Which distribution?
Which configuration files?
Distributions as a whole are simply collection of applications and the linux kernel. Configuration files vary wildly among each distribution and each version there of.
To manage most configs you simply need to be able to parse a text file.
Some applications are a little more complicated and use various others means to store data, but it would be difficult to go into all of them.
What I've seen from most utilities that manage multiple configuration files. They tend to store data in a central location and rewrite the config file in question on the fly. (Or lack of storage, simply recreate the configuration file based on user input).
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