Dotfiles

Personal config managed with GNU Stow.

Setup

From this repo:

cd ~/dotfiles
stow <package>    # e.g. stow fish

Each package mirrors paths under $HOME. Example: stow direnv links direnv/.config/direnv/direnv.toml → ~/.config/direnv/direnv.toml.

On macOS, install Homebrew dependencies first and then run the macOS setup helper:

brew bundle
./setup/macos.sh

setup/macos.sh creates ~/.docker/cli-plugins/ and links Homebrew's docker-compose binary into Docker's CLI plugin path as docker-compose, so docker compose can find the Compose plugin.

Packages

Package	Main targets
alacritty	~/.config/alacritty/
atuin	~/config.toml
colima	~/.colima/_templates/default.yaml
direnv	~/.config/direnv/
fish	~/.config/fish/
git	~/.gitconfig
herdr	~/.config/herdr/config.toml
lmod	modulefiles under ~/dotfiles/lmod/modules (used from fish)
lsd	~/.config/lsd/config.yml
nix	~/.config/nix/nix.conf
nvim	~/.config/nvim/
proxychains	~/.proxychains/proxychains.conf
tmux	~/.tmux.conf
tmuxinator	~/.config/tmuxinator/
vim	~/.vscodevimrc

Stow multiple at once: stow fish git tmux.

If a target file already exists, adopt it into the repo first:

stow --adopt colima

Helper Scripts

The setup/ directory is not a stow package. It contains host setup scripts for machine-level steps that do not map cleanly to symlinked dotfiles.

• setup/macos.sh: macOS post-Homebrew setup. Requires brew and the docker-compose formula from Brewfile; links the Compose plugin into ~/.docker/cli-plugins/docker-compose.

Colima

Template for new Colima profiles (M-series baseline: 4 CPU, 8 GiB RAM, 60 GiB disk, vz, virtiofs, rosetta):

stow colima

• Template (versioned): colima/.colima/_templates/default.yaml → ~/.colima/_templates/default.yaml
• Active profile (not in dotfiles): ~/.colima/default/colima.yaml — Colima rewrites this on start, so do not stow it as a symlink.

Edit the template in dotfiles, or run colima template after stowing.

To apply template changes to an existing VM (cpu/memory/disk/vmType are fixed at create time):

colima stop
colima delete
colima start

Do not commit runtime state under ~/.colima/ (_lima/, sockets, daemon/, etc.).

Fish

HPC: ssh-cluster

VITO_PASSWORD is not stored on the SLURM cluster. On macOS it lives in Keychain; for cluster sessions, inject it per login:

ssh-cluster mycluster    # or: sshc mycluster

Same flags and host completion as ssh. Reads Keychain item VITO_PASSWORD for $USER, exports it on the remote shell for that session only.

Store the password in Keychain once:

security add-generic-password -a "$USER" -s "VITO_PASSWORD" -w

Use plain ssh when you do not need VITO_PASSWORD on the remote host. Batch jobs (sbatch) and VS Code Remote-SSH do not use ssh-cluster automatically.