Issue
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You want to add Command Line Jenkins Parameter arguments to Tomcat as specified in https://www.jenkins.io/doc/book/installing/
Resolution
The major part of these parameters are useless if you deploy the war within Tomcat. They are useful only if you are using the embedded (jetty) web server.
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httpPort, httpListenAddress, httpsPort, httpsListenAddress, ajp13Port, ajp13ListenAddress are all set in your server.xml at tomcat level.
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prefix will be the war name (/jenkins by default) but you can change it like any other webapp in tomcat with a context.xml file (or in server.xml)
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argumentsRealm.* are usable only with the embedded web server ( https://www.jenkins.io/doc/book/installing/war-file/ ) and for tomcat you have to consider to use the Standard Security Setup ( https://www.jenkins.io/doc/book/security/managing-security/ )
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Xdebug .. in Tomcat you have to use the JPDA_xx settings if you want to do a remote debugging ( https://cwiki.apache.org/confluence/display/TOMCAT/Developing#Developing-Debugging )