refactor(nix): extract settings.nix to root nix/ directory

Extract settings.nix from nix/modules/shared/ to nix/ for better
consistency with the modular flake-parts architecture.

## Changes

- Moved `nix/modules/shared/settings.nix` → `nix/settings.nix`
- Updated `nix/modules/shared/default.nix` to remove settings.nix import
- Updated `flake-modules/hosts.nix` to import settings.nix in both:
  - darwinConfigurations
  - nixosConfigurations
- Updated FLAKE-PARTS-MIGRATION.md documentation

## Rationale

This creates a consistent structure where all core system modules are
at the same level:

```
nix/
├── settings.nix              # Custom options & config
├── shared-configuration.nix  # Core system configuration
└── overlays.nix              # Package overlays
```

All three modules are platform-aware (handling both Darwin and Linux)
and are imported by all system configurations, maintaining a single
unified configuration across all managed systems.

## Content

The settings.nix module remains functionally unchanged:
- Defines custom `config.my.*` options
- Sets up home-manager aliases
- Configures XDG directories
- Manages environment variables
- Platform-specific home directory logic (Darwin vs Linux)

Only the file location has changed for better organization.

Author: claude

FLAKE-PARTS-MIGRATION.md

@@ -45,17 +45,26 @@ outputs = inputs @ {flake-parts, ...}:
 │   ├── per-system.nix                 # Per-system outputs (formatter, devShells, apps)
 │   └── hosts.nix                      # Darwin & NixOS configurations
 ├── nix/
-│   ├── shared-configuration.nix       # Shared config for all systems (NEW)
-│   ├── overlays.nix                   # Nixpkgs overlays (NEW)
+│   ├── settings.nix                   # Custom options & config (EXTRACTED)
+│   ├── shared-configuration.nix       # Shared config for all systems (EXTRACTED)
+│   ├── overlays.nix                   # Nixpkgs overlays (EXTRACTED)
 │   ├── modules/
-│   │   ├── shared/                    # Shared modules
-│   │   │   └── settings.nix           # Custom options (UNCHANGED)
+│   │   ├── shared/                    # Shared feature modules (shell, git, vim, etc)
 │   │   └── darwin/                    # Darwin-specific modules
 │   └── hosts/                         # Host-specific configs
 ```
 
 #### Module Breakdown
 
+**`nix/settings.nix`** (Extracted from `nix/modules/shared/`)
+- Defines custom `config.my.*` options (username, timezone, email, etc.)
+- Sets up home-manager aliases (`my.hm.file`, `my.hm.configFile`, etc.)
+- Configures XDG directories (platform-aware)
+- Environment variable management
+- Platform-specific home directory logic (Darwin vs Linux)
+
+This is a NixOS/nix-darwin module that defines reusable options and configuration used across all systems.
+
 **`nix/shared-configuration.nix`** (Extracted from original `sharedConfiguration`)
 - Core Nix settings (experimental features, substituters, GC)
 - Font configuration (platform-specific)
@@ -87,16 +96,17 @@ This is a NixOS/nix-darwin module that gets imported by all system configuration
 
 The migration achieves a **single Nix configuration that works on any system** managed by the flake:
 
-1. **`nix/shared-configuration.nix`**: Applied to ALL systems (Darwin and NixOS)
-2. **`nix/overlays.nix`**: Applied to ALL systems
-3. **`nix/modules/shared/settings.nix`**: Custom options available to ALL systems
+1. **`nix/settings.nix`**: Custom options and config applied to ALL systems
+2. **`nix/shared-configuration.nix`**: Core system config applied to ALL systems (Darwin and NixOS)
+3. **`nix/overlays.nix`**: Package customizations applied to ALL systems
 4. Platform-specific logic handled via `pkgs.stdenv.isDarwin` conditionals
 
 All systems share the same:
-- Nix settings
+- Custom options (`config.my.*`)
+- Nix settings and configuration
 - Overlays and custom packages
 - Base home-manager configuration
-- Custom options defined in settings.nix
+- XDG directory structure
 
 ## Benefits of This Migration
 
@@ -107,15 +117,27 @@ All systems share the same:
 5. **Single Source of Truth**: shared-configuration.nix applies universally
 6. **Better Organization**: Clear separation between flake outputs and system modules
 
-## settings.nix Unchanged
+## Extracted Core Modules
+
+Three core modules have been extracted to the `nix/` directory for better organization:
+
+**`nix/settings.nix`** (moved from `nix/modules/shared/settings.nix`)
+- Defines custom `config.my.*` options
+- Sets up home-manager aliases
+- Configures XDG directories
+- Manages environment variables
+- Platform-aware home directory logic
+
+**`nix/shared-configuration.nix`** (extracted from `sharedConfiguration` function)
+- Core Nix daemon settings
+- Cache configuration
+- Font packages
+- System-wide settings
 
-The `nix/modules/shared/settings.nix` file remains **completely unchanged**. It continues to:
-- Define custom `config.my.*` options
-- Set up home-manager aliases
-- Configure XDG directories
-- Manage environment variables
+**`nix/overlays.nix`** (extracted from `sharedConfiguration` function)
+- All package overlays and customizations
 
-This is because settings.nix is a NixOS/nix-darwin module (not a flake-parts module), and the migration only affects the flake structure, not the system module structure.
+These are NixOS/nix-darwin modules (not flake-parts modules), imported directly by system configurations. The content remains functionally identical, only the organization has changed.
 
 ## How to Use
 

flake-modules/hosts.nix

@@ -31,6 +31,7 @@ in {
             specialArgs = {inherit inputs self;};
             inherit system;
             modules = [
+              ../nix/settings.nix
               ../nix/shared-configuration.nix
               ../nix/overlays.nix
               inputs.home-manager.darwinModules.home-manager
@@ -52,6 +53,7 @@ in {
             specialArgs = {inherit inputs self;};
             inherit system;
             modules = [
+              ../nix/settings.nix
               ../nix/shared-configuration.nix
               ../nix/overlays.nix
               inputs.home-manager.nixosModules.home-manager

nix/modules/shared/default.nix

@@ -1,6 +1,5 @@
 {lib, ...}: {
   imports = [
-    ./settings.nix
     ./user-shell.nix
     ./mail.nix
     ./gpg.nix