.dotfiles

Cross-platform dotfiles managed with GNU Stow. One repo. Many machines. Zero friction.

Table of Contents

• Overview
• Quick Start
• Structure
• Packages
• Hosts
• How It Works
• Pre-commit Hooks
• Adding a New Package
• License

Overview

Shared defaults live in common/. Host-specific overlays layer on top, so each machine gets exactly the config it needs — no conditionals, no templating.

Quick Start

git clone https://github.com/FridrichMethod/dotfiles.git ~/dotfiles
cd ~/dotfiles
git submodule update --init --recursive
./stow-all.sh <host-dir>   # e.g. mac, wsl-ubuntu, sherlock

.stowrc sets --target=~, so Stow links everything into your home directory.

Structure

dotfiles/
├── common/          shared defaults (stowed first)
│   ├── aria2/
│   ├── bash/
│   ├── conda/
│   ├── git/
│   ├── kitty/
│   ├── pymol/       submodule — auto-updated daily via GitHub Actions
│   ├── sh/
│   ├── ssh/
│   ├── tcsh/
│   ├── vim/
│   ├── wezterm/
│   ├── xonsh/
│   └── zsh/
│
├── mac/             macOS overrides
├── wsl-ubuntu/      WSL Ubuntu overrides
├── lab-ubuntu/      lab Ubuntu overrides
├── fedora/          Fedora overrides
├── ubuntu/          Ubuntu overrides
├── sherlock/        Stanford Sherlock HPC
├── marlowe/         host overrides
├── win/             Windows-side config (WezTerm, .wslconfig)
│
├── stow-all.sh      one-command installer
├── dotfiles-update.sh
└── .stowrc          Stow defaults (target = ~)

Packages

Category	Tools
Shell	Zsh, Bash, POSIX sh, tcsh, xonsh
Terminal	Kitty, WezTerm
Editor	Vim
Version Control	Git, SSH
Science	Conda, PyMOL scripts
Utilities	Aria2

Hosts

Host	Platform	Layers
mac	macOS	bash, git, sh, ssh, zsh
wsl-ubuntu	WSL 2	bash, git, sh, ssh, zsh
lab-ubuntu	Ubuntu (lab)	bash, git, sh, ssh, zsh
fedora	Fedora	bash, zsh
ubuntu	Ubuntu	bash, zsh
sherlock	Stanford HPC	bash, sh, zsh
marlowe	Custom host	bash, sh, zsh
win	Windows	wezterm, wsl

How It Works

common/zsh/.zshrc  ──stow──▶  ~/.zshrc
mac/git/.gitconfig ──stow──▶  ~/.gitconfig   (overrides common)

1. common/ is stowed first — shared baseline for every machine.
2. <host>/ is stowed second — host-specific files override or extend common.
3. Stow runs with --no-folding, so individual files are linked (not entire directories).

Pre-commit Hooks

Optional but recommended — keeps configs clean before every commit:

pip install pre-commit   # or: brew install pre-commit
pre-commit install
pre-commit run --all-files

Hook	Scope
shellcheck	.sh, .bash*
shfmt	.sh, .bash*, .zsh*
stylua	*.lua
built-in	whitespace, EOF, merge conflicts, YAML, JSON, TOML

Adding a New Package

# 1. Create the package directory mirroring $HOME paths
mkdir -p common/newtool/.config/newtool

# 2. Add your config files
cp ~/.config/newtool/config.toml common/newtool/.config/newtool/

# 3. Stow it
stow --dir=common newtool

License

MIT