stream: fix sequence number on smsg

Set correct starting sequence on the smsg. This causes smsg to be
inspected slightly earlier.
detect: only inspect smsg for valid tcp packets

Packets that are rejected by the stream engine are not considered
part of an established tcp session. By allowing them to inspect
an smsg, some smsgs would not be properly inspected.
delayed detect: init threshold at proper time

Don't initialize threshold before rules on delayed detect. Bug #1000.
Bug 1061: fix multiple vars per sig in ordering

In sigordering rules that had multiple vars doing the same operation,
like setting multiple flowbits, would not be considered correctly.

Bug 1061.
iprep: fix reputation loading and reloading

When an IP is listed in multiple categories, each new "load" would clear the
previous loads for that IP.

Bug #976
Fix parsing of 'custom' detect grouping values

Also, add error checking

Bug 892