nix-os

name	nix-os
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

0. Required Workflow

Every config change follows this sequence — no shortcuts:

1. Discover — use mcp-nixos to find correct package attr or option path. Never guess.
2. Inspect — read the target file before editing (inspect_state or Read tool).
3. Patch — edit the module. Minimal diff.
4. Validate — targeted eval before deploying (see §3).
5. Apply — zcli deploy <host> for system switches.
6. Report — surface rollback_generation so user can recover: sudo nixos-rebuild switch --rollback.

On validation failure: extract the first error: line, surface it, stop. Don't retry blind.

System config vs Home Manager:

• System modules (/mnt/repository/nix-os/hosts/, modules/) → zcli deploy <host>
• Home Manager config → home-manager build then home-manager switch (no sudo)

1. Understand Repository Context

Check current Nix setup:

• Flake location: /mnt/repository/nix-os/
• Package management: Declarative NixOS configuration via flakes.
• Update mechanism: zcli deploy <host>

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

2. Package Management Operations

Install New Package

Process:

1. Query mcp-nixos for correct package attribute name
2. Add package to appropriate module in /mnt/repository/nix-os/
3. Validate (§3)
4. Run zcli deploy <host> to apply
5. Verify package availability

Update All Packages

Process:

# Update flake inputs
nix flake update -C /mnt/repository/nix-os

# Apply updates to mesh host
zcli deploy <host>

Remove Package

Process:

1. Remove from flake configuration
2. Run zcli deploy <host> or nh os switch
3. Old package remains in store but not in PATH

Note: Garbage collection removes unreferenced packages:

nh clean all

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 host-specific packages:

paths = [
  # Universal packages
  git gh lazygit
] ++ lib.optionals (config.networking.hostName == "nxiz") [
  # nxiz-only
  nvidia-vaapi-driver
];

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 "Ready for development."
    '';
  };
});

Validate Before Applying

Choose the right tool for the scope of change:

# Dry-run full host eval (standard gate before deploy)
zcli deploy <host> --dry

# Evaluate a specific attribute without building
nix eval /mnt/repository/nix-os#nixosConfigurations.<host>.config.<attr.path>

# Check a specific package is resolvable
nix eval /mnt/repository/nix-os#nixosConfigurations.<host>.config.environment.systemPackages --json

# Build only the system closure, no switch
nix build /mnt/repository/nix-os#nixosConfigurations.<host>.config.system.build.toplevel --dry-run

# Fast syntax+eval check without building anything
nix flake check /mnt/repository/nix-os --no-build

# Quick metadata check (no eval)
nix flake metadata /mnt/repository/nix-os

On error: extract the first error: line and surface it. Stop. Don't retry blind.

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

Generation Issues

Rollback to previous generation: Use the boot menu on restart, or temporarily switch:

/nix/var/nix/profiles/system-*-link/bin/switch-to-configuration test

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 flake check                # Pure evaluation

Incorrect:

nix flake check --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)

Enable Flakes in Config

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

experimental-features = nix-command flakes

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. Transient Agent Tooling (Daemon Profile)

This skill enables agents to maintain a local Nix profile in a user-provided directory, allowing dynamic installation of tools without requiring system-wide package management or sudo access.

Quick Start: Setting Up a Local Profile

The DAEMON_PROFILE env var is automatically set to ~/.local/state/daemon-profile and its bin directory is added to the $PATH via Home Manager. The agent can use:

nix profile add --profile "$DAEMON_PROFILE" "nixpkgs#git"

The --profile flag stores the profile metadata in that location. (Note: on older Nix versions, the add sub-command was called install).

Essential Commands for Agents

Search for Packages:

# Search in nixpkgs flake
nix search nixpkgs git

# Search in specific (fully qualified) flake
nix search "github:user/repo[/branch]" <package-name>

# Get detailed JSON output
nix search nixpkgs python3 --json | jq '.[].pname'

Manage Daemon Profile:

# Add package
nix profile add --profile "$DAEMON_PROFILE" "<flake>#<package>"

# List installed packages
nix profile list --profile "$DAEMON_PROFILE"

# Remove by index or element number
nix profile remove --profile "$DAEMON_PROFILE" 0

# Upgrade packages
nix profile upgrade --profile "$DAEMON_PROFILE" <package_name>
nix profile upgrade --profile "$DAEMON_PROFILE" --all

General Agent Workflow

# 1. Verify profile path
echo $DAEMON_PROFILE

# 2. Search for the package
nix search nixpkgs git

# 3. Add it
nix profile add --profile "$DAEMON_PROFILE" "nixpkgs#git"

# 4. Use it!
git --version

Important Details:

• Path: The directory containing the profile ($DAEMON_PROFILE/bin) is automatically in $PATH.
• Immutability: nixpkgs#git resolves to the current nixpkgs version. Use github:user/repo/ref#package to pin.
• Locking: Only one agent should modify a profile at a time; locking is not automatic.

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: targeted nix eval or zcli deploy <host> --dry
2. Apply: zcli deploy <host>
3. Report rollback generation to user

Include testing commands:

# Validate changes
nix flake check

# Show what changed
nix flake show

Repository Patterns

This NixOS mesh repository follows these conventions:

File Structure:

• flake.nix - Package definitions and outputs
• flake.lock - Pinned dependency versions
• hosts/ - Host-specific configuration (nxiz, zrrh, adeck)
• modules/ - Shared configuration modules

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
];

Common Commands:

• zcli deploy <host> --dry - Dry-run eval without applying
• zcli deploy <host> - Build and apply to a host
• nh clean all - Garbage collect

Mesh Flake Idioms

Patterns this flake uses that agents must recognize and preserve.

Custom my.* Option Namespace

Host identity and opt-in features flow through my.* options defined in modules/system.nix and modules/performance.nix:

# modules/system.nix
options.my.host = lib.mkOption {
  type = lib.types.enum [ "nxiz" "adeck" "zrrh" ];
  description = "Host identifier — selects per-host blocks in shared modules";
};

# modules/performance.nix
options.my.performance.enable = lib.mkEnableOption "system-wide performance optimizations";

Each host's configuration.nix sets my.host = "<name>"; — every shared module keys off this.

perHost Lookup Tables

Instead of cascading lib.mkIf checks, shared modules declare a perHost attrset and select with h = perHost.${config.my.host}. Found in modules/{boot,networking,storage,nh}.nix:

let
  perHost = {
    nxiz  = { flake = "/mnt/repository/nix-os"; resolvedDns = true; };
    adeck = { flake = "/etc/nixos"; resolvedDns = false; };
    zrrh  = { flake = "/etc/nixos"; resolvedDns = true; };
  };
  h = perHost.${config.my.host};
in {
  programs.nh.flake = h.flake;
  services.resolved.enable = h.resolvedDns;
}

When adding host-divergent config, extend perHost rather than sprinkling conditionals.

Home Manager Integrated into NixOS

HM is bound into each nixosConfiguration via home-manager.nixosModules.home-manager in flake.nix. Key settings:

home-manager.useGlobalPkgs = true;        # share nixpkgs with system
home-manager.useUserPackages = true;      # install to /etc/profiles/per-user/zk
home-manager.backupFileExtension = "hm-bak";
home-manager.overwriteBackup = true;      # resolves dotfile collisions on deploy
home-manager.extraSpecialArgs = { inherit inputs; };  # threads flake inputs into HM

HM modules live under modules/home/** and per-host HM entry is hosts/<host>/home.nix.

Inline Derivations in home.packages

Ad-hoc derivations live next to their install site — avoid creating separate files for one-off packages. Found in hosts/{nxiz,adeck,zrrh}/home.nix:

# Prebuilt binary with ELF patch
pkgs.runCommand "nullclaw-2026.3.1" {
  src = pkgs.fetchurl { url = "..."; hash = "..."; };
  nativeBuildInputs = [ pkgs.autoPatchelfHook ];
} ''install -Dm755 $src $out/bin/nullclaw''

# Go module from GitHub
pkgs.buildGoModule {
  pname = "picoclaw";
  src = pkgs.fetchFromGitHub { owner = "..."; repo = "..."; rev = "..."; hash = "..."; };
  vendorHash = "...";
}

# Shell wrapper with runtime deps
pkgs.writeShellApplication {
  name = "fzf-emoji";
  runtimeInputs = [ fzf jq wl-clipboard curl coreutils ];
  text = ''...'';
}

Rule of thumb: if it's one derivation used in one place, inline it. If it's used across hosts, make it a module with options.programs.<name> (see modules/home/msgvault.nix for the reference pattern: mkEnableOption + mkOption + lib.mkIf cfg.enable).

Overlays for Upstream Fixes

modules/overlays.nix holds all overrideAttrs surgeries. Pattern is always _final: prev: { pkg = prev.pkg.overrideAttrs (old: {...}); }. Real examples:

• tumbler rebuilt without libgepub to drop webkitgtk dep
• lmstudio rebuilt with patchelf to fix Bun ELF layout corruption
• yaziPlugins namespace created from flake = false input source tree

Input-provided overlays are applied per-host in flake.nix via nixpkgs.overlays = [ inputs.nix-cachyos-kernel.overlays.pinned ];.

agenix Secret Flow

Secrets encrypted with recipient SSH keys, decrypted at boot into /run/secrets/:

# modules/user.nix
age.identityPaths = [
  "/etc/ssh/ssh_host_ed25519_key"
  "/home/zk/.ssh/id_ed25519"
];

age.secrets.github-token = {
  file = ../secrets/github-token.age;
  owner = "zk"; group = "users"; mode = "0400";
  path = "/run/secrets/github-token";
};

Recipients declared in secrets/secrets.nix (per-file publicKeys list). To add a new secret: agenix -e secrets/new.age (after adding to secrets.nix), then reference via config.age.secrets.new.path in the module.

Home Activation + DAG Ordering

HM activation scripts use config.lib.dag.entryAfter [ "writeBoundary" ] to run after file symlinks are in place:

home.activation.ensureLocalBin = config.lib.dag.entryAfter [ "writeBoundary" ] ''
  mkdir -p "$HOME/.local/bin"
'';

System activation uses system.activationScripts.<name> = { text = "..."; deps = [ "etc" ]; } — the deps list controls ordering (e.g. SSH host key staging runs after /etc is populated).

mkOutOfStoreSymlink for Live Files

For dotfiles that point at mutable paths outside /nix/store (edited live, not baked into the system closure):

home.file.".pi".source = config.lib.file.mkOutOfStoreSymlink
  "/mnt/repository/daemonturgy/pi/.pi";

Use for editable config dirs, large data caches, or anything that shouldn't trigger a rebuild on change.

Flake Outputs (Current)

• nixosConfigurations.{nxiz,adeck,zrrh} — host configs
• formatter.x86_64-linux — nixfmt-rfc-style (run nix fmt)
• devShells.x86_64-linux.default — includes nixd, nil, nixfmt, statix, deadnix (nix develop)
• checks.x86_64-linux.{statix,deadnix} — lint gates (nix flake check)

Run nix fmt before committing .nix changes. Run nix flake check --no-build to catch lint regressions cheaply.

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

Quick Reference

Essential Commands:

# Deploy
zcli deploy <host>                   # Apply flake changes
zcli deploy <host> --dry             # Dry-run eval, no switch
zcli deploy all                      # Deploy all mesh hosts

# Targeted evaluation (prefer over full deploy for validation)
nix eval /mnt/repository/nix-os#nixosConfigurations.<host>.config.<attr>
nix build /mnt/repository/nix-os#nixosConfigurations.<host>.config.system.build.toplevel --dry-run
nix flake check /mnt/repository/nix-os --no-build

# Package discovery (use mcp-nixos first)
nix search nixpkgs <package>         # Fallback search

# Flake management
nix flake update /mnt/repository/nix-os   # Update all inputs
nix flake show /mnt/repository/nix-os     # Display outputs
nix flake metadata /mnt/repository/nix-os # Show metadata

# Garbage collection
nh clean all                         # Clean old generations
nix store gc --dry-run               # Preview cleanup

# Development
nix develop                          # Enter dev shell
nix fmt                              # Format Nix code
nix shell nixpkgs#<tool>             # Transient tool (one-shot)