (currently $30) after a free trial. I just discovered they offer a Pro version which does some stuff I really like... but it's an extra $30. I highly recommend this tool.