As a rule I try to avoid cPanel for hosting sites, I find the overhead of the control panel and the limited flexibility too confining for all but the simplest of sites. Occasionally though I need to deploy sites at work though to cPanel servers due to client requirements.
The default web location ( ~/public_html ) for an account works well in most instances. But this default can cause issues when deploying certain applications such as Zend Framework. in which you do not want the web server serving the root of application codebase as the site root.
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