The Tomcat managed container adapter assumes that catalina.base is the same as catalina.home.
However, this is not necessary true. For instance, when using Tomcat from Eclipse, the catalina.base (which includes the configuration files) is managed inside the Eclipse workspace. This allows the developer to modify Tomcat settings without affecting the system installation.
The fix for this problem is to add a configuration property named "catalinaBase" and honor if it's set when building the startup script.
This affects all the Tomcat managed containers (5, 6 and 7).