Bean folder location

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I have an ear file that has an ejb.jar, web.war and others items(I will upload the ear file).

I have two items/issues:
1) We put the class files in the ejb.jar. When I do that my injection fails issues(I'm sorry but I don't have that message at this point but if u must have it, I can recreate). What I did was put the .java files in ejb.jar.
2). I would have expected to access the bean in the portalapplication/ejb/... but it's in the portalapplication/web folder. I think I can override this w/annotation in the bean but was curious if I did something in the setup causing this situation.

I had to remove some source files to get below 5 MB but nothing of reference to assist in determining the answers for the ?'s.

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I'm sorry but what is the actual question? Can you post the error?