Config fixes for Ubuntu 14.04

refs #7293

Apache now expects sites-[available|enabled] to end in .conf, so update dev
creation to create 000-default.conf

Gearman no longer creates a PID file that can be checked for. Instead,
check for the existance of the gearman process directly.
Dev-install: Do not install AtoM 1.3
Upstart: Add timeout waiting for Gearman