WARNING: [SetPropertiesRule]{Server/Service/Engine/Host/Context} Setting property 'source' to 'org.eclipse.jst.jee.server:AppName' did not find a matching property.

You can change the eclipse tomcat server configuration. Open the server view, double click on you server to open server configuration. Then click to activate "Publish module contents to separate XML files". Finally, restart your server, the message must disappear.