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First of all, Jandex is a separate technology which doesn't need to be used by Weld depending in EE server and/or environment. It is used by default in WildFly and can be used in Weld SE, but I think other EE servers do no use it.
The code and code docs around Jandex can be seen here.
I am no Jandex expert myself, but what it creates (mkouba correct me if I am wrong ) is an index of all annotations that you can then easily browse/query for a complete information on a deployment without ever actually touching the java classes.
That means without the need to load them among other things. So while there is some footprint, it should be rather miniature and save you resources on other fronts.
As for how to configure it, I am pretty sure there has to be some way, but if you are talking WildFly, then it is WFLY that does Jandex building and Weld merely consumes the built index (which is another plus of Jandex, it is built once and many technologies consume it without the need to scan the deployment again). So this question would probably be a better fit for WFLY forums?
Hello and Thank you,
I will close this question and post it under the WFLY forums.