Rob Stryker [https://community.jboss.org/people/rob.stryker] created the 
discussion

"Re: JBoss Dev Studio: jars from dependant projects disappearing from deployed 
wars"

To view the discussion, visit: https://community.jboss.org/message/751827#751827

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I have added the test over at:   
https://source.jboss.org/browse/~raw,r=42846/JBossTools/trunk/as/tests/org.jboss.tools.as.test.core/src/org/jboss/tools/as/test/core/parametized/server/publishing/defect/PublishWeb2DeletesWeb1LibsTest.java
 
https://source.jboss.org/browse/~raw,r=42846/JBossTools/trunk/as/tests/org.jboss.tools.as.test.core/src/org/jboss/tools/as/test/core/parametized/server/publishing/defect/PublishWeb2DeletesWeb1LibsTest.java

THe test imports the 5 projects with the structure you mentioned above. IT adds 
them to the server one by one, executing a full publish each time. It then 
verifies the new module publishes properly with its libs, and also, that the 
previouspublished modules libs still exist. 

The unit test fails to replicate your issue.     
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