Secret Management Best Practices

Keep secrets out of your dotfiles repository. This step-by-step guide covers three production-tested methods for managing API keys, tokens, and credentials safely with Chezmoi: age encryption for local-first security, SOPS for structured YAML/JSON secret storage, and 1Password CLI for zero-disk-exposure retrieval at apply time.

Why This Matters

Dotfiles repositories are often public. A single committed API key, token, or password can lead to:

• Account compromise within minutes of push.
• Cloud billing abuse from leaked cloud credentials.
• Supply-chain attacks when CI tokens are exposed.

Golden Rules

1. Never store plaintext secrets in version control.
2. Encrypt at rest — use age, SOPS, or a secrets manager.
3. Verify before every commit — automate with pre-commit hooks.

Method 1: Chezmoi + age (Recommended)

age is a simple, modern file encryption tool. Chezmoi has native integration.

Setup

# Install age
brew install age    # macOS
sudo apt install age  # Ubuntu

# Generate a key pair
age-keygen -o ~/.config/chezmoi/key.txt

# Tell Chezmoi to use it
chezmoi edit-config

Add to ~/.config/chezmoi/chezmoi.toml:

encryption = "age"

[age]
identity = "~/.config/chezmoi/key.txt"
recipient = "age1xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"

Encrypt a file

# Add a secret file as encrypted
chezmoi add --encrypt ~/.config/gh/hosts.yml

# The file is stored encrypted in the source directory
cat "$(chezmoi source-path)/encrypted_dot_config/gh/hosts.yml.age"

Template secrets

# Use Chezmoi templates for inline secrets
chezmoi edit ~/.bashrc

export GITHUB_TOKEN="{{ (bitwarden "github-token").notes }}"
export AWS_ACCESS_KEY_ID="{{ pass "aws/access-key-id" }}"

Method 2: Chezmoi + SOPS

SOPS (Secrets OPerationS) encrypts specific keys in YAML/JSON files, keeping structure visible.

Setup

# Install SOPS
brew install sops   # macOS
sudo apt install sops  # Ubuntu

# Create a SOPS config
cat > .sops.yaml << 'EOF'
creation_rules:
  - age: >-
      age1xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
EOF

Encrypt

# Create a secrets file
cat > chezmoi-data.yaml << 'EOF'
github_token: ghp_xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
aws_key: AKIAIOSFODNN7EXAMPLE
EOF

# Encrypt with SOPS
sops --encrypt --in-place chezmoi-data.yaml

Use in templates

Add to chezmoi.toml:

[data]
[data.secrets]
source = "sops"
path = "chezmoi-data.yaml"

Method 3: 1Password CLI

1Password CLI (op) retrieves secrets at apply-time without storing them locally.

Setup

# Install 1Password CLI
brew install --cask 1password-cli   # macOS

# Sign in
op signin

Use in Chezmoi templates

export GITHUB_TOKEN="{{ onepasswordRead "op://Private/GitHub Token/credential" }}"
export NPM_TOKEN="{{ onepasswordRead "op://Development/npm/token" }}"

Advantages

• Secrets never touch disk unencrypted.
• Team sharing through 1Password vaults.
• Automatic rotation support.

Pre-commit Safety Net

git-secrets

# Install
brew install git-secrets  # macOS
sudo apt install git-secrets  # Ubuntu

# Configure for your repo
git secrets --install
git secrets --register-aws

# Add custom patterns
git secrets --add 'ghp_[A-Za-z0-9_]{36}'
git secrets --add 'sk-[A-Za-z0-9]{48}'

.gitignore

Always exclude sensitive paths:

# Secrets - never commit
*.age
*.enc
*.key
.sops.yaml
chezmoi-data.yaml
key.txt

.chezmoiignore

Prevent Chezmoi from managing sensitive files:

.ssh/id_*
.gnupg/
.config/chezmoi/key.txt

Audit Checklist

• [ ] No plaintext secrets in source state: chezmoi archive | tar -tf - | grep -v '.age'
• [ ] age key is not committed: git ls-files | grep key.txt returns nothing
• [ ] git-secrets hook is active: git secrets --scan
• [ ] .gitignore covers *.age, *.key, .sops.yaml
• [ ] dot doctor passes with no warnings
• [ ] SOPS-encrypted files decrypt correctly: sops --decrypt chezmoi-data.yaml

Tested On

Platform	age	SOPS	1Password CLI
macOS Sonoma+	✅	✅	✅
Ubuntu 24.04	✅	✅	✅
WSL2 (Ubuntu)	✅	✅	⚠️

Related

• About
• Compatibility Matrix
• Security Aliases