Changes to deployment process.

+ Grab a fresh copy of the code base rather than merging into the previous copy.
+ Copy over setup.php.
+ Note that this is intended for use when the media directory is OUTSIDE of the code base.
+ Note also that temporary files are not copied over, but this should be fine as they are after all temporary.
Add symlink to media path as part of deployment.
Being pedantic
Fix problem with undefined array, and skip linking non-existent setup.php.
Add missing trailing slash for correct rsync operation, and delete existing (empty) media directory.
Merge pull request #14 from leftclickben/FreshCopyOfCodeAndCopyInSetupPhp

Changes to deployment process.
Add init script
Merge branch 'InitScript' of https://github.com/leftclickben/cmis-tools into InitScript