Re: doomed to fail
One more thing came to mind. C4G could add special sections to all configuration files as soon as it first sees them and user approves. These sections could be marked with special comments.
There could be predefined places for eg. things to keep, things to ask user about, security critical stuff and stuff that can be removed (and archived) if need be.
Btw. Thanks for this discussion.
Re: doomed to fail
There is always a point, where this (it's called Configuration 4 GNU (C4G) :), has to throw it's hands in the air and admit it has no clue about a given file. However it can try to do it gracefully and it can also try to push that point as far as possible. Anyway, C4G will probably have to check software versions and inform the user if it is not familiar with given version.
If it can't fully understand a file, it could offer to revert the file to previous version. It could also try to identify the weird bits and ask the user for a policy about them. Maybe it could even give the user searches to documentation of the particular package version.
If a more sophisticated user or program added the weird bits manually it/he could have also added special comments telling both C4G and regular user what to think about them. Some config files have some syntactical structure that could also help with these kind of decisions.
Many users also only upgrade their system with full releases of given distro (+ security upgrades hopefully). Then it could be expected that C4G and the all packages around are fairly well in sync.
Also, C4G will hopefully have modular enough architecture that only small part of it will need to be changed/upgraded when any given package is changed. Maybe there could even be some-kind of online service that given specific software versions, would provide new versions of some C4G modules and metadata.
PS. Apologies for everybody about that duplicate link I posted above :) I thought I was so clever to stumble upon it :I