I am Using GNU Stow to manage my dotfiles, I arrange my all dotfiles here, and there are many comments and references to ArchWiki inside them, which are very helpful.
Let me explain some diretories.
I follow Desktop entries to set my Default applications, and I do not use any DE, so there are only a $HOME/.config/mimeapps.list inside, at the same time, I set some environments to appoint default applications in the Shell sections.
I use less as the pager for git, and set some aliases.
I use meld as the differ for git.
No .gitignore, I advise that set .gitgnore for every program by yourself, just pull github/gitignore immediately.
.config/gtk-3.0/bookmarks: use for Nautilus. .config/gtk-3.0/setting.ini: GTK+ 3 config. .config/.gtkrc-2.0: GTK+ 2 config. .xinitrc & .Xmodmap: X11 config.
By the way, I write some scripts to reinstall Arch Linux quickly, but they are not practical as so far.