It is suggested that you can uncomment and set initial variable values in settings.php with the $conf array.  In doing so, and not seeing my variables set when retrieving using variable_get, I discovered that conf_init(), when called to initialize the configure file path, it sets $conf to a string.  I know that since it initializes settings.php within the context it conceptually SHOULD reset it to a variable, but it doesn't.   I proved this by changing the variable array name in settings.php, variable_get, variable_set, variable_init and conf_init to $config_vars and the values I initialized in settings.php were reflected when my application later retrieved them using variable_get.

This bug is currently hindering the flexibility of an application that I'm writing that will be deployed to different environments.  I initially tried to set the variables in the 'variable' table of the Database in order to retrieve them with variable_get but that method only accesses the cached variables in $conf (or in my case, $config_vars.  Is this on purpose?  I see that variable_set will not only set the cached variable but will also set into the database.  This seems to be a bug as well to me.  Can someone clarify this for me?