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What is the proper way to checkout a bunch of .*rc files into a home directory?

I've seen lots of github repos online and people usually name them dotfiles, and I guess they get checked out into their home directory; but what I don't understand is...

How does one keep their other home files (specific to that machine) separate from their .*rc related files?

For instance, you would not want to store /home/<username>/Documents in the dotfiles git repo, but you would want to store .vimrc, /home/vim in the repository.

I'm aware of using .gitignore to ignore files for a repository, but I don't want to add an entry to .gitignore every single time I add a file to /home/<username>/Documents. Is there a way to do this the opposite way, that I only specify the files and directories related to my dotfiles project to be included in the repository?

Also, if I create a new feature branch for something that I'm already developing, and I check it out, I don't want it to "blow away" the non-dotfiles folders etc when I check it out, or have git complain that the working directory isn't clean before cutting a new branch.

Would this somehow require the use of git submodules?

What I'd really like to do with this is be able to get on a new Linux box and with the required dependencies installed check out a common version of my .*rc files and related files from my repo, so if I fix it on one, I can just pull the changes to the other machines.

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An option is to use symbolic links. For example, say I have my git checkout out in ~/.dotfiles. I might have:

.vimrc      -> ~/.dotfiles/vimrc
.bashrc     -> ~/.dotfiles/bashrc
.bash_login _. ~/.dotfiles/bash_profile
...

I would not, personally, check my home directory itself into the repo.

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