Just to clarify: the applications folder for these applications are not part of the installation. They are generated when these applications are deployed (the first server start up after installation). Your log showed that subsequent loading of these applications in later server start ups failed, that is due to the applications folder not present. We need to figure out why these application folders were not created the first time. Seems the applications may fail to deploy for some reason when the server first starts up after installation.
Can you re-install the server and start the server and look at the log? That log should tell you whether the applications were deployed successfully or not, and if not, the exception associated with it.
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