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No extra tooling, no symlinks, files are tracked on a version control system, you can use different branches for different computers, you can replicate you configuration easily on new installation.

The technique consists in storing a Git bare repo in a "side" folder (like $HOME/.dots or $HOME/src/dotfiles) using a specially crafted alias so that commands are run against that repo and not the usual .git local folder, which would interfere with any other Git repositories around.

If you haven't been tracking your configurations in a Git repo before, you can start using this technique easily with these lines:

git init --bare "$HOME"/src/dotfiles
alias dot_git='/usr/bin/git --git-dir=$HOME/src/dotfiles/ --work-tree=$HOME'
dot_git config --local status.showUntrackedFiles no
echo "alias dot_git='/usr/bin/git --git-dir=$HOME/src/dotfiles/ --work-tree=$HOME'" >> "$HOME"/.bashrc

• The first line creates a folder ~/src/dotfiles which is a Git bare repo that will track our files.
• Then we create an alias dot_git which we will use instead of the regular git when we want to interact with our configuration repo.
• We set a flag - local to the repo - to hide files we are not explicitly tracking yet. This is so that when you type dot_git status and other commands later, files you are not interested in tracking will not show up as untracked.
• Also you can add the alias definition by hand to your .bashrc or use the the fourth line provided for convenience.

After you've executed the setup any file within the $HOME folder can be versioned with normal commands, replacing git with your newly created dot_git alias, like:

dot_git status
dot_git add .vimrc
dot_git commit -m "Add vimrc"
dot_git add .bashrc
dot_git commit -m "Add bashrc"
dot_git push

If you already store your configuration/dotfiles in a Git repo, on a new system you can migrate to this setup with the following steps:

• Prior to the installation make sure you have committed the alias to your .bashrc:

    alias dot_git='/usr/bin/git --git-dir=$HOME/src/dotfiles/ --work-tree=$HOME'
  

• And that your source repo ignores the folder where you'll clone it, so that you don't create weird recursion problems:

    echo "dotfiles" >> .gitignore
  

• Now clone your dotfiles into a bare repo in a "dot" folder of your $HOME:

    git clone --bare [email protected]:bongardino/dotfiles.git "$HOME"/src/dotfiles
  

• Define the alias in the current shell scope:

    alias dot_git='/usr/bin/git --git-dir=$HOME/.dots/ --work-tree=$HOME'
  

• Checkout the actual content from the bare repo to your $HOME:

    dot_git checkout
  

• The step above might fail with a message like:

        error: The following untracked working tree files would be overwritten by checkout:
        .bashrc
        .gitignore
    Please move or remove them before you can switch branches.
    Aborting

This is because your $HOME folder might already have some stock configuration files which would be overwritten by Git. The solution is simple: back up the files if you care about them, remove them if you don't care. I provide you with a possible rough shortcut to move all the offending files automatically to a backup folder:

    mkdir -p /Desktop/config-backup && 
    dots2git checkout 2>&1 | egrep "[.]+[a-z]" | awk {'print $1'} | xargs -I{} mv {} "$HOME"/Desktop/config-backup/

• Re-run the check out if you had problems:

    dot_git checkout
  

• Set the flag showUntrackedFiles to no on this specific (local) repo:

    dot_git config --local status.showUntrackedFiles no
  

• You're done, from now on you can now type dot_git commands to add and update your dotfiles:

    dot_git status
    dot_git add .vimrc
    dot_git commit -m "Add vimrc"
    dot_git add .bashrc
    dot_git commit -m "Add bashrc"
    dot_git push

For completeness this is what I ended up with for OS X

#!/bin/bash
# this is terrible and not safe dont use it I was up late

bakup_dir="$HOME"/Desktop/dot-backup
git_dir="$HOME"/src/dotfiles
dots=$(curl https://raw.githubusercontent.com/bongardino/dotfiles/master/.gitignore)

function dot_git {
   /usr/bin/git --git-dir="$git_dir" --work-tree="$HOME" "$@"
}

git init --bare "$git_dir"
git clone --bare https://github.com/bongardino/dotfiles.git "$git_dir"

mkdir -p "$bakup_dir"

for dots in "${dots[@]}"
do
   : 
   file=$(echo "$dot" | cut -c2-)
   mv "$HOME/$file" "$backup_dir" || true
done

dot_git checkout
dot_git config status.showUntrackedFiles no