Allow protocols to have both app layer keywords, as well as transaction
based ones.

Our general logic and assumption is protocols either support one of the
above and not have both.
1. Fix assignment of signums, which affected how we used read
   sigs(priority wise) inside staging.

   Previously we would assign signums before sig ordering, and hence the
   order didn't actually reflect the order of the sig in the
   sig_list(assuming sig reordering changed the sig_list).  Staging would
   use the old sig_nums to decide the priority of sigs.
2. Fix sig ordering for flowvar, flowbits, flowint, pktvar sigs.   We have
   introduced a new priority to treat sigs with set + read as lower
   priority compared to set only sigs.
3. Previously we treated sigs with a "priority(keyword)" > another sig's
   priority, as a sig with greater priority than the later.  We have
   reversed it.  Now the sig priority ordering is 1,2,.etc.  Updated
   sigordering unittests to reflect the same.
Removed Signature->order_id and replaced it with Signature->num.