There was a problem with the logs directory. It contained logfiles that varied with each run thus
triggering the VCS to spot a change and want the logs checking in. These can be ignored in the .gitignore file
but by doing this the directory becomes empty and so doesnt get cloned. The next time the server is run then
it falls over because the directory doesnt exist. The fix is to put a blank .gitignore file in the logs directory.