How to use Github to manage dotfiles?

The above answers are excellent and are exactly how I would do it on "real operating systems".

I ran into an issue with this on a well-known commercial OS using cygwin/msys whereby using symlinks can sometimes be problematic with "native" ports of some of my favorite software.

To work around this I experimented with just making the folder $HOME be a git repository directly. After some failures I found the key is all in the .gitignore file.

So the setup I've been using for a while was created by making $HOME a repository, making a .gitignore file, and adding the required "dotfiles" files individually. I also added a repository on a backup up drive (z: in this case) as an upstream just to gain the automatic backups. If you're folder is already backed up, adding an upstream is an unnecessary complication. So, assuming "/z/Backups/Dotfiles.git" is a pre-existing "bare" repository, in msys shell, the steps to set things up are:

$ cd $HOME
$ git init
Initialised empty Git repository in $HOME
$ git add .bashrc .emacs .gitconfig # for example
$ git commit -m "Initial import of dotfiles"
[master (root-commit) xxxxxxxx] Initial import for dotfiles
 3 files changed, xxx instertions(+)
 create mode 100644 .bashrc
 create mode 100644 .emacs
 create mode 100644 .gitconfig

# The following two lines just add an "upstream" purely for backup purposes.
$ git remote add origin /z/Backups/Dotfiles.git
$ git push -u origin master
<< snip >>

Next I put the following into $HOME/.gitignore:

# First exclude everything.
*
# then re-include all "dotfiles"
!/.*
# then a bunch of specific excludes as they are more-or-less "cache" data rather than configuration.
/.bash_history
/.dbus-keyrings/
/.emacs.d/
/.gimp-2.8/
/.git/
/.gitk
/.idlerc/
/.lesshst
/.saves/
/.thumbnails/

Finally the following commands (apologies I didn't capture the output from these) add the .gitignore itself to the repository:

$ cd $HOME
$ git add .gitignore
$ git commit -m "Added some rules so git status on the dotfiles is useful."
$ git push

Now any "normal" files you add to your home dir get ignored by the dotfiles repo, but any new dotfiles show up in git status e.g.:

$ cd $HOME
$ touch NewFile.txt
$ git status
On branch master
Your branch is up-to-date with 'origin/master'.

nothing to commit, working directory clean

$ touch .funkychicken
$ git status
On branch master
Your branch is up-to-date with 'origin/master'.

Untracked files:
  (use "git add <file>..." to include in what will be committed)

        .funkychicken

nothing added to commit but untracked files present (use "git add" to track)

So far this has been working well, even with some subdirs being their own (unrelated) git repository. Sometimes there are "quirks" with non-git subdirs, but so far nothing problematic.

I'm using git repository (github) and bash script to creating symlinks. But now I found this tool which seems to be more powerful. Check it out: https://github.com/shanx/python-dotfiles.

The main source of information about dotfiles is dotfiles.github.io.

It references blog posts like Using Git and Github to Manage Your Dotfiles, based on a symlink method.

For starters, we’ll be putting all of our dotfiles into a folder called dotfiles, like so: /home/smalleycreative/dotfiles/vimrc.
Then, we’ll simply symlink to them from our home directory.

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Jaime mentions the Atlassian tutorial "The best way to store your dotfiles: A bare Git repository"

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

Well, it's three years later and nobody has come up with anything great so i took a stab at this problem. It's platform agnostic and shell agnostic with no dependancies other then the bourne compatible shell you have available(bash, zsh, ksh, etc). It works on mac, linux, & windows:

dotsys

It will automatically synchronize changes to your dotfiles with github and multiple machines, along with many other features.