> Why does standalone Tomcat need any more integration with the system than an app with embedded Tomcat? They are both Java applications.

With an embedded Jetty my app can just be a jar or set of jars. Tomcat has a directory structure and ships as a binary rather than a jar so I'd need to unpack it and worry about it being linked correctly for the target system.

> Tool support is not server specific. In both cases you set the appropriate VM arguments. What XML file would you have to edit?

I forget the name - catalina.xml or something? You can't just run ./tomcat -agent:myagent.jar. because it won't pass the arguments through to the JVM, unless that's changed.