A lot of folks seem to like storing their sites in the webapps directory, so performing a tomcat upgrade and wiping out the existing webapps directory is bad for those people.
Usually it's bad practice to customize a widely used installer to support a specific use case, but in this case enough people use the webapps directory that it would be better if we took some extra time to not wipe out the entire directory.
webapps directory contents is preserved (index.cfm and index.jsp is still overwritten with new versions for Tomcat 7 and Railo 3.3) in Railo 3.3.1.000 pl1
A lot of folks seem to like storing their sites in the webapps directory, so performing a tomcat upgrade and wiping out the existing webapps directory is bad for those people.
Usually it's bad practice to customize a widely used installer to support a specific use case, but in this case enough people use the webapps directory that it would be better if we took some extra time to not wipe out the entire directory.