Various setup.sh fixes

This was failing on a brand new installation (worked fine for redeploying where it had already been used).  Some fixes.  Works here now on a brand new Ubuntu 12.04 install.
This is what the next lines do (if this doesn't already exist - i.e. existing production deployment - check if this was configured in the directory the script is being ran from - which will be the dev/test directory - and copy these over).  Unless I'm misunderstanding the purpose of this...