Convention for primary app deployment dir structure on a Unix-like app server

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http://unix.stackexchange.com – The client I am working for deploys their application to a directory they created at the root level. While acknowledging it is a matter of local preference, I am unsure if this is in accordance with the generally accepted standard how to distribute an application's components across a Unix-like system. E.g. normally, I would put the binaries for my deployed app to /opt, conf files in /etc, logs under /var etc. But then again, this is the primary application the server is used for so it isn't exactly equivalent to untaring some 3rd party software into /opt. Still, personally, I would prefer (HowTos)