I truly wasn’t able to follow everything you wrote. But just to those auto generated files: It’s not Lucee which creates them… it’s Tomcat according to the definitions of your server.xml. That is how Tomcat runs its servlets and Lucee is nothing more than a Java servlet. I’ve read you are using/changing webapps and docBase paths. You need to be very careful changing those, cause it might happen in certain configurations, that Tomcat will autogenerate web contexts and these can be identified by Tomcat again and regenerate Web Context for those Web Contexts, having a recursive newer ending generation.
Please read as an example: