Rename "site" to "domain" in code

We deprecated site in favor of domain in user interfaces.
There are still some references to "site" in the code.
This will help prevent confusion for helios developers.
Also, there's stuff in puppet to set the HELIOS_MASTER env var to site:// blah on the machines in the cluster itself, so after this goes in, do the appropriate puppet change to change the env var to domain:// blah.