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I'm not able to replicate your issue using JBoss Tools 4.2.0 release. Can you tell me what version of JBoss Tools / JBDS you are using? It would also be helpful if you could outline your failing workflow a bit. The workflow I'm using is as follows:
1) Open server view
2) right-click, new -> Server
3) Expand the "Red Hat JBoss Middleware" category and select the "JBoss Enterprise Application Platform 6.1+" server type.
4) Click 'next'
5) Keep the server marked as "Local" and controlled by "Filesystem and Shell Operations"
6) click next
7) Fill in the runtime's home directory, specifically, point to your unzipped eap6.3 folder.
This is the point in the past where such errors would appear, but I am unable to make this error appear at this time.
Finally, are you using Windows, Linux, or Mac?
Thank you for your help. The problem was that the jboss-eap-6.3.0.zip had a different path from that required by eclipse (had extra unnecessary folders).
Your workflow steps were very useful and it helped a lot.
Thank you and have a nice day!