Pre-forwardServer config requirement

There's a bunch of stuff in here but nothing that should really change any behaviour, with the possible exception of server output. I've changed the log method so that it no longer prints to the server STDOUT as it was simply duplicating output. Everything still goes to the log file, and only summary server init messages go to the server STDOUT. I also standardised some of the server init log messages in preparation for the startCGSServers.sh script.

I've added support in the config and various modules to enable having reference/input data and output data outside of the main code directory. Your current relative paths(in ini files) should still work. As part of this I also split the settings file as previously discussed (setting_default.py and settings.example.py). I have added what I think is a working settings.MPII.py file. Take a look and check it out, simply copy it to settings.py to see if it works.  You'll be able to see what I've tried to do in settings.example.py, some of this didn't directly translate to the current MPII set up, so I've had to redefine a few things. If you happy with this, we should remove settings.py from the repo. (it's up to you whether you want to remove settings.MPII.py, but my choice would be to maintain this locally in case of accidental internal info being leaked). If you need to look at our setting.EBI.py I can send this via email.

Other than that the rest is random bug fixes and optimisation.

This is the 'Pre-forwardServer config requirement' pull request, as the next thing I need to do is remove the CGSServer.py round robin to server.php to get it's own settings. This will remove the config/startup inter-dependancy between the back and the front end. This make the new forwardServer settings mandatory.

Nath