docs(README): update configuration details and migrate from Home Manager to nix-wrappers

Enhanced the README to reflect the migration of user program configurations from Home Manager to nix-wrappers. Updated module structure and added new wrapper configurations for Git, Ghostty, Fuzzel, and Neovim. Clarified system tuning and desktop configurations, and included migration notes for users transitioning from the old setup.

Author: kzndotsh

README.md

@@ -1,11 +1,12 @@
 # NixOS Configuration
 
-A modular, reproducible NixOS configuration optimized for development and professional audio work. Built with flakes, Home Manager, and modern tooling.
+A modular, reproducible NixOS configuration optimized for development and professional audio work. Built with flakes, nix-wrappers, and modern tooling.
 
 ## Features
 
 - **Flake-based** - Reproducible, atomic updates with flake inputs
 - **Modular architecture** - Shared modules under `modules/common/` for easy reuse
+- **Wrapper-based user programs** - User applications configured via nix-wrappers (migrated from Home Manager)
 - **Professional audio** - Low-latency PipeWire configuration with realtime scheduling
 - **System tuning** - Optimized for AMD Ryzen 7 5800X and RX 6700 XT
 - **Code quality** - treefmt with 10+ formatters, git-hooks.nix pre-commit hooks, CI checks
@@ -62,34 +63,25 @@ nixos/
 │   ├── ikigai.nix         # Main host (ikigai)
 │   └── test-vm.nix        # VM variant
 │
-├── modules/common/        # Shared modules
-│   ├── desktop/           # Sway, theming, audio
-│   ├── hardware/          # GPU configuration
-│   ├── i18n/              # Locale, keyboard, timezone
-│   ├── network/           # DNS, firewall, IPv6
-│   ├── nix/               # Nix settings, registry, substituters
-│   ├── packages/          # System packages, git config
-│   ├── security/          # 1Password, SOPS, PAM
-│   ├── services/          # Docker, Cachix, systemd services
-│   └── tuning/            # Kernel, sysctl, I/O, power, audio
-│
-├── home/                  # Home Manager configuration
-│   └── kaizen/            # User-specific configuration
+├── modules/
+│   ├── common/            # Shared system modules
+│   │   ├── desktop/       # Sway, theming, audio, XDG, greetd
+│   │   ├── hardware/      # GPU configuration
+│   │   ├── i18n/          # Locale, keyboard, timezone
+│   │   ├── network/       # DNS, firewall, IPv6
+│   │   ├── nix/           # Nix settings, registry, substituters
+│   │   ├── packages/      # System packages, SSH config
+│   │   ├── security/      # 1Password, SOPS, PAM
+│   │   ├── services/      # Docker, Cachix, systemd services
+│   │   ├── system/        # System environment variables
+│   │   └── tuning/        # Kernel, sysctl, I/O, power, audio
+│   │
+│   └── wrappers/          # User program wrappers (nix-wrappers)
 │       ├── default.nix    # Main entry point
-│       ├── packages.nix   # Packages without HM modules
-│       ├── programs/      # Program configurations
-│       │   ├── cli/       # CLI tools (htop, btop, eza, etc.)
-│       │   ├── editors/   # VS Code, Neovim
-│       │   ├── terminal/  # Ghostty
-│       │   ├── wayland/   # Sway, Waybar
-│       │   └── git.nix    # Git configuration
-│       ├── services/      # User services
-│       └── system/        # System-level configs
-│           ├── audio.nix  # ALSA user config
-│           ├── env.nix    # Environment variables
-│           ├── fonts.nix  # Font configuration
-│           ├── shell.nix # Zsh configuration
-│           └── xdg.nix   # XDG base directories
+│       ├── git.nix        # Git wrapper with config
+│       ├── ghostty.nix    # Ghostty terminal wrapper
+│       ├── fuzzel.nix     # Fuzzel launcher wrapper
+│       └── neovim.nix     # Neovim wrapper
 │
 ├── users/                 # User definitions
 ├── lib/                   # Helper functions
@@ -132,7 +124,6 @@ pre-commit run --all-files  # Run all hooks manually
 
 ```bash
 just build           # Build NixOS configuration
-just build-home      # Build Home Manager config
 just eval-config     # Evaluate config (no build)
 just syntax-check <file>  # Check Nix syntax
 ```
@@ -186,6 +177,17 @@ nix run .#treefmt
 
 ## Configuration Modules
 
+### Wrappers (`modules/wrappers/`)
+
+User programs are configured via **nix-wrappers** (migrated from Home Manager):
+
+- **Git** (`git.nix`): Git wrapper with global configuration, aliases, SSH signing
+- **Ghostty** (`ghostty.nix`): Terminal emulator with theme and font configuration
+- **Fuzzel** (`fuzzel.nix`): Application launcher with styling
+- **Neovim** (`neovim.nix`): Editor wrapper (minimal, config can be extended)
+
+Wrappers automatically add programs to `environment.systemPackages` when `systemWide = true` is set.
+
 ### System Tuning (`modules/common/tuning/`)
 
 Hardware-optimized configuration for AMD Ryzen 7 5800X and RX 6700 XT:
@@ -198,9 +200,11 @@ Hardware-optimized configuration for AMD Ryzen 7 5800X and RX 6700 XT:
 
 ### Desktop (`modules/common/desktop/`)
 
-- **Sway** (`sway.nix`): Window manager configuration
-- **Theming** (`theming.nix`): Tokyo Night theme via base16.nix
+- **Sway** (`sway.nix`): Window manager configuration (config written to `/etc/sway/config`)
+- **Theming** (`theming.nix`): Tokyo Night theme via base16.nix, GTK/Qt theming
 - **Audio** (`audio.nix`): PipeWire, WirePlumber, realtime scheduling
+- **XDG** (`xdg.nix`): XDG portal configuration, desktop/session environment variables
+- **Greetd** (`greetd.nix`): Display manager configuration
 
 ### Security (`modules/common/security/`)
 
@@ -219,24 +223,19 @@ Hardware-optimized configuration for AMD Ryzen 7 5800X and RX 6700 XT:
 - **Substituters** (`substituters.nix`): Binary cache configuration
 - **Settings** (`default.nix`): Nix experimental features, performance settings
 
-### Home Manager (`home/kaizen/`)
-
-- **Programs** (`programs/`): All program configurations organized by category
-- **System** (`system/`): XDG, environment variables, fonts, shell, audio
-- **Services** (`services/`): User services (systemd user units)
-- **Packages** (`packages.nix`): Packages without Home Manager modules
-
 ## Flake Inputs
 
 - `nixpkgs` - Stable (nixos-25.11)
 - `nixpkgs-unstable` - For newer packages
-- `home-manager` - User configuration
+- `wrappers` - nix-wrappers library for user program configuration
 - `sops-nix` - Secret management
 - `base16` - Theming support
 - `treefmt-nix` - Code formatting
 - `git-hooks` - Pre-commit hooks
 - `nix-topology` - Infrastructure visualization
 
+**Note**: Home Manager has been deprecated and migrated to nix-wrappers for user program configuration.
+
 ## Hardware
 
 Optimized for:
@@ -296,13 +295,47 @@ networking.firewall.enable = false;
 environment.systemPackages = with pkgs; [
   # Add packages here
 ];
+
+# Zsh configuration
+programs.zsh = {
+  enable = true;
+  # ... configuration
+};
 ```
 
 ### Add Packages
 
 - **System packages**: Edit `modules/common/packages/default.nix`
-- **User packages**: Edit `home/kaizen/packages.nix`
-- **Programs with HM modules**: Add to `home/kaizen/programs/`
+- **User programs via wrappers**: Add to `modules/wrappers/` (e.g., `modules/wrappers/myapp.nix`)
+
+### Add a Wrapper
+
+Create a new wrapper file in `modules/wrappers/`:
+
+```nix
+# modules/wrappers/myapp.nix
+{
+  pkgs,
+  ...
+}:
+{
+  wrappers.myapp = {
+    basePackage = pkgs.myapp;
+    systemWide = true;  # Automatically add to systemPackages
+    executables.myapp = {
+      environment = {
+        MYAPP_CONFIG = {
+          value = pkgs.writeText "myapp.conf" ''
+            # Configuration here
+          '';
+        };
+      };
+    };
+  };
+}
+```
+
+Then import it in `modules/wrappers/default.nix`.
 
 ### Modify Tuning
 
@@ -339,11 +372,22 @@ sudo nixos-rebuild switch
 sudo modprobe -r <module>  # Manually unload
 ```
 
+## Migration Notes
+
+This configuration migrated from Home Manager to nix-wrappers. The old Home Manager configuration is preserved in `home.old/` for reference.
+
+Key differences:
+
+- User programs are now configured via wrappers in `modules/wrappers/`
+- System-wide configuration remains in `modules/common/`
+- Zsh configuration is now in host files (`hosts/ikigai.nix`) via `programs.zsh`
+- Git configuration is in `modules/wrappers/git.nix` as a wrapper
+
 ## References
 
 - [NixOS Manual](https://nixos.org/manual/nixos/stable/)
 - [NixOS Wiki](https://wiki.nixos.org/)
-- [Home Manager](https://nix-community.github.io/home-manager/)
+- [nix-wrappers](https://codeberg.org/midischwarz12/nix-wrappers)
 - [treefmt](https://treefmt.com/)
 - [SOPS-nix](https://github.com/Mic92/sops-nix)
 - [nh](https://github.com/nix-community/nh)