Here's a list of files that had major changes since 0.6.3:

[ Administration ]
- due to directory structure change nearly all important adminminstration files

[ Main ]
- due to directory structure change nearly all important main files 

[ Template ]
- templates/mgbModern/main/newentry_bbcodes.tpl
- templates/mgbModern/main/newentry_body.tpl
- templates/mgbModern/main/newentry_preview.tpl [NEW]
- templates/mgbModern/general/captcha.tpl

[ Language ]
- language/[language]/lang_main.php