Optimizations to reduce branch misses
Counters: remove unused updated field
Counter: fix accidental logic change
Counters: move perf critical var to the top of the SCPerfContext struct
Counters: fix delayed-detect counter registration

Make sure we register the detect.alerts counter before packet runtime starts
even in delayed detect mode. The registration of new counters at packet
runtime is not supported by the counters api and might lead to crashes as there
is no proper locking to allow for this operation.

This changes how delayed detect works a bit. Now we call the ThreadInit
callback twice. The first call will only register the counter. The 2nd call
will do all the other setup. This way the counter is registered before the
counters api starts operating in the packet runtime.

Fixes the segv reported in ticket #1018.
Support for configuration include files.
directory fixup
directory fixup
another fixup