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docs: move STRUCTURE.md to docs/ and update README.md reference

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# Nomarchy - Architecture & Directory Structure
Nomarchy is a NixOS-based distribution characterized by its **Modular Merging Architecture**. This design strictly separates the "Upstream" core (the distro's logic) from the "Downstream" configuration (the user's personal setup), while allowing for dynamic, state-based theming and a highly modular desktop environment.
## Table of Contents
1. [Core Principles](#core-principles)
2. [Root Directory](#root-directory)
3. [The `core/` Directory (Foundational)](#the-core-directory-foundational)
4. [The `features/` Directory (Apps & Desktop)](#the-features-directory-apps--desktop)
5. [The `themes/` Directory (Dynamic Theming)](#the-themes-directory-dynamic-theming)
6. [The `lib/` Directory (Shared Library)](#the-lib-directory-shared-library)
7. [The `installer/` & `hosts/` Directories (Deployment)](#the-installer--hosts-directories-deployment)
---
## Core Principles
### Upstream vs. Downstream
- **Upstream:** The code in this repository is treated as the "Upstream" source. It provides the base OS configurations, dynamic theming engine, and modular application logic.
- **Downstream:** A user's installation (typically in `/etc/nixos/`) imports the Upstream flake. The user layers their own `system.nix` and `home.nix` on top, overriding or extending the Upstream settings using native NixOS `lib.mkDefault` and `lib.mkForce` patterns.
### Hybrid Declarative State
While the system is defined declaratively, Nomarchy uses a small, local state file (`~/.config/nomarchy/state.json`) to manage user preferences like the active theme, fonts, and feature toggles. This allows for instant UI feedback (via the `env-update` script) without requiring a full system rebuild for every cosmetic change.
---
## Root Directory
- **`flake.nix`**: The master entry point for the entire distribution.
- **Inputs:** Defines external dependencies like `nixpkgs`, `home-manager`, `disko`, `stylix`, and others.
- **Outputs:**
- `nixosModules.system`: Exports the foundational OS logic (`./core`).
- `nixosModules.home`: Exports the application and desktop logic (`./features`).
- `nixosConfigurations`: Defines pre-configured targets like `installerIso`, `live-iso`, and a testing `vm`.
- **`flake.lock`**: Locks dependency versions for reproducible builds.
- **`GEMINI.md`**: Foundational mandates and architectural rules for the Nomarchy Agent.
- **`STRUCTURE.md`**: (This file) Detailed architectural documentation.
- **`README.md`**: Project overview, installation instructions, and basic usage.
- **`TODO.md`**: Roadmap and pending tasks.
---
## The `core/` Directory (Foundational)
The `core/` directory contains the foundational modules required for a functional system and user environment.
### `core/system/` (OS-Level)
- **`default.nix`**: The central entry point for the system module, importing all OS components.
- **`options.nix`**: Defines the `nomarchy.system` configuration options (e.g., DNS, Timezone, Feature toggles).
- **`state.nix`**: Loads and applies the system-level state (from `/etc/nixos/state.json`).
- **`audio.nix`**: Configures Pipewire, Wireplumber, and audio-related settings.
- **`bluetooth.nix`**: Bluetooth stack and management tools.
- **`browser.nix`**: System-level browser configurations and protocols.
- **`network.nix`**: NetworkManager configuration, DNS optimization, and Wi-Fi powersave settings.
- **`hardware.nix`**: Generic hardware support and hardware-specific script triggers.
- **`virtualization.nix`**: Libvirtd, Docker, and VM guest support.
- **`impermanence.nix`**: Root-on-RAM/Impermanence setup for ephemeral root filesystems.
- **`scripts/`**: A collection of low-level system scripts (e.g., `nomarchy-hw-match`, `nomarchy-setup-dns`).
### `core/home/` (User-Level)
- **`default.nix`**: The entry point for the base Home Manager module.
- **`options.nix`**: Defines the `nomarchy` user options (Toggles, Theme, Fonts, etc.).
- **`state.nix`**: Loads and applies user-level state (from `~/.config/nomarchy/state.json`).
- **`behavior.nix`**: Deploys non-visual configs (Keybindings, Input settings, Window rules) with `lib.mkDefault`.
- **`configs.nix`**: Manages static configuration files and directories in `~/.config/`.
- **`bash.nix`**: Shell environment, aliases, and specialized `env-update` hooks.
- **`security.nix`**: Polkit, keyring management, and GPG settings.
- **`config/`**: Contains the physical source files for the base user configuration (e.g., `starship.toml`, `hypr/` behavior configs).
---
## The `features/` Directory (Apps & Desktop)
The `features/` directory contains optional, modular components that define the user's interactive environment.
- **`default.nix`**: Aggregates and enables all sub-modules in `features/`.
- **`apps/`**: Individual application modules.
- Each app (e.g., `alacritty`, `btop`, `vscode`, `ghostty`) has its own directory containing a `default.nix` and a `config/` subdirectory.
- Apps are configured using the "Individual File Management" pattern to avoid directory symlink conflicts with the theme loader.
- **`desktop/`**: The graphical environment core.
- **`hyprland/`**: The primary tiling window manager configuration.
- **`waybar/`**: The status bar configuration, including dynamic CSS generation.
- **`idle.nix`** & **`nightlight.nix`**: Management of screen timeouts and blue light filters.
- **`scripts/`**: High-level utility scripts (e.g., `nomarchy-update`, `nomarchy-theme-set`).
- **`utils/`**: Helper scripts like `nomarchy-launch-or-focus-tui` or `nomarchy-restart-*`.
---
## The `themes/` Directory (Dynamic Theming)
The theming system is the "soul" of Nomarchy, providing dynamic, consistent aesthetics across all applications.
### `themes/engine/` (The Logic)
- **`loader.nix`**: The core theme loader. It reads the active theme from state and selectively deploys app-specific themed configs (e.g., `btop.theme`, `kitty.conf`) to `~/.config/`.
- **`stylix.nix`**: Integration with Stylix for base color palette and wallpaper management.
- **`switcher.nix`**: Provides the `nomarchy-theme-selector` and `nomarchy-wallpaper-selector` tools.
- **`plymouth.nix`** & **`sddm.nix`**: System-level theming for the boot screen and login manager.
### `themes/palettes/` (The Data)
- Contains subdirectories for every available theme (e.g., `summer-night`, `nord`, `tokyo-night`).
- Each theme directory includes:
- `colors.toml`: The Base16 color definition.
- `backgrounds/`: A collection of theme-aware wallpapers.
- `apps/`: Themed overrides for specific applications (e.g., `btop.theme`, `vscode.json`).
### `themes/templates/` (The Blueprints)
- Contains `.tpl` files (e.g., `waybar.css.tpl`, `hyprland.conf.tpl`) used to generate dynamic configuration files that incorporate the current theme's color palette.
---
## The `lib/` Directory (Shared Library)
The `lib/` directory provides centralized logic and data structures to maintain consistency.
- **`default.nix`**: A shared Nix library providing helper functions:
- `readState`: Safely reads JSON/text state files.
- `getPalette` / `getColorScheme`: Resolves theme names to color data.
- `resolveWallpaper`: Logic for choosing the correct background image.
- `getIconsTheme`: Resolves the appropriate icon set for a theme.
- **`state-schema.nix`**: Defines the single source of truth for the shape and default values of the Nomarchy state (both system and home).
---
## The `installer/` & `hosts/` Directories (Deployment)
### `installer/` (Bootstrap)
- **`install.sh`**: The interactive TTY-based installer. It handles disk partitioning, NixOS installation, and generating a clean "Downstream" flake for the user.
- **`disko-golden.nix`**: The standard partition layout (BTRFS on top of LUKS2).
- **`disko-btrfs-luks.nix`**: A simpler reference layout for disk management.
### `hosts/` (Targets)
- **`installer-iso.nix`**: Configuration for the minimal, TTY-based installation ISO.
- **`live-iso.nix`**: Configuration for the full graphical live environment, used for testing and GUI-based installation.