see: ppsi#25

softPLL was set in BC mode and current_reference changed during
the measurment. The problemw as that the before-measurement
setting was not recovered. This caused problems, in particular
during LPDC rx calibration of other ports.

printf makes the messages to be logged in syslog in strange order
with respect to the other messages. It's best to use pr_* consistently.

NC: Add patches for 1GB NAND flash on SCB3.4.1. These patches are (tested) backwards compatible with the original SCB3.4.

In the rx calib FSM, this is needed to over the case when the
calibration is re-started (INIT state entered) during execution
of the FSM (e.g. due to link unplugging, or timeout).

In the tx calib FSM, in theory this is not needed, yet it seems
clean and it might be needed in the future if some sort of
reset is implemented.

changed from daemon.info to a new option default_syslog that
uses daemon.info as default and additionally parses syslog
messages for info about facility,priority and uses this info
if available.

Some deamons/etc that log messages to syslog do not specify facility.level
in their messages. The logger is configured to parse the message looking
for facility.level (option: --prio-prefix). If the message does not include
If no facility.priority is specified, the logger will use the one specified
after -p, this is now provided. For example, PPSi does not specify
facility.priority in messages (hopefully, this will change), without
"-p daemon.info", it was reported as user.info. If user wishes to,
he/she can override. This is the default config

Signed-off-by: Maciej Lipinski <maciej.lipinski@cern.ch>

- behavior for different VLAN modes was incorrect (in table and text)
- updates per changes in v6.0 were needed.