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At the moment, I am using rsync to backup my /home directory. At the moment, I am excluding some 'dot directories' like ~/.cache, ~/.mozilla, etc. The problem with this is that most of the time spent during a backup is updating all the dotfiles or directories, must of which I don't [think] I care about.

If, instead, I switched to excluding all but certain hidden directories, which ones are important to have backed up? I will, of course, backup things like .zshrc and .emacs, but what else (if anything) is important?

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This is subjective as it depends on what applications you use and what you think is important.

For me I back up .gitconfig .subversion/ .ssh/ .my.cnf .face .thunderbird/ .liferea/

How many of those do you have? Would they be important to you.

Here is a good way to find out:

Set up a new user, log out an log in as that new user, then copy over all the files and directories from your real home directory that you need to get your new user to a working state.

Then that is what you need to backup.

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