You can download Dolphin 6.0.0003 to 6.0.0004 Diff to see file changes.

http://www.boonex.com/trac/dolphin/wiki/6.0.0003to6.0.0004

We keep in mind that you are modifying the default set up. So Diff is the best tool to see the difference and perform the upgrade without any loss.
Though, this will take much time and efforts.