One thing we'll have to make sure is that AFTv5 and AFT can be deployed in parallel (because we'll be continuing use of the old system while we're trying the new one). This will likely mean changing message key prefixes, table prefixes, and other unique identifiers to avoid conflicts. We should aim to have both versions running on the prototype server ASAP.
So did you copy the extension on your local system, modify it, then commit it? That's the worst thing you could've done with regards to preserving history. You should use svn copy to make sure the history is preserved, and you shouldn't copy and modify in the same revision.
I outlined this in an e-mail I sent to Fabrice and Yoni on October 25th:
Also, please use svn copy to fork the extension, and svn rename to rename the files in your copy; that way history is preserved. Also, do not copy/rename and change a file in the same commit, doing so makes review harder. All this means you'll probably need 3 commits to fork the extension: one for a verbatim copy, one to rename all the files, and one to update the contents of the files to match the changed extension name, file names, prefixes, etc.
Please revert this revision and execute the clone properly. If you have trouble doing these things, I'm willing to do it for you.