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Distro hoppers, how do you manage your config files?

I am currently trying to keep track of my config files in a repo to be able to get the configa back together easily if/when I change distro, but I am not sure if that's the best way or if I should be using some tool to help me since I some programs keep preferences in other directories other then $HOME (at least I think so). Can you guys share with me your must used/trusted simple process for this?

Thank you and specially thanks to everyone who is being helpful in this community for the past few weeks, I've learned much and got some very useful tips from the comments in my posts and in other people posts too.

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