Adds subdirectories to submit test
new_job no longer creates the 'stage' directory

It still returns its full path, but the directory doesn't exist yet at
that point.
Uploads the job directory in one go

scp.py crashes when uploading multiple directories at this point. Until
this is fixed, let's work around it.
Merge branch 'avoid-scp-bug' into 'master'
Merge branch 'master' into 'vistrails'