App Layer v13

This is #745 plus my own set of fixes, cleanups and name changes. It's huge.

prscript:
build ok: https://buildbot.suricata-ids.org/builders/inliniac/builds/117
pcap expected fail: https://buildbot.suricata-ids.org/builders/inliniac-pcap/builds/38
This is one test failing because we disabled ssh keyword for now.