flow timeout v2.1

Rebase and small cleanup of https://github.com/inliniac/suricata/pull/1256

Prscript:
- PR build: https://buildbot.openinfosecfoundation.org/builders/inliniac/builds/94
- PR pcaps: https://buildbot.openinfosecfoundation.org/builders/inliniac-pcap/builds/94