Organize Dotfiles Per-App with GNU Stow

Most dotfiles tutorials use a flat structure where the repo mirrors $HOME directly. There’s another approach — organizing configs by app — that makes it easy to selectively install only what you need on a given machine.

Flat structure (common)

dotfiles/
├── .zshrc
└── .config/
    ├── ghostty/
    └── zed/

Running stow . symlinks everything at once, but you can’t easily install just one app’s config.

Per-app structure (stow packages)

dotfiles/
├── zsh/
│   └── .zshrc
├── ghostty/
│   └── .config/
│       └── ghostty/
│           └── config
└── zed/
    └── .config/
        └── zed/
            └── settings.json

Each app gets its own top-level folder that mirrors $HOME. Stow creates symlinks in the parent directory matching the internal structure.

Usage

Symlink everything:

stow */

Or install just one app — useful when setting up a server that doesn’t need a GUI config:

stow ghostty

Source: Dotfiles + Claude Code = my tiny config workshop