I have been managing my dotfiles using the alias below.

alias dot="git --git-dir=$HOME/.dotfiles.git --work-tree=$HOME"

Credits to StreakyCobra

To avoid committing your whole $HOME directory to git, use a .gitignore file:

# Ignore all files
/*
# but keep .ssh
!.ssh
# ignore everything under .ssh, to avoid committing rsa keys, known hosts, etc
.ssh/*
# but keep your config under vcs
!.ssh/config