Use PacketGetFromAlloc() instead of malloc and PACKET_INITIALIZE().

Replaces:

  Packet *p = SCMalloc(SIZE_OF_PACKET);
  memset(p, 0, SIZE_OF_PACKET);
  PACKET_INITIALIZE(p);

with:
  Packet *p = PacketGetFromAlloc();

In some cases, also remove redundant:

  p->pkt = (uint8_t *)(p + 1);

Since that is done in PACKET_INITIALIZE() inside PacketGetFromAlloc().

This has the same effect, but is more clear and simpler. All the places
where PACKET_INITIALIZE() was used are updated. There are more cases
that SCMalloc() memory, but don't use PACKET_INITIALIZE().

Also fixes some indentation problems in affected code.