The messages are produced as a consequence of your project's dependencies.For example:Verification of class org.hibernate.metamodel.source.annotations.JandexHelper failed and will not be available for authoring. Please check the necessary external dependencies for this project are configured correctly.This is caused by failure to effectively instantiate JandexHelper (see here).
If a class cannot be instantiated then it is not available for rule authoring. We show the warning to alert the user.
The Project Editor only exposes course grained features for the average user. You can edit the underlying pom.xml, adding whatever fine-grained exclusions you may require, for your project using the Administration Perspective.
There are some occasions when you receive an error popup. We are currently working to address this (they'll become errors in the Problems Panel).
With kind regards,
Mike