Update first deployment clean logic, it used to be that we removed the entire content on the first deployment (before the actual deployment),
Now we will only remove the file that is initially created by IIS (or Azure) using a default manifest file.
Also updated the defualt site generated when creating a new site to be the same as Azure: hostingstart.html.

Fixes #397.
Fixes #376.
On delete repository, if delete wwwroot is not set, clean from wwwroot only files from the deployment/repository.
Fixes #398.
CR related fixes.