query about creating CLI installer from source code

The same way tigase-xmltools and tigase-utils are separate projects in different SVN repositories, extras, pubsub and muc are also separate projects and are located in separate SVN repositories.
Please have a look at this address for a list of all projects available: https://svn.tigase.org/reps/

tigase-extras.jar tigase-muc.jar tigase-pubsub.jar missing when compiling server build but present in pre-compiled builds (tigase-server-4.3.1-b1858) available on tigase.org.

How are these jar files built?

If you compile Tigase code from sources and you are going to manually modify config files you can just forget about the installer.
After you compiled the Tigase from sources it is actually read to be run, no other installation is needed. Typical Tigase installation directory contains following subdirectories:

certs/     with certification files
etc/        with configuration files
jars/       with tigase-server.jar
libs/       with all other JAR libs
logs/      here are all logs created
scripts/  startup and administrator

And they all should be part of the SVN repository.

If you really want to create an installer version of the package you have to execute two scripts in the following order:

prepare-installer.sh
generate-installer.sh

Please note above scripts will pull the IzPack in correct version, patch it and generate the installer. There is no separate CLI and GUI installer. This is the same file which can be executed in two modes.