use fewer 'run' methods when deploying

each run method is a separate ssh call to the server
remove unused applications
clean up more unused applications
fix 'clone' bug when updating jnlp snapshot

In rails >= 3.1, the clone method copies the id, so the code changed here
doesn't actually create a new object, it just modifies an existing one.
This could be replaced with dupe, but that isn't really useful because
all the properties are being modified anyhow.
fix syntax error
our servers don't have X-Sendfile support
Merge branch 'master' into topic_np_student_offerings_page2