In the development documentation the description for the jandex indexes (Creating a Jandex Index) is not clear. It is important to emphasize two points:

1. The creation of the jandex index is recommended. The automatic scanning can be a long process and CPU consuming (CPU spikes). So manual operation avoids those penalties.
2. The current implementation is an all or nothing. If the index is added to a jar file in the module no scanning at all is done.

For example something like this could be added at the beginning of the chapter (but feel free to change it):

"The annotations flag requires that the module contain a Jandex index. In ProductShortName ProductVersion, this is generated automatically. However, adding the index manually is still recommended for performance reasons (automatic scanning can be a long and cpu consuming process that increases the deployment time). To add the index manually create a new "index JAR" to add to the module. Use the Jandex JAR to build the index, and then insert it into a new JAR file. The current implementation is an all or nothing, if the index is added to a jar file in the module no scanning at all is executed."