I am experiencing a very similar problem deploying an application on a Linux server. Although this is a GlassFish related post and the application is deployed under Tomcat, I don't think this problem is limited to GlassFish. I can confirm that the application successfully deploys under Windows and even an almost identical virtual machine to the Linux server running the same versions etc. Restarting/redeploying or any of the other suggestions above did not help in getting the application to work. Any ideas?
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