Nix Os

name: nix-manager description: Manage Nix packages, flakes, and configurations using Determinate Nix installer patterns. Use when installing/updating packages, creating flakes, troubleshooting Nix issues, or optimizing Nix workflows. Keywords: nix, flake, package, nixpkgs, nix profile, flake.nix, flake.lock, determinate, nix-installer

Nix Package & Configuration Manager

Comprehensive Nix management following Determinate Systems best practices and this repository's patterns.

Core Architecture Components

1. agent-skills-nix (Framework)

The primary orchestrator for Declarative Skill Management.

• The Concept: Skills are self-contained directories with a SKILL.md (instructions/YAML frontmatter).
• The Mechanism: Uses a Home Manager module to "sync" selected skills into agent configuration directories (e.g., ~/.claude/skills).
• Key Feature: Supports Markdown Transformations. You can inject local paths to binaries (like jq or curl) directly into the SKILL.md so the agent doesn't have to guess where they are or download them, saving context tokens.

2. llm-agents.nix (Distribution)

A daily-updated collection of Nix packages for AI agents.

• Provides ready-to-use derivations for claude-code, codex, amp, and more.
• This is your source for the actual agent binaries.

3. khanelinix (System-Level context engine)

Beyond just "skills," this repo is a masterclass in Nix Meta-Programming for AI context.

• The Transformation Engine: Uses custom Nix logic (lib.importSubdirs + mapAttrs) to translate a single source of truth for agents and commands into:
  • Claude Code: Multi-part Markdown with YAML frontmatter.
  • Gemini CLI: JSON-friendly descriptors and prompt blocks.
  • OpenCode: Specialized frontmatter for tool permissions (bash, edit, write).
• MCP Integration: Directly imports mcp-servers-nix, treats MCP tools as system-level resources available across all host archetypes.
• Flake-Parts Partitioning: The entire system is modularly partitioned. You can swap neovim flavors (khanelivim) or shell environments without breaking the core system logic.

Instructions

1. Understand Repository Context

Check current Nix setup:

• Flake location: /Users/wcygan/Development/dotfiles/flake.nix
• Installation script: scripts/install-packages.sh
• Package management: nix profile (user-scoped, modern approach)
• Installer: Determinate Systems installer (macOS/Linux)
• Update mechanism: make update or nix flake update && nix profile upgrade

Read current flake.nix to understand:

• Input sources (currently: nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable")
• Package definitions (buildEnv with ~60+ packages)
• Outputs: packages, devShells, formatter
• Supported systems: x86_64-linux, aarch64-linux, x86_64-darwin, aarch64-darwin

2. Package Management Operations

Install New Package

Process:

1. Add package to flake.nix in appropriate category
2. Run nix flake check to validate
3. Run nix profile upgrade dotfiles to apply changes
4. Test package availability

Example:

# flake.nix packages section
paths = [
  # ... existing packages ...

  # New package
  cowsay  # Fun terminal tool
];

# Validate and install
nix flake check
nix profile upgrade dotfiles
which cowsay  # Verify installation

Update All Packages

Process:

# Update flake inputs (updates nixpkgs revision)
nix flake update

# Apply updates to installed profile
nix profile upgrade dotfiles

# Verify no breakage
nix profile list

Or use Makefile shortcut:

make update  # Runs both commands above

Remove Package

Process:

1. Remove from flake.nix
2. Run nix flake check
3. Run nix profile upgrade dotfiles
4. Old package remains in store but not in PATH

Note: Garbage collection removes unreferenced packages:

make clean  # or: nix-collect-garbage -d

3. Flake Configuration

Modify flake.nix

Common operations:

Add new input:

inputs = {
  nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";

  # Add new input
  home-manager.url = "github:nix-community/home-manager";
  home-manager.inputs.nixpkgs.follows = "nixpkgs";  # Prevent duplicate nixpkgs
};

Add platform-specific packages:

paths = [
  # Universal packages
  git gh lazygit
] ++ lib.optionals stdenv.isDarwin [
  # macOS-only
  darwin.apple_sdk.frameworks.Security
] ++ lib.optionals stdenv.isLinux [
  # Linux-only
  libnotify
];

Modify devShell:

devShells = forAllSystems ({ pkgs }: {
  default = pkgs.mkShell {
    packages = with pkgs; [
      fish
      nixpkgs-fmt
      shellcheck
      # Add development tools here
    ];
    inputsFrom = [ self.packages.${pkgs.system}.default ];
    shellHook = ''
      echo "🐠 Dotfiles development environment"
      echo "Run: make test-pre"
    '';
  };
});

Validate Flake

Always validate before applying:

nix flake check        # Full validation (slow, builds everything)
nix flake metadata     # Quick metadata check
nix flake show         # Show outputs without building

Common issues:

• Package renamed in nixpkgs (e.g., du-dust → dust)
• Missing comma in package list
• Invalid attribute path
• Syntax errors in Nix expressions

Update Lock File

When to update:

• Regular maintenance (weekly/monthly)
• Security updates needed
• Specific package version required

How:

# Update all inputs
nix flake update

# Update specific input only
nix flake lock --update-input nixpkgs

# Verify changes
git diff flake.lock

4. Troubleshooting

Slow Nix Operations

Diagnosis:

nix store info             # Check store size
nix store gc --dry-run     # See what can be cleaned

Solutions:

• Run nix-collect-garbage -d to remove old generations
• Run nix store optimise to deduplicate files
• Check network connectivity (binary cache downloads)

Package Not Found

Error: error: attribute 'package-name' missing

Solutions:

1. Check nixpkgs version: some packages only in unstable
2. Search for package: nix search nixpkgs package-name
3. Check if package was renamed
4. Try alternative package names

Evaluation Errors

Error: error: ... while evaluating ...

Common causes:

• Syntax error in flake.nix
• Recursive attribute access
• Type mismatch (string vs list)

Debug:

nix eval .#packages.aarch64-darwin.default.name  # Test specific attribute
nix repl                                          # Interactive REPL
:lf .                                             # Load flake in REPL
packages.aarch64-darwin.default.name              # Evaluate in REPL

Lock File Conflicts

Error: error: flake.lock is dirty

Solutions:

# Regenerate lock file
rm flake.lock
nix flake update

# Or accept uncommitted changes
nix flake check --impure  # NOT recommended for reproducibility

Profile Issues

List installed profiles:

nix profile list

Output format:

Index:              0
Flake attribute:    legacyPackages.aarch64-darwin.dotfiles
Original flake URL: git+file:///Users/wcygan/Development/dotfiles
Locked flake URL:   git+file:///Users/wcygan/Development/dotfiles?rev=...
Store paths:        /nix/store/...-system-packages

Rollback to previous generation:

nix profile rollback

Remove specific profile:

nix profile remove <index-number>

5. CI/CD Integration

This repository uses Determinate Systems GitHub Actions for CI.

GitHub Actions setup (.github/workflows/ci.yml):

- name: Setup Nix cache
  uses: DeterminateSystems/magic-nix-cache-action@v2

- name: Install Nix
  uses: DeterminateSystems/nix-installer-action@v14
  with:
    extra-conf: |
      experimental-features = nix-command flakes

- name: Run install script
  run: ./install.sh

Benefits:

• Magic Nix Cache: ~90% faster CI (uses GitHub Actions cache)
• Automatic cache population
• No configuration required

Local equivalent:

# Test installation in Docker
make test-docker

# Test idempotency
./install.sh && ./install.sh  # Should succeed twice

6. Best Practices (Determinate Nix Patterns)

Use nixos-unstable Instead of master

Reasoning:

• nixos-unstable: Tested, passes Hydra CI
• master: Untested, may have broken packages

Current setup:

inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";

Never Use --impure

Problem: Breaks reproducibility by allowing environment variable access

Correct:

nix profile add .              # Pure evaluation
nix profile upgrade dotfiles   # Pure evaluation

Incorrect:

nix profile add . --impure     # BAD: non-reproducible

Exception: Only use --impure if flake explicitly uses getEnv or similar

Pin Dependencies in Lock File

Why:

• Ensures reproducible builds across machines
• Prevents "works on my machine" issues
• Required for CI/CD reliability

How:

# Always commit flake.lock
git add flake.lock
git commit -m "chore: update flake lock"

Use buildEnv for Package Groups

Pattern in this repo:

packages.default = pkgs.buildEnv {
  name = "system-packages";
  paths = [ git gh lazygit ... ];
};

Benefits:

• Single derivation for all packages
• Atomic updates (all packages succeed or fail together)
• Easier to manage than individual nix profile install calls

Enable Flakes in Config

User-level config (~/.config/nix/nix.conf):

experimental-features = nix-command flakes

This is automatically set by scripts/install-packages.sh

7. Development Workflows

Create New Project Flake

Use repository root as template:

# Copy flake structure
cp flake.nix /path/to/new-project/

# Customize for project needs
cd /path/to/new-project
$EDITOR flake.nix

Or use templates directory:

# Use template (if available in .claude/skills/nix-manager/templates/)
nix flake init -t .#template-name

Test Flake Locally

Without installing:

# Enter dev shell
nix develop

# Build without installing
nix build

# Run specific package
nix run .#package-name

Format Nix Code

Using formatter output:

nix fmt  # Uses nixpkgs-fmt (defined in flake.nix)

Manual formatting:

nixpkgs-fmt flake.nix

8. Migration Guidance

From Homebrew

Don't uninstall Homebrew—it coexists peacefully. Fish PATH priority:

1. Homebrew (/opt/homebrew/bin) - highest priority
2. User bins (~/.local/bin, ~/bin)
3. Language toolchains (~/.cargo/bin, ~/go/bin)
4. Nix (~/.nix-profile/bin) - lowest priority

Migration strategy:

# 1. Install package via Nix
# (add to flake.nix and run nix profile upgrade)

# 2. Test package works
which package-name  # Should show Homebrew path (higher priority)

# 3. Uninstall from Homebrew
brew uninstall package-name

# 4. Verify Nix version now active
which package-name  # Should show /nix/store/... path

From apt/dnf

Linux distros:

• Nix coexists with system package managers
• System packages have priority over Nix (via PATH ordering)
• Use Nix for tools not in distro repos or needing newer versions

9. Output Format

When modifying flake.nix:

Use Edit tool for existing files:

• Modify specific sections
• Preserve comments and formatting
• Minimize diff size

Use Write tool for new files:

• Complete flake.nix from scratch
• Include comments explaining choices
• Follow repository formatting style

After changes, always:

1. Validate: nix flake check
2. Test build: nix build --dry-run
3. Apply: nix profile upgrade dotfiles
4. Verify: nix profile list

Include testing commands:

# Validate changes
nix flake check

# Show what changed
nix flake show

# Apply updates
nix profile upgrade dotfiles

Repository Patterns

This dotfiles repository follows these conventions:

File Structure:

• flake.nix - Package definitions and outputs
• flake.lock - Pinned dependency versions
• scripts/install-packages.sh - Installation wrapper
• scripts/link-config.sh - Dotfile symlinking
• config/ - Dotfile configurations (fish, starship, etc.)

Package Organization: Packages grouped by purpose with comments:

paths = [
  # Version control
  git gh lazygit

  # Build tools
  gnumake cmake pkg-config

  # Programming languages
  rustup go python3 deno

  # ... etc
];

Testing:

• make test-pre - Pre-flight validation
• make test-local - Ephemeral HOME test
• make test-docker - Multi-distro Docker matrix

Common Commands:

• make install - Run full installation
• make update - Update flake + upgrade packages
• make clean - Garbage collect
• make verify - Check Nix installation health

Reference Documentation

• Determinate Installer: https://determinate.systems/blog/determinate-nix-installer/
• Zero to Nix (Flakes): https://zero-to-nix.com/concepts/flakes/
• Nix.dev (Flakes): https://nix.dev/concepts/flakes.html
• NixOS Wiki: https://nixos.wiki/wiki/Flakes
• Repository: /Users/wcygan/Development/dotfiles/

Quick Reference

Essential Commands:

# Package management
nix search nixpkgs <package>     # Search for package
nix profile list                 # List installed packages
nix profile upgrade dotfiles     # Apply flake changes
nix-collect-garbage -d           # Clean old generations

# Flake management
nix flake update                 # Update all inputs
nix flake check                  # Validate flake
nix flake show                   # Display outputs
nix flake metadata               # Show metadata

# Development
nix develop                      # Enter dev shell
nix build                        # Build package
nix fmt                          # Format Nix code
nix run .#package                # Run package

# Troubleshooting
nix store info                   # Store statistics
nix store gc --dry-run           # Preview cleanup
nix profile rollback             # Revert to previous