Dan,
Some files do have special handling and merging. Take a look at the
files in the directory /etc/mcp/templates/
For example,
/etc/mcp/templates/apache2.conf
begins with the comments:
# X: ----------------
# X: This file is used to automatically generate the httpd configuration
# X: file based on configuration information obtained from the Isilon
# X: Web UI.
# X: The resulting configuration file is stored at
# X: /usr/local/apache2/conf/httpd.conf
# X: ----------------
So I'd put modifications for the web server into the template file
/etc/mcp/templates/apache2.conf
You can then restart the web server from the UI, at which point it
will splice in any parameters it gets from the UI (for example,
filling in the DocumentRoot) and sends the merged httpd.conf to all
the nodes.
The catch is that if/when you upgrade, you can lose the changes. So
keep track of what you have changed.
Eric