Once you start getting into Linux, you'll notice that most applications are configurable through dotfiles; files like .bashrc, .vimrc, .inputrc et cetera. These files normally reside inside your home directory, and this is often the cause of severe file clutter.

There's multiple ways to make this mess a lot more manageable. I personally use GNU Stow, a tool to manage symlinking packages of software/data.

At one point, my home directory looked approximately like this:

├── .bashrc
├── .gitconfig
├── .i3
├── .tmux.conf
├── .vim
├── .vimrc
├── .Xresources
├── ...

A bunch of files and folders related to configuration of applications I use daily. When your dotfiles are structured like this, you have practically no way to use version control and/or keep track of every single file. Migrating your configurations to another machine is even more of a hellish task.

Enter Stow and Git! You can create a single folder ~/dotfiles that will contain all of your configuration files and folders split up into packages. My dotfiles folder looks like this (I left out the Git folders):

├── bash
   ├── .bashrc
   └── .inputrc
├── git
   └── .gitconfig
├── i3
   └── .i3
├── powerline
   └── .config
├── tmux
   └── .tmux.conf
├── vim
   ├── .vim
   └── .vimrc
└── x
    ├── .xinitrc
    └── .Xresources

The dotfiles folder is also a Git repository with a remote on Github. I use Stow to manage symlinking for me:

cd ~/dotfiles
stow bash
stow vim
stow i3

Stow will symlink to the contents of the specified folder from the home directory (you can also specify a target by using -t).

That's all there is to it! If anything is unclear, feel free to contact me.