Git not working over AFP
We've run into the same issue repeatedly, especially as we try to use XCode 6. I'm currently changing over my connect to our server to WebDAV (connecting to our server via Finder > Go (menubar) > Connect to Server... > https://localnetworkIP/userfolder/).

This is working for us (so far).

UPDATE: After a few days, I noticed a new issue using WebDAV: files would disappear from view in the Finder causing XCode/Git to think that the file had been deleted. Looking at the server showed that the files were still there.

I then changed my connection type to SMB. This has worked well for me: Git no longer encounters file permission errors, and Finder (OSX 10.10 Yosemite) doesn't "loose" files.