I would add that the configured program should spit its final configuation back out as it starts up, either as a set of command line parameters into a log file,

I would add that the configured program should spit its final configuation back out as it starts up, either as a set of command line parameters into a log file, or if that gets out of hand, as a file in /tmp with all external cofigurable values explicitly written out. This simplifies the 3am fix problem somewhat, since some values will always be missing.