Dotfiles, (i.e. configuration files) are a mess. The XDG Base Directory Specification would be a good solution, if only applications would stick to it. As it is, there are a number of applications that are all too happy to dump their .app_cache, .apprc or .appdata into your $HOME directory, regardless of how you set $XDG_*_HOME environment variables.

If you want to version-control your configuration files, this is a problem.

Using dotlink, you can not only treat your configuration as code, but their location in your system as well. This means you can write an user.link file like the following:

# You can specify which files to link where
link "dotfiles/xinitrc" "$HOME/.xinitrc"
link "dotfiles/Xresources" "$HOME/.Xresources"
link "dotfiles/zprofile" "$HOME/.zprofile"
link "dotfiles/profile" "$HOME/.profile"
link "dotfiles/zshrc" "$HOME/.zshrc"
link "dotfiles/inputrc" "$HOME/.inputrc"
link "dotfiles/bashrc" "$HOME/.bashrc"
link "dotfiles/bash_profile" "$HOME/.bash_profile"
link "dotfiles/Xresources.d" "$HOME/.Xresources.d"

# And you can hierarchycally include other .link files 
include "config.link"
include "scripts.link"

and dotlink will link all the files to their correct locations by simply running:

$ dotlink path/to/user.link

Dotlink also performs all the operations atomically, it will not make any changes to your system unless it has verified that you can make all the changes (for example, the link names are not existing non-symbolic-link files and you have relevant permissions to create such links).

Finally, you can keep all your configuration files in the same place commit them to a source control repository with ease!