I found that I can use:
ignore.default = \A#.*\Z
\A.*~\Z
\A.*\.py[oc]\Z
\A.*\.sw[nopx]\Z
\A.*\.swpx\Z
\A\..*\.tmp\Z
\A.*\.git\Z
In /etc/xdg/ubuntuone/syncdaemon.conf to ignore files. I'm not really up on regex so I tried to add the last line to ignore the .git folder. It doesn't appear to be working though. Anyone have a correct solution?
A friend of mine suggested \A.git\Z for the .git folder. It seems to work effectively. The end result was the following ignore.default in /etc/xdg/ubuntuone/syncdaemon.conf: