log: change default log level to notice

This patch updates the log level of meaningful start messages to
notice. It also sets the default log level to notice.
suricata: reorder start

Initalizing output just after configuration file parsing allow to
log almost all messages accordingly to configuration.
suricata: info message after log init

This patch moves version display after log init so we can have an
homogeneous display.
suricata: add -v[v] option to increase verbosity

This patch adds a -v option to suricata. It increases the log level
defined in the YAML.
Bug 640: add more tests to validate that issue is fixed
htp: for apache and apache_2_2 personalities, that are no longer supported by libhtp, fall back to apache_2 with a warning.
Store TX id with alerts

When generating an alert and storing it in the packet, store the tx_id
as well. This way the output modules can log the tx_id and access the
proper tx for logging.

Issue #904.
Display TX id in alert debuglog.
XFF: use per alert tx id

Use the tx id stored for each alert to find the correct XFF address
to add to the extra-data field.

In overwrite mode we still only grab the first available XFF addr,
as this address is set in the header preceeding the individual alerts.

Issue #904.
Update ssl parser protocol detection pattern strings.
Inside PP parser, we were using the return value from DetectPortParse as
the ip_proto value,  which is wrong.  We have fixed this now.
Reset app layer processed flag for segments that have been sent for proto
detection, but we failed to figure out the proto.

Updated a unittest to reflect the above change.
Fix for bug #989.

In case of recursive call to protocol detection from within protocol
detection, and the recursively invoked stream still hasn't been ack'ed
yet, protocol detection doesn't take place.  In such cases we will end up
still calling the app layer with the wrong direction data.  Introduce a
check to not call app layer with wrong direction data.

When sockets are re-used reset all relevant vars correctly.

This commit fixes a bug where we were not reseting app proto detection
vars.

While fixing #989, we discovered some other bugs which have also been
fixed, or rather some features which are now updated.  One of the feature
update being if we recieve wrong direction data first, we don't reset the
protocol values for the flow.  We let the flow retain the detected
values.

Unittests have been modified to accomodate the above change.
API renaming/beautification.
fix for bug #987.

We don't support jabber protocol detection atm.  Disable the code check
inside suricata to check if jabber protocol detection is enabled in the
yaml file.

Also updated an error log message for app layer.
Clean up rule reload logging
tag: add some debug statements
tag: fix session seconds tracking

Fix bug #995. Tag time setting was initialized using "usec" field
instead of "sec" field. This led to immediate timing out of tag.

Added proper matching unittests for all tagging types.

Bug #995.
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
Don't initialize threshold before rules on delayed detect. Bug #999.