Before 5-oh, it has been possible to install the Alfresco Repo directly in the server root.
Since 5-oh, we have two additional deployments that need to be installed on the same server. One of these need to be installed in the server root. Thus, it is no longer possible to install the Alfresco Repo in the server root.
It would be possible for the alfresco.war deployment to take over the functionality of these two web-apps so that it is still possible to install Alfresco in the server root. (We are already using this mechanism in the cloud deployment).
The optimal solution would be to make this configurable.