This is an issue with Git darn it. A folder with no files simply doesnt exist... I will add an index.html in there to protect it.
2.) I thought a fix went in for that a while back. Check your assets/js/front.js and see if it says /applicaion/ in there anywhere. If so, git has stolen another commit from me.
3.) Good point. They should probably just be md5'ed to be certain.
