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Isn't it good idea to detect already installed (not runned) ASes and check configured ports or at least make a suggestion to user to check ports' numbers twice before installation to avoid future conflicts?
Very-very valid. And not a difficult task.
A warning "banner" should now appear is at least one of the installed GlassFishes or SJSAS'es is using one of the selected ports as its http/https/admin port. That's the best we can do at the moment. -> FIXED