Rework Tile CPU affinity setting to handle non-contiguous sets of CPUs.

It is possible to have a non-contiguous CPU set, which was not being
handled correctly on the TILE architecture.

Added a "rank" field in the ThreadVar to store the worker's rank separately
from the cpu for this case.
unix-manager: fix crash when client disconnect

This patch fixes an issue in unix socket handling. It is possible
that a socket did disconnect when analysing a command and because
the data treatment is done in a loop on clients this was leading
to a update of the list of clients during the loop. So we need
in fact to use TAILQ_FOREACH_SAFE instead of TAILQ_FOREACH.

Reported-by: Luigi Sandon <luigi.sandon@gmail.com>
Fix-suggested-by: Luigi Sandon <luigi.sandon@gmail.com>
unix socket: fix valgrind issue

This patch fixes the following issue reported by valgrind:
 31 errors in context 1 of 1:
 Conditional jump or move depends on uninitialised value(s)
    at 0x8AB2F8: UnixSocketPcapFilesCheck (runmode-unix-socket.c:279)
    by 0x97725D: UnixCommandBackgroundTasks (unix-manager.c:368)
    by 0x97BC52: UnixManagerThread (unix-manager.c:884)
    by 0x6155F6D: start_thread (pthread_create.c:311)
    by 0x6E3A9CC: clone (clone.S:113)

The running field in PcapCommand was not initialized.
defrag: fix reconstruction

This patch is fixing an issue in defragmentation code. The
insertion of a fragment in the list of fragments is done with
respect to the offset of the fragment. But the code was using
the original offset of the fragment and not the one of the
new reconstructed fragment (which can be different in the
case of overlapping segment where the left part is trimmed).

This case could lead to some evasion techniques by causing
Suricata to analyse a different payload.
defrag: fix timeout setting when config is missing

When the config is missing, DefragPolicyGetHostTimeout will default
to returning -1. This will effectively set no timeout at all, leading
to defrag trackers being freed too early.
lua: fix liblua use on OS X with macports

Set the correct lua pkg-config name used by macports.
Update Changelog for 2.0.2 release
Fix lowercase table initialization (bug 1221)

The for loop needed to check for < 256, not < 255.
valgrind/magic: add suppression for known issue

Add suppression for Ubuntu 14.04 64bit.
Fix __thread configure check on Clang

AC_TRY_COMPILE puts the code in a function already, and Clang didn't like
the function within the function declaration. This lead to test failure.

Clang now properly detects __thread support.
Add initial travis-ci integration.
Update log-file.c

test whether tx_ud is NULL
Fix compile-time error on old kernels and ethtool.h
ethtool: add missing include necessary for CentOS5
htp: init memuse atomics

In case of the spinlocked fallback code the lock was uninitialized.
Profiling: fix compilation on CentOS5

Bug #1207
Open 2.1 development in the master branch.
autotools: enable silent mode

Add check to make sure that if the functionality isn't available, we
don't error out.
Update version number to 2.1dev
profiling: add pcap logger profiling

Tracks: file open, file close, file rotate (which includes open and
close), file write and open handles.

Open handles measures the cost of open the libpcap handles.