Typically, installed applications have their own configuration files, with their own syntax, etc. It is important that these files be kept separate from the base system, so that they may be easily located and managed by the package management tools.
Typically, these files are installed in /usr/local/etc. In the case where an application has a large number of configuration files, a subdirectory will be created to hold them.
Normally, when a port or package is installed, sample configuration files are also installed. These are usually identified with a .default suffix. If there are no existing configuration files for the application, they will be created by copying the .default files.
For example, consider the contents of the directory /usr/local/etc/apache:
-rw-r--r-- 1 root wheel 2184 May 20 1998 access.conf -rw-r--r-- 1 root wheel 2184 May 20 1998 access.conf.default -rw-r--r-- 1 root wheel 9555 May 20 1998 httpd.conf -rw-r--r-- 1 root wheel 9555 May 20 1998 httpd.conf.default -rw-r--r-- 1 root wheel 12205 May 20 1998 magic -rw-r--r-- 1 root wheel 12205 May 20 1998 magic.default -rw-r--r-- 1 root wheel 2700 May 20 1998 mime.types -rw-r--r-- 1 root wheel 2700 May 20 1998 mime.types.default -rw-r--r-- 1 root wheel 7980 May 20 1998 srm.conf -rw-r--r-- 1 root wheel 7933 May 20 1998 srm.conf.default
The file sizes show that only srm.conf has been changed. A later update of the Apache port would not overwrite this changed file.