1. Create two java project, Project1 and Project2
2. Project1 depends on Project2
3. Enable KB support for Project1 (Proejct Properties->JBoss Tools Knowledge Base)
4. ASSERT: There is a warning on Project1 that there is no KB nature installed on required Projet2.
5. Go to Preferences->JBoss Tools->Web->Knowledge Base->Validator
6. Uncheck Enable Validation
7. Clean/rebuild Project1
8. FAILURE: The warning is still there

If you set "Capabilities are not enabled in Java uitl module" to "Ignore" then the warning disappears.
It looks like when we disable the KB validator at all then the old warning is not removed.