output: clean file desc at exit.

This is a beginning of implementation for bug #1660:
 https://redmine.openinfosecfoundation.org/issues/1160

This patch adds a cleaning function for each logger of new type
(packet, tx and file). These functions are called in RunModeShutDown().

The state of this patch is that it is crashing suricata when sending
pcap to analyse:
 - At first pcap if tx and file cleaning function are called
 - At second pcap if only packet cleaning function is called

The cause in first case is unknown. In second case this is due to
the necessity of cleaning the list of logger registered to a logging
type.