fix: forced logging in the docker compose file

Reviewed-on: https://gitea.iswearihadsomethingforthis.net/francwa/alfred/pulls/18

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.1.6"
+current_version = "0.1.7"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

.dockerignore

@@ -22,8 +22,7 @@ venv
 .venv
 env
 .env
-.env.*
-
+.env-
 # IDE
 .vscode
 .idea

.env.example

@@ -1,53 +1,93 @@
-# Configuration
-LIBRECHAT_VERSION=v0.8.1
-RAG_VERSION=v0.7.0
+MAX_HISTORY_MESSAGES=10
+MAX_TOOL_ITERATIONS=10
+REQUEST_TIMEOUT=30
 
-# Keys
-# - Deepseek API
-DEEPSEEK_API_KEY=
+# LLM Settings
+LLM_TEMPERATURE=0.2
 
-# - Google API
-GOOGLE_API_KEY=
-#GOOGLE_MODELS=gemini-2.5-pro,gemini-2.5-flash,gemini-2.5-flash-lite,gemini-2.0-flash,gemini-2.0-flash-lite #TODO:Update models
+# Persistence
+DATA_STORAGE_DIR=data
 
-# - Anthropic API
-ANTHROPIC_API_KEY=
+# Network configuration
+HOST=0.0.0.0
+PORT=3080
 
-# - Kimi API
-KIMI_API_KEY=
+# Build informations (Synced with pyproject.toml via bootstrap)
+ALFRED_VERSION=
+IMAGE_NAME=
+LIBRECHAT_VERSION=
+PYTHON_VERSION=
+PYTHON_VERSION_SHORT=
+RAG_VERSION=
+RUNNER=
+SERVICE_NAME=
 
-# - ChatGPT/Open API
-OPENAI_API_KEY=
-
-# - Themoviedb.org API (media metadata)
-TMDB_API_KEY=
-
-# - Security keys
+# --- SECURITY KEYS (CRITICAL) ---
+# These are used for session tokens and encrypting sensitive data in MongoDB.
+# If you lose these, you lose access to encrypted stored credentials.
 JWT_SECRET=
 JWT_REFRESH_SECRET=
 CREDS_KEY=
 CREDS_IV=
 
-# Local LLM
-OLLAMA_BASE_URL=
-OLLAMA_MODEL=
+# --- DATABASES (AUTO-SECURED) ---
+# Alfred uses MongoDB for application state and PostgreSQL for Vector RAG.
+# Passwords will be generated as 24-character secure tokens if left blank.
 
-# Alfred Configuration
-LLM_PROVIDER=deepseek
+# MongoDB (Application Data)
+MONGO_URI=
+MONGO_HOST=mongodb
+MONGO_PORT=27017
+MONGO_USER=alfred
+MONGO_PASSWORD=
+MONGO_DB_NAME=LibreChat
 
-# Memory storage directory (inside container)
-MEMORY_STORAGE_DIR=/data/memory
-
-# qBittorrent Configuration
-QBITTORRENT_URL=
-QBITTORRENT_USERNAME=admin
-QBITTORRENT_PASSWORD=adminadmin
-
-# Debug Options
-DEBUG_LOGGING=false
-DEBUG_CONSOLE=false
-
-# Postgres (RAG)
-POSTGRES_DB=
-POSTGRES_USER=
+# PostgreSQL (Vector Database / RAG)
+POSTGRES_URI=
+POSTGRES_HOST=vectordb
+POSTGRES_PORT=5432
+POSTGRES_USER=alfred
 POSTGRES_PASSWORD=
+POSTGRES_DB_NAME=alfred
+
+# --- EXTERNAL SERVICES ---
+# Media Metadata (Required)
+# Get your key at https://www.themoviedb.org/
+TMDB_API_KEY=
+TMDB_BASE_URL=https://api.themoviedb.org/3
+
+# qBittorrent integration
+QBITTORRENT_URL=http://qbittorrent:16140
+QBITTORRENT_USERNAME=admin
+QBITTORRENT_PASSWORD=
+QBITTORRENT_PORT=16140
+
+# Meilisearch
+MEILI_ENABLED=FALSE
+MEILI_NO_ANALYTICS=TRUE
+MEILI_HOST=http://meilisearch:7700
+MEILI_MASTER_KEY=
+
+# --- LLM CONFIGURATION ---
+# Providers: 'local', 'openai', 'anthropic', 'deepseek', 'google', 'kimi'
+DEFAULT_LLM_PROVIDER=local
+
+# Local LLM (Ollama)
+OLLAMA_BASE_URL=http://ollama:11434
+OLLAMA_MODEL=llama3.3:latest
+
+# --- API KEYS (OPTIONAL) ---
+# Fill only the ones you intend to use.
+ANTHROPIC_API_KEY=
+DEEPSEEK_API_KEY=
+GOOGLE_API_KEY=
+KIMI_API_KEY=
+OPENAI_API_KEY=
+
+# --- RAG ENGINE ---
+# Enable/Disable the Retrieval Augmented Generation system
+RAG_ENABLED=TRUE
+RAG_API_URL=http://rag_api:8000
+RAG_API_PORT=8000
+EMBEDDINGS_PROVIDER=ollama
+EMBEDDINGS_MODEL=nomic-embed-text

.gitea/workflows/ci.yml

@@ -34,6 +34,9 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
 
+      - name: Generate build variables
+        run: python scripts/generate_build_vars.py
+
       - name: Load config from Makefile
         id: config
         run: make -s _ci-dump-config >> $GITHUB_OUTPUT

CONTRIBUTE.md

@@ -0,0 +1,261 @@
+# Contributing to Alfred
+
+## Settings Management System
+
+Alfred uses a **declarative, schema-based configuration system** that ensures type safety, validation, and maintainability.
+
+### Architecture Overview
+
+```
+settings.toml          # Schema definitions (single source of truth)
+    ↓
+settings_schema.py     # Parser & validation
+    ↓
+settings_bootstrap.py  # Generation & resolution
+    ↓
+.env                   # Runtime configuration
+.env.make              # Build variables for Makefile
+    ↓
+settings.py            # Pydantic Settings (runtime validation)
+```
+
+### Key Files
+
+- **`settings.toml`** — Declarative schema for all settings
+- **`alfred/settings_schema.py`** — Schema parser and validation logic
+- **`alfred/settings_bootstrap.py`** — Bootstrap logic (generates `.env` and `.env.make`)
+- **`alfred/settings.py`** — Pydantic Settings class (runtime)
+- **`.env`** — Generated configuration file (gitignored)
+- **`.env.make`** — Build variables for Makefile (gitignored)
+
+### Setting Sources
+
+Settings can come from different sources:
+
+| Source | Description | Example |
+|--------|-------------|---------|
+| `toml` | From `pyproject.toml` | Version numbers, build config |
+| `env` | From `.env` file | User-provided values, API keys |
+| `generated` | Auto-generated secrets | JWT secrets, passwords |
+| `computed` | Calculated from other settings | Database URIs |
+
+### How to Add a New Setting
+
+#### 1. Define in `settings.toml`
+
+```toml
+[tool.alfred.settings_schema.MY_NEW_SETTING]
+type = "string"                    # string, integer, float, boolean, secret, computed
+source = "env"                     # env, toml, generated, computed
+default = "default_value"          # Optional: default value
+description = "Description here"   # Required: clear description
+category = "app"                   # app, api, database, security, build
+required = true                    # Optional: default is true
+validator = "range:1:100"          # Optional: validation rule
+export_to_env_make = false         # Optional: export to .env.make for Makefile
+```
+
+#### 2. Regenerate Configuration
+
+```bash
+make bootstrap
+```
+
+This will:
+- Read the schema from `settings.toml`
+- Generate/update `.env` with the new setting
+- Generate/update `.env.make` if `export_to_env_make = true`
+- Preserve existing secrets
+
+#### 3. Validate
+
+```bash
+make validate
+```
+
+This ensures all settings are valid according to the schema.
+
+#### 4. Use in Code
+
+The setting is automatically available in `settings.py`:
+
+```python
+from alfred.settings import settings
+
+print(settings.my_new_setting)
+```
+
+### Setting Types
+
+#### String Setting
+
+```toml
+[tool.alfred.settings_schema.API_URL]
+type = "string"
+source = "env"
+default = "https://api.example.com"
+description = "API base URL"
+category = "api"
+```
+
+#### Integer Setting with Validation
+
+```toml
+[tool.alfred.settings_schema.MAX_RETRIES]
+type = "integer"
+source = "env"
+default = 3
+description = "Maximum retry attempts"
+category = "app"
+validator = "range:1:10"
+```
+
+#### Secret (Auto-generated)
+
+```toml
+[tool.alfred.settings_schema.API_SECRET]
+type = "secret"
+source = "generated"
+secret_rule = "32:b64"  # 32 bytes, base64 encoded
+description = "API secret key"
+category = "security"
+```
+
+Secret rules:
+- `"32:b64"` — 32 bytes, URL-safe base64
+- `"16:hex"` — 16 bytes, hexadecimal
+
+#### Computed Setting
+
+```toml
+[tool.alfred.settings_schema.DATABASE_URL]
+type = "computed"
+source = "computed"
+compute_from = ["DB_HOST", "DB_PORT", "DB_NAME"]
+compute_template = "postgresql://{DB_HOST}:{DB_PORT}/{DB_NAME}"
+description = "Database connection URL"
+category = "database"
+```
+
+#### From TOML (Build Variables)
+
+```toml
+[tool.alfred.settings_schema.APP_VERSION]
+type = "string"
+source = "toml"
+toml_path = "tool.poetry.version"
+description = "Application version"
+category = "build"
+export_to_env_make = true  # Available in Makefile
+```
+
+### Validators
+
+Available validators:
+
+- **`range:min:max`** — Numeric range validation
+  ```toml
+  validator = "range:0.0:2.0"  # For floats
+  validator = "range:1:100"    # For integers
+  ```
+
+### Categories
+
+Organize settings by category:
+
+- **`app`** — Application settings
+- **`api`** — API keys and external services
+- **`database`** — Database configuration
+- **`security`** — Secrets and security keys
+- **`build`** — Build-time configuration
+
+### Best Practices
+
+1. **Always add a description** — Make it clear what the setting does
+2. **Use appropriate types** — Don't use strings for numbers
+3. **Add validation** — Use validators for numeric ranges
+4. **Categorize properly** — Helps with organization
+5. **Use computed settings** — For values derived from others (e.g., URIs)
+6. **Mark secrets as generated** — Let the system handle secret generation
+7. **Export build vars** — Set `export_to_env_make = true` for Makefile variables
+
+### Workflow Example
+
+```bash
+# 1. Edit settings.toml
+vim settings.toml
+
+# 2. Regenerate configuration
+make bootstrap
+
+# 3. Validate
+make validate
+
+# 4. Test
+python -c "from alfred.settings import settings; print(settings.my_new_setting)"
+
+# 5. Commit (settings.toml only, not .env)
+git add settings.toml
+git commit -m "Add MY_NEW_SETTING"
+```
+
+### Commands
+
+```bash
+make bootstrap  # Generate .env and .env.make from schema
+make validate   # Validate all settings against schema
+make help       # Show all available commands
+```
+
+### Troubleshooting
+
+**Setting not found in schema:**
+```
+KeyError: Missing [tool.alfred.settings_schema] section
+```
+→ Check that `settings.toml` exists and has the correct structure
+
+**Validation error:**
+```
+ValueError: MY_SETTING must be between 1 and 100, got 150
+```
+→ Check the validator in `settings.toml` and adjust the value in `.env`
+
+**Secret not preserved:**
+→ Secrets are automatically preserved during `make bootstrap`. If lost, they were never in `.env` (check `.env` exists before running bootstrap)
+
+### Testing
+
+When adding a new setting, consider adding tests:
+
+```python
+# tests/test_settings_schema.py
+def test_my_new_setting(self, create_schema_file):
+    """Test MY_NEW_SETTING definition."""
+    schema_toml = """
+[tool.alfred.settings_schema.MY_NEW_SETTING]
+type = "string"
+source = "env"
+default = "test"
+"""
+    base_dir = create_schema_file(schema_toml)
+    schema = load_schema(base_dir)
+
+    definition = schema.get("MY_NEW_SETTING")
+    assert definition.default == "test"
+```
+
+### Migration from Old System
+
+If you're migrating from the old system:
+
+1. Settings are now in `settings.toml` instead of scattered across files
+2. No more `.env.example` — schema is the source of truth
+3. Secrets are auto-generated and preserved
+4. Validation happens at bootstrap time, not just runtime
+
+---
+
+## Questions?
+
+Open an issue or check the existing settings in `settings.toml` for examples.

Dockerfile

@@ -43,6 +43,9 @@ RUN --mount=type=cache,target=/root/.cache/pip \
         uv pip install --system -r pyproject.toml; \
     fi
 
+COPY scripts/ ./scripts/
+COPY .env.example ./
+
 # ===========================================
 # Stage 2: Testing
 # ===========================================
@@ -60,7 +63,8 @@ RUN --mount=type=cache,target=/root/.cache/pip \
     fi
 
 COPY alfred/ ./alfred
-COPY tests/ ./tests
+COPY scripts ./scripts
+COPY tests/  ./tests
 
 # ===========================================
 # Stage 3: Runtime
@@ -69,10 +73,11 @@ FROM python:${PYTHON_VERSION}-slim-bookworm AS runtime
 
 ARG PYTHON_VERSION_SHORT
 
+# TODO: A-t-on encore besoin de toutes les clés  ?
 ENV LLM_PROVIDER=deepseek \
     MEMORY_STORAGE_DIR=/data/memory \
     PYTHONDONTWRITEBYTECODE=1 \
-    PYTHONPATH=/home/appuser/app \
+    PYTHONPATH=/home/appuser \
     PYTHONUNBUFFERED=1
 
 # Install runtime dependencies (needs root)
@@ -85,8 +90,8 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 RUN useradd -m -u 1000 -s /bin/bash appuser
 
 # Create data directories (needs root for /data)
-RUN mkdir -p /data/memory /data/logs \
-    && chown -R appuser:appuser /data
+RUN mkdir -p /data /logs \
+    && chown -R appuser:appuser /data /logs
 
 # Switch to non-root user
 USER appuser
@@ -100,9 +105,13 @@ COPY --from=builder /usr/local/bin /usr/local/bin
 
 # Copy application code (already owned by appuser)
 COPY --chown=appuser:appuser alfred/ ./alfred
+COPY --chown=appuser:appuser scripts/ ./scripts
+COPY --chown=appuser:appuser .env.example ./
+COPY --chown=appuser:appuser pyproject.toml ./
+COPY --chown=appuser:appuser settings.toml ./
 
 # Create volumes for persistent data
-VOLUME ["/data/memory", "/data/logs"]
+VOLUME ["/data", "/logs"]
 
 # Expose port
 EXPOSE 8000
@@ -111,5 +120,4 @@ EXPOSE 8000
 HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
     CMD python -c "import requests; requests.get('http://localhost:8000/health', timeout=5).raise_for_status()" || exit 1
 
-# Run the application
-CMD ["python", "-m", "uvicorn", "app:app", "--host", "0.0.0.0", "--port", "8000"]
+CMD ["python", "-m", "uvicorn", "alfred.app:app", "--host", "0.0.0.0", "--port", "8000"]

Makefile

@@ -1,83 +1,81 @@
 .DEFAULT_GOAL := help
 
-# --- Config ---
-export IMAGE_NAME			:= alfred_media_organizer
-export LIBRECHAT_VERSION 	:= v0.8.1
-export PYTHON_VERSION		:= 3.14.2
-export PYTHON_VERSION_SHORT	:= 3.14
-export RAG_VERSION 			:= v0.7.0
-export RUNNER				:= poetry
-export SERVICE_NAME			:= alfred
+# --- Load Config from pyproject.toml ---
+-include .env.make
+
+# --- Profiles management ---
+# Usage: make up p=rag,meili
+p ?= full
+PROFILES_PARAM	:= COMPOSE_PROFILES=$(p)
 
 # --- Commands ---
-CLI				:= python3 cli.py
 DOCKER_COMPOSE	:= docker compose
-DOCKER_BUILD	:= docker build \
+DOCKER_BUILD	:= docker build --no-cache \
 					--build-arg PYTHON_VERSION=$(PYTHON_VERSION) \
 					--build-arg PYTHON_VERSION_SHORT=$(PYTHON_VERSION_SHORT) \
 					--build-arg RUNNER=$(RUNNER)
 
 # --- Phony ---
-.PHONY: setup status check
-.PHONY: up down restart logs ps shell
-.PHONY: build build-test
-.PHONY: install update install-hooks
-.PHONY: test coverage lint format clean prune
-.PHONY: major minor patch
-.PHONY: help
+.PHONY: .env bootstrap validate up down restart logs ps shell build build-test install \
+	update install-hooks test coverage lint format clean major minor patch help
 
 # --- Setup ---
-setup:
+.env:
 	@echo "Initializing environment..."
-	@$(CLI) setup \
-		&&  echo "✓ Environment ready" \
-		|| (echo "✗ Setup failed" && exit 1)
+	@python scripts/bootstrap.py \
+		&& echo "✓ Environment ready" \
+		|| (echo "✗ Environment setup failed" && exit 1)
 
-status:
-	@$(CLI) status
+# .env.make is automatically generated by bootstrap.py when .env is created
+.env.make: .env
 
-check:
-	@$(CLI) check
+bootstrap: .env
+
+validate:
+	@echo "Validating settings..."
+	@python scripts/validate_settings.py \
+		&& echo "✓ Settings valid" \
+		|| (echo "✗ Settings validation failed" && exit 1)
 
 # --- Docker ---
-up: check
-	@echo "Starting containers..."
-	@$(DOCKER_COMPOSE) up -d --remove-orphans \
+up: .env
+	@echo "Starting containers with profiles: [full]..."
+	@$(PROFILES_PARAM) $(DOCKER_COMPOSE) up -d --remove-orphans \
 		&& echo "✓ Containers started" \
 		|| (echo "✗ Failed to start containers" && exit 1)
 
 down:
 	@echo "Stopping containers..."
-	@$(DOCKER_COMPOSE) down \
+	@$(PROFILES_PARAM) $(DOCKER_COMPOSE) down \
 		&& echo "✓ Containers stopped" \
 		|| (echo "✗ Failed to stop containers" && exit 1)
 
 restart:
 	@echo "Restarting containers..."
-	@$(DOCKER_COMPOSE) restart \
+	@$(PROFILES_PARAM) $(DOCKER_COMPOSE) restart \
 		&& echo "✓ Containers restarted" \
 		|| (echo "✗ Failed to restart containers" && exit 1)
 
 logs:
 	@echo "Following logs (Ctrl+C to exit)..."
-	@$(DOCKER_COMPOSE) logs -f
+	@$(PROFILES_PARAM) $(DOCKER_COMPOSE) logs -f
 
 ps:
 	@echo "Container status:"
-	@$(DOCKER_COMPOSE) ps
+	@$(PROFILES_PARAM) $(DOCKER_COMPOSE) ps
 
 shell:
 	@echo "Opening shell in $(SERVICE_NAME)..."
 	@$(DOCKER_COMPOSE) exec $(SERVICE_NAME) /bin/bash
 
 # --- Build ---
-build: check
+build: .env.make
 	@echo "Building image $(IMAGE_NAME):latest ..."
 	@$(DOCKER_BUILD) -t $(IMAGE_NAME):latest . \
 		&& echo "✓ Build complete" \
 		|| (echo "✗ Build failed" && exit 1)
 
-build-test: check
+build-test: .env.make
 	@echo "Building test image $(IMAGE_NAME):test..."
 	@$(DOCKER_BUILD) --target test -t $(IMAGE_NAME):test . \
 		&& echo "✓ Test image built" \
@@ -90,18 +88,18 @@ install:
 		&& echo "✓ Dependencies installed" \
 		|| (echo "✗ Installation failed" && exit 1)
 
-update:
-	@echo "Updating dependencies with $(RUNNER)..."
-	@$(RUNNER) update \
-		&& echo "✓ Dependencies updated" \
-		|| (echo "✗ Update failed" && exit 1)
-
 install-hooks:
 	@echo "Installing pre-commit hooks..."
 	@$(RUNNER) run pre-commit install \
 		&& echo "✓ Hooks installed" \
 		|| (echo "✗ Hook installation failed" && exit 1)
 
+update:
+	@echo "Updating dependencies with $(RUNNER)..."
+	@$(RUNNER) update \
+		&& echo "✓ Dependencies updated" \
+		|| (echo "✗ Update failed" && exit 1)
+
 # --- Quality ---
 test:
 	@echo "Running tests..."
@@ -133,12 +131,6 @@ clean:
 	@find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null || true
 	@echo "✓ Cleanup complete"
 
-prune:
-	@echo "Pruning Docker system..."
-	@docker system prune -af \
-		&& echo "✓ Docker pruned" \
-		|| (echo "✗ Prune failed" && exit 1)
-
 # --- Versioning ---
 major minor patch: _check-main
 	@echo "Bumping $@ version..."
@@ -151,6 +143,7 @@ major minor patch: _check-main
 		&& echo "✓ Tags pushed" \
 		|| (echo "✗ Push failed" && exit 1)
 
+# CI/CD helpers
 _ci-dump-config:
 	@echo "image_name=$(IMAGE_NAME)"
 	@echo "python_version=$(PYTHON_VERSION)"
@@ -173,31 +166,29 @@ _check-main:
 
 # --- Help ---
 help:
-	@echo "Usage: make [target]"
+	@echo "Cleverly Crafted Unawareness - Management Commands"
+	@echo ""
+	@echo "Usage: make [target] [p=profile1,profile2]"
 	@echo ""
 	@echo "Setup:"
-	@echo "  setup       Initialize .env"
-	@echo "  status      Show project status"
+	@echo "  bootstrap   Generate .env and .env.make from schema"
+	@echo "  validate    Validate settings against schema"
 	@echo ""
 	@echo "Docker:"
-	@echo "  up          Start containers"
-	@echo "  down        Stop containers"
-	@echo "  restart     Restart containers"
-	@echo "  logs        Follow logs"
-	@echo "  ps          Container status"
-	@echo "  shell       Shell into container"
-	@echo "  build       Build image"
+	@echo "  up          Start containers (default profile: full)"
+	@echo "              Example: make up p=rag,meili"
+	@echo "  down        Stop all containers"
+	@echo "  restart     Restart containers (supports p=...)"
+	@echo "  logs        Follow logs (supports p=...)"
+	@echo "  ps          Status of containers"
+	@echo "  shell       Open bash in the core container"
+	@echo "  build       Build the production Docker image"
 	@echo ""
-	@echo "Dev:"
-	@echo "  install     Install dependencies"
-	@echo "  update      Update dependencies"
-	@echo "  test        Run tests"
-	@echo "  coverage    Run tests with coverage"
-	@echo "  lint        Lint code"
-	@echo "  format      Format code"
-	@echo "  clean       Clean artifacts"
+	@echo "Dev & Quality:"
+	@echo "  install     Install dependencies via $(RUNNER)"
+	@echo "  test        Run pytest suite"
+	@echo "  coverage    Run tests and generate HTML report"
+	@echo "  lint/format Quality and style checks"
 	@echo ""
 	@echo "Release:"
-	@echo "  patch       Bump patch version"
-	@echo "  minor       Bump minor version"
-	@echo "  major       Bump major version"
+	@echo "  major|minor|patch  Bump version and push tags (main branch only)"

README.md

@@ -1,89 +1,277 @@
-# Agent Media 🎬
+# Alfred Media Organizer 🎬
 
-An AI-powered agent for managing your local media library with natural language. Search, download, and organize movies and TV shows effortlessly.
+An AI-powered agent for managing your local media library with natural language. Search, download, and organize movies and TV shows effortlessly through a conversational interface.
 
-## Features
+[![Python 3.14](https://img.shields.io/badge/python-3.14-blue.svg)](https://www.python.org/downloads/)
+[![Poetry](https://img.shields.io/badge/dependency%20manager-poetry-blue)](https://python-poetry.org/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://github.com/astral-sh/ruff)
 
-- 🤖 **Natural Language Interface**: Talk to your media library in plain language
-- 🔍 **Smart Search**: Find movies and TV shows via TMDB
-- 📥 **Torrent Integration**: Search and download via qBittorrent
-- 🧠 **Contextual Memory**: Remembers your preferences and conversation history
-- 📁 **Auto-Organization**: Keeps your media library tidy
-- 🌐 **API Compatible**: OpenAI-compatible API for easy integration
+## ✨ Features
 
-## Architecture
+- 🤖 **Natural Language Interface** — Talk to your media library in plain language
+- 🔍 **Smart Search** — Find movies and TV shows via TMDB with rich metadata
+- 📥 **Torrent Integration** — Search and download via qBittorrent
+- 🧠 **Contextual Memory** — Remembers your preferences and conversation history
+- 📁 **Auto-Organization** — Keeps your media library tidy and well-structured
+- 🌐 **OpenAI-Compatible API** — Works with any OpenAI-compatible client
+- 🖥️ **LibreChat Frontend** — Beautiful web UI included out of the box
+- 🔒 **Secure by Default** — Auto-generated secrets and encrypted credentials
 
-Built with **Domain-Driven Design (DDD)** principles:
+## 🏗️ Architecture
+
+Built with **Domain-Driven Design (DDD)** principles for clean separation of concerns:
 
 ```
-agent_media/
-├── agent/          # AI agent orchestration
-├── application/    # Use cases & DTOs
-├── domain/         # Business logic & entities
-└── infrastructure/ # External services & persistence
+alfred/
+├── agent/              # AI agent orchestration
+│   ├── llm/            # LLM clients (Ollama, DeepSeek)
+│   └── tools/          # Tool implementations
+├── application/        # Use cases & DTOs
+│   ├── movies/         # Movie search use cases
+│   ├── torrents/       # Torrent management
+│   └── filesystem/     # File operations
+├── domain/             # Business logic & entities
+│   ├── movies/         # Movie entities
+│   ├── tv_shows/       # TV show entities
+│   └── subtitles/      # Subtitle entities
+└── infrastructure/     # External services & persistence
+    ├── api/            # External API clients (TMDB, qBittorrent)
+    ├── filesystem/     # File system operations
+    └── persistence/    # Memory & repositories
 ```
 
-See [architecture_diagram.md](docs/architecture_diagram.md) for architectural details.
+See [docs/architecture_diagram.md](docs/architecture_diagram.md) for detailed architectural diagrams.
 
-## Quick Start
+## 🚀 Quick Start
 
 ### Prerequisites
 
-- Python 3.12+
-- Poetry
-- qBittorrent (optional, for downloads)
-- API Keys:
-  - DeepSeek API key (or Ollama for local LLM)
-  - TMDB API key
+- **Python 3.14+** (required)
+- **Poetry** (dependency manager)
+- **Docker & Docker Compose** (recommended for full stack)
+- **API Keys:**
+  - TMDB API key ([get one here](https://www.themoviedb.org/settings/api))
+  - Optional: DeepSeek, OpenAI, Anthropic, or other LLM provider keys
 
 ### Installation
 
 ```bash
 # Clone the repository
-git clone https://github.com/your-username/agent-media.git
-cd agent-media
+git clone https://github.com/francwa/alfred_media_organizer.git
+cd alfred_media_organizer
 
 # Install dependencies
-poetry install
+make install
 
-# Copy environment template
-cp .env.example .env
+# Bootstrap environment (generates .env with secure secrets)
+make bootstrap
 
 # Edit .env with your API keys
 nano .env
 ```
 
-### Configuration
-
-Edit `.env`:
+### Running with Docker (Recommended)
 
 ```bash
-# LLM Provider (deepseek or ollama)
-LLM_PROVIDER=deepseek
-DEEPSEEK_API_KEY=your-api-key-here
+# Start all services (LibreChat + Alfred + MongoDB + Ollama)
+make up
 
-# TMDB (for movie/TV show metadata)
-TMDB_API_KEY=your-tmdb-key-here
+# Or start with specific profiles
+make up p=rag,meili      # Include RAG and Meilisearch
+make up p=qbittorrent    # Include qBittorrent
+make up p=full           # Everything
 
-# qBittorrent (optional)
-QBITTORRENT_HOST=http://localhost:8080
-QBITTORRENT_USERNAME=admin
-QBITTORRENT_PASSWORD=adminadmin
+# View logs
+make logs
+
+# Stop all services
+make down
 ```
 
-### Run
+The web interface will be available at **http://localhost:3080**
+
+### Running Locally (Development)
 
 ```bash
+# Install dependencies
+poetry install
+
 # Start the API server
-poetry run uvicorn app:app --reload
-
-# Or with Docker
-docker-compose up
+poetry run uvicorn alfred.app:app --reload --port 8000
 ```
 
-The API will be available at `http://localhost:8000`
+## ⚙️ Configuration
 
-## Usage
+### Environment Bootstrap
+
+Alfred uses a smart bootstrap system that:
+
+1. **Generates secure secrets** automatically (JWT tokens, database passwords, encryption keys)
+2. **Syncs build variables** from `pyproject.toml` (versions, image names)
+3. **Preserves existing secrets** when re-running (never overwrites your API keys)
+4. **Computes database URIs** automatically from individual components
+
+```bash
+# First time setup
+make bootstrap
+
+# Re-run after updating pyproject.toml (secrets are preserved)
+make bootstrap
+```
+
+### Configuration File (.env)
+
+The `.env` file is generated from `.env.example` with secure defaults:
+
+```bash
+# --- CORE SETTINGS ---
+HOST=0.0.0.0
+PORT=3080
+MAX_HISTORY_MESSAGES=10
+MAX_TOOL_ITERATIONS=10
+
+# --- LLM CONFIGURATION ---
+# Providers: 'local' (Ollama), 'deepseek', 'openai', 'anthropic', 'google'
+DEFAULT_LLM_PROVIDER=local
+
+# Local LLM (Ollama - included in Docker stack)
+OLLAMA_BASE_URL=http://ollama:11434
+OLLAMA_MODEL=llama3.3:latest
+LLM_TEMPERATURE=0.2
+
+# --- API KEYS (fill only what you need) ---
+TMDB_API_KEY=your-tmdb-key-here        # Required for movie search
+DEEPSEEK_API_KEY=                       # Optional
+OPENAI_API_KEY=                         # Optional
+ANTHROPIC_API_KEY=                      # Optional
+
+# --- SECURITY (auto-generated, don't modify) ---
+JWT_SECRET=<auto-generated>
+JWT_REFRESH_SECRET=<auto-generated>
+CREDS_KEY=<auto-generated>
+CREDS_IV=<auto-generated>
+
+# --- DATABASES (auto-generated passwords) ---
+MONGO_PASSWORD=<auto-generated>
+POSTGRES_PASSWORD=<auto-generated>
+```
+
+### Security Keys
+
+Security keys are defined in `pyproject.toml` and generated automatically:
+
+```toml
+[tool.alfred.security]
+jwt_secret = "32:b64"           # 32 bytes, base64 URL-safe
+jwt_refresh_secret = "32:b64"
+creds_key = "32:hex"            # 32 bytes, hexadecimal (AES-256)
+creds_iv = "16:hex"             # 16 bytes, hexadecimal (AES IV)
+mongo_password = "16:hex"
+postgres_password = "16:hex"
+```
+
+**Formats:**
+- `b64` — Base64 URL-safe (for JWT tokens)
+- `hex` — Hexadecimal (for encryption keys, passwords)
+
+## 🐳 Docker Services
+
+### Service Architecture
+
+```
+┌─────────────────────────────────────────────────────────────┐
+│                     alfred-net (bridge)                      │
+├─────────────────────────────────────────────────────────────┤
+│                                                              │
+│  ┌──────────────┐    ┌──────────────┐    ┌──────────────┐  │
+│  │  LibreChat   │───▶│    Alfred    │───▶│   MongoDB    │  │
+│  │   :3080      │    │   (core)     │    │   :27017     │  │
+│  └──────────────┘    └──────────────┘    └──────────────┘  │
+│         │                   │                               │
+│         │                   ▼                               │
+│         │            ┌──────────────┐                       │
+│         │            │    Ollama    │                       │
+│         │            │   (local)    │                       │
+│         │            └──────────────┘                       │
+│         │                                                   │
+│  ┌──────┴───────────────────────────────────────────────┐  │
+│  │              Optional Services (profiles)             │  │
+│  ├──────────────┬──────────────┬──────────────┬─────────┤  │
+│  │ Meilisearch  │  RAG API     │  VectorDB    │qBittor- │  │
+│  │   :7700      │   :8000      │   :5432      │  rent   │  │
+│  │  [meili]     │   [rag]      │   [rag]      │[qbit..] │  │
+│  └──────────────┴──────────────┴──────────────┴─────────┘  │
+│                                                              │
+└─────────────────────────────────────────────────────────────┘
+```
+
+### Docker Profiles
+
+| Profile | Services | Use Case |
+|---------|----------|----------|
+| (default) | LibreChat, Alfred, MongoDB, Ollama | Basic setup |
+| `meili` | + Meilisearch | Fast search |
+| `rag` | + RAG API, VectorDB | Document retrieval |
+| `qbittorrent` | + qBittorrent | Torrent downloads |
+| `full` | All services | Complete setup |
+
+```bash
+# Start with specific profiles
+make up p=rag,meili
+make up p=full
+```
+
+### Docker Commands
+
+```bash
+make up              # Start containers (default profile)
+make up p=full       # Start with all services
+make down            # Stop all containers
+make restart         # Restart containers
+make logs            # Follow logs
+make ps              # Show container status
+make shell           # Open bash in Alfred container
+make build           # Build production image
+make build-test      # Build test image
+```
+
+## 🛠️ Available Tools
+
+The agent has access to these tools for interacting with your media library:
+
+| Tool | Description |
+|------|-------------|
+| `find_media_imdb_id` | Search for movies/TV shows on TMDB by title |
+| `find_torrent` | Search for torrents across multiple indexers |
+| `get_torrent_by_index` | Get detailed info about a specific torrent result |
+| `add_torrent_by_index` | Download a torrent by its index in search results |
+| `add_torrent_to_qbittorrent` | Add a torrent via magnet link directly |
+| `set_path_for_folder` | Configure folder paths for media organization |
+| `list_folder` | List contents of a folder |
+| `set_language` | Set preferred language for searches |
+
+## 💬 Usage Examples
+
+### Via Web Interface (LibreChat)
+
+Navigate to **http://localhost:3080** and start chatting:
+
+```
+You: Find Inception in 1080p
+Alfred: I found 3 torrents for Inception (2010):
+        1. Inception.2010.1080p.BluRay.x264 (150 seeders) - 2.1 GB
+        2. Inception.2010.1080p.WEB-DL.x265 (80 seeders) - 1.8 GB
+        3. Inception.2010.1080p.REMUX (45 seeders) - 25 GB
+
+You: Download the first one
+Alfred: ✓ Added to qBittorrent! Download started.
+        Saving to: /downloads/Movies/Inception (2010)/
+
+You: What's downloading right now?
+Alfred: You have 1 active download:
+        - Inception.2010.1080p.BluRay.x264 (45% complete, ETA: 12 min)
+```
 
 ### Via API
 
@@ -91,219 +279,177 @@ The API will be available at `http://localhost:8000`
 # Health check
 curl http://localhost:8000/health
 
-# Chat with the agent
+# Chat with the agent (OpenAI-compatible)
 curl -X POST http://localhost:8000/v1/chat/completions \
   -H "Content-Type: application/json" \
   -d '{
-    "model": "agent-media",
+    "model": "alfred",
     "messages": [
-      {"role": "user", "content": "Find Inception 1080p"}
+      {"role": "user", "content": "Find The Matrix 4K"}
     ]
   }'
+
+# List available models
+curl http://localhost:8000/v1/models
+
+# View memory state (debug)
+curl http://localhost:8000/memory/state
+
+# Clear session memory
+curl -X POST http://localhost:8000/memory/clear-session
 ```
 
-### Via OpenWebUI
+### Via OpenWebUI or Other Clients
 
-Agent Media is compatible with [OpenWebUI](https://github.com/open-webui/open-webui):
+Alfred is compatible with any OpenAI-compatible client:
 
 1. Add as OpenAI-compatible endpoint: `http://localhost:8000/v1`
-2. Model name: `agent-media`
-3. Start chatting!
+2. Model name: `alfred`
+3. No API key required (or use any placeholder)
 
-### Example Conversations
+## 🧠 Memory System
 
-```
-You: Find Inception in 1080p
-Agent: I found 3 torrents for Inception:
-       1. Inception.2010.1080p.BluRay.x264 (150 seeders)
-       2. Inception.2010.1080p.WEB-DL.x265 (80 seeders)
-       3. Inception.2010.720p.BluRay (45 seeders)
-
-You: Download the first one
-Agent: Added to qBittorrent! Download started.
-
-You: List my downloads
-Agent: You have 1 active download:
-       - Inception.2010.1080p.BluRay.x264 (45% complete)
-```
-
-## Available Tools
-
-The agent has access to these tools:
-
-| Tool | Description |
-|------|-------------|
-| `find_media_imdb_id` | Search for movies/TV shows on TMDB |
-| `find_torrents` | Search for torrents |
-| `get_torrent_by_index` | Get torrent details by index |
-| `add_torrent_by_index` | Download torrent by index |
-| `add_torrent_to_qbittorrent` | Add torrent via magnet link |
-| `set_path_for_folder` | Configure folder paths |
-| `list_folder` | List folder contents |
-
-## Memory System
-
-Agent Media uses a three-tier memory system:
+Alfred uses a three-tier memory system for context management:
 
 ### Long-Term Memory (LTM)
-- **Persistent** (saved to JSON)
-- Configuration, preferences, media library
-- Survives restarts
+- **Persistent** — Saved to JSON files
+- **Contents:** Configuration, user preferences, media library state
+- **Survives:** Application restarts
 
 ### Short-Term Memory (STM)
-- **Session-based** (RAM only)
-- Conversation history, current workflow
-- Cleared on restart
+- **Session-based** — Stored in RAM
+- **Contents:** Conversation history, current workflow state
+- **Cleared:** On session end or restart
 
 ### Episodic Memory
-- **Transient** (RAM only)
-- Search results, active downloads, recent errors
-- Cleared frequently
+- **Transient** — Stored in RAM
+- **Contents:** Search results, active downloads, recent errors
+- **Cleared:** Frequently, after task completion
 
-## Development
+## 🧪 Development
 
-### Project Structure
+### Project Setup
 
-```
-agent_media/
-├── agent/
-│   ├── agent.py          # Main agent orchestrator
-│   ├── prompts.py        # System prompt builder
-│   ├── registry.py       # Tool registration
-│   ├── tools/            # Tool implementations
-│   └── llm/              # LLM clients (DeepSeek, Ollama)
-├── application/
-│   ├── movies/           # Movie use cases
-│   ├── torrents/         # Torrent use cases
-│   └── filesystem/       # Filesystem use cases
-├── domain/
-│   ├── movies/           # Movie entities & value objects
-│   ├── tv_shows/         # TV show entities
-│   ├── subtitles/        # Subtitle entities
-│   └── shared/           # Shared value objects
-├── infrastructure/
-│   ├── api/              # External API clients
-│   │   ├── tmdb/         # TMDB client
-│   │   ├── knaben/       # Torrent search
-│   │   └── qbittorrent/  # qBittorrent client
-│   ├── filesystem/       # File operations
-│   └── persistence/      # Memory & repositories
-├── tests/                # Test suite (~500 tests)
-└── docs/                 # Documentation
+```bash
+# Install all dependencies (including dev)
+poetry install
+
+# Install pre-commit hooks
+make install-hooks
+
+# Run the development server
+poetry run uvicorn alfred.app:app --reload
 ```
 
 ### Running Tests
 
 ```bash
-# Run all tests
-poetry run pytest
+# Run all tests (parallel execution)
+make test
 
-# Run with coverage
-poetry run pytest --cov
+# Run with coverage report
+make coverage
 
 # Run specific test file
-poetry run pytest tests/test_agent.py
+poetry run pytest tests/test_agent.py -v
 
 # Run specific test
-poetry run pytest tests/test_agent.py::TestAgent::test_step
+poetry run pytest tests/test_config_loader.py::TestBootstrapEnv -v
 ```
 
 ### Code Quality
 
 ```bash
-# Linting
-poetry run ruff check .
+# Lint and auto-fix
+make lint
 
-# Formatting
-poetry run black .
+# Format code
+make format
 
-# Type checking (if mypy is installed)
-poetry run mypy .
+# Clean build artifacts
+make clean
 ```
 
 ### Adding a New Tool
 
-Quick example:
+1. **Create the tool function** in `alfred/agent/tools/`:
 
 ```python
-# 1. Create the tool function in agent/tools/api.py
-def my_new_tool(param: str) -> Dict[str, Any]:
-    """Tool description."""
+# alfred/agent/tools/api.py
+def my_new_tool(param: str) -> dict[str, Any]:
+    """
+    Short description of what this tool does.
+    
+    This will be shown to the LLM to help it decide when to use this tool.
+    """
     memory = get_memory()
-    # Implementation
-    return {"status": "ok", "data": "result"}
-
-# 2. Register in agent/registry.py
-Tool(
-    name="my_new_tool",
-    description="What this tool does",
-    func=api_tools.my_new_tool,
-    parameters={
-        "type": "object",
-        "properties": {
-            "param": {"type": "string", "description": "Parameter description"},
-        },
-        "required": ["param"],
-    },
-),
+    
+    # Your implementation here
+    result = do_something(param)
+    
+    return {
+        "status": "success",
+        "data": result
+    }
 ```
 
-## Docker
+2. **Register in the registry** (`alfred/agent/registry.py`):
 
-### Build
+```python
+tool_functions = [
+    # ... existing tools ...
+    api_tools.my_new_tool,  # Add your tool here
+]
+```
+
+The tool will be automatically registered with its parameters extracted from the function signature.
+
+### Version Management
 
 ```bash
-docker build -t agent-media .
+# Bump version (must be on main branch)
+make patch    # 0.1.7 -> 0.1.8
+make minor    # 0.1.7 -> 0.2.0
+make major    # 0.1.7 -> 1.0.0
 ```
 
-### Run
-
-```bash
-docker run -p 8000:8000 \
-  -e DEEPSEEK_API_KEY=your-key \
-  -e TMDB_API_KEY=your-key \
-  -v $(pwd)/memory_data:/app/memory_data \
-  agent-media
-```
-
-### Docker Compose
-
-```bash
-# Start all services (agent + qBittorrent)
-docker-compose up -d
-
-# View logs
-docker-compose logs -f
-
-# Stop
-docker-compose down
-```
-
-## API Documentation
+## 📚 API Reference
 
 ### Endpoints
 
 #### `GET /health`
 Health check endpoint.
 
-**Response:**
 ```json
 {
   "status": "healthy",
-  "version": "0.2.0"
+  "version": "0.1.7"
 }
 ```
 
 #### `GET /v1/models`
 List available models (OpenAI-compatible).
 
+```json
+{
+  "object": "list",
+  "data": [
+    {
+      "id": "alfred",
+      "object": "model",
+      "owned_by": "alfred"
+    }
+  ]
+}
+```
+
 #### `POST /v1/chat/completions`
 Chat with the agent (OpenAI-compatible).
 
 **Request:**
 ```json
 {
-  "model": "agent-media",
+  "model": "alfred",
   "messages": [
     {"role": "user", "content": "Find Inception"}
   ],
@@ -317,7 +463,7 @@ Chat with the agent (OpenAI-compatible).
   "id": "chatcmpl-xxx",
   "object": "chat.completion",
   "created": 1234567890,
-  "model": "agent-media",
+  "model": "alfred",
   "choices": [{
     "index": 0,
     "message": {
@@ -330,71 +476,120 @@ Chat with the agent (OpenAI-compatible).
 ```
 
 #### `GET /memory/state`
-View full memory state (debug).
+View full memory state (debug endpoint).
 
 #### `POST /memory/clear-session`
 Clear session memories (STM + Episodic).
 
-## Troubleshooting
+## 🔧 Troubleshooting
 
 ### Agent doesn't respond
-- Check API keys in `.env`
-- Verify LLM provider is running (Ollama) or accessible (DeepSeek)
-- Check logs: `docker-compose logs agent-media`
+
+1. Check API keys in `.env`
+2. Verify LLM provider is running:
+   ```bash
+   # For Ollama
+   docker logs alfred-ollama
+   
+   # Check if model is pulled
+   docker exec alfred-ollama ollama list
+   ```
+3. Check Alfred logs: `docker logs alfred-core`
 
 ### qBittorrent connection failed
-- Verify qBittorrent is running
-- Check `QBITTORRENT_HOST` in `.env`
-- Ensure Web UI is enabled in qBittorrent settings
+
+1. Verify qBittorrent is running: `docker ps | grep qbittorrent`
+2. Check Web UI is enabled in qBittorrent settings
+3. Verify credentials in `.env`:
+   ```bash
+   QBITTORRENT_URL=http://qbittorrent:16140
+   QBITTORRENT_USERNAME=admin
+   QBITTORRENT_PASSWORD=<check-your-env>
+   ```
+
+### Database connection issues
+
+1. Check MongoDB is healthy: `docker logs alfred-mongodb`
+2. Verify credentials match in `.env`
+3. Try restarting: `make restart`
 
 ### Memory not persisting
-- Check `memory_data/` directory exists and is writable
-- Verify volume mounts in Docker
+
+1. Check `data/` directory exists and is writable
+2. Verify volume mounts in `docker-compose.yaml`
+3. Check file permissions: `ls -la data/`
+
+### Bootstrap fails
+
+1. Ensure `.env.example` exists
+2. Check `pyproject.toml` has required sections:
+   ```toml
+   [tool.alfred.settings]
+   [tool.alfred.security]
+   ```
+3. Run manually: `python scripts/bootstrap.py`
 
 ### Tests failing
-- Run `poetry install` to ensure dependencies are up to date
-- Check logs for specific error messages
 
-## Contributing
+1. Update dependencies: `poetry install`
+2. Check Python version: `python --version` (needs 3.14+)
+3. Run specific failing test with verbose output:
+   ```bash
+   poetry run pytest tests/test_failing.py -v --tb=long
+   ```
 
-Contributions are welcome!
+## 🤝 Contributing
 
-### Development Workflow
+Contributions are welcome! Please follow these steps:
 
-1. Fork the repository
-2. Create a feature branch: `git checkout -b feature/my-feature`
-3. Make your changes
-4. Run tests: `poetry run pytest`
-5. Run linting: `poetry run ruff check . && poetry run black .`
-6. Commit: `git commit -m "Add my feature"`
-7. Push: `git push origin feature/my-feature`
-8. Create a Pull Request
+1. **Fork** the repository
+2. **Create** a feature branch: `git checkout -b feature/my-feature`
+3. **Make** your changes
+4. **Run** tests: `make test`
+5. **Run** linting: `make lint && make format`
+6. **Commit**: `git commit -m "feat: add my feature"`
+7. **Push**: `git push origin feature/my-feature`
+8. **Create** a Pull Request
 
-## Documentation
+### Commit Convention
 
-- [Architecture Diagram](docs/architecture_diagram.md) - System architecture overview
-- [Class Diagram](docs/class_diagram.md) - Class structure and relationships
-- [Component Diagram](docs/component_diagram.md) - Component interactions
-- [Sequence Diagram](docs/sequence_diagram.md) - Sequence flows
-- [Flowchart](docs/flowchart.md) - System flowcharts
+We use [Conventional Commits](https://www.conventionalcommits.org/):
 
-## License
+- `feat:` New feature
+- `fix:` Bug fix
+- `docs:` Documentation
+- `refactor:` Code refactoring
+- `test:` Adding tests
+- `chore:` Maintenance
 
-MIT License - see [LICENSE](LICENSE) file for details.
+## 📖 Documentation
 
-## Acknowledgments
+- [Architecture Diagram](docs/architecture_diagram.md) — System architecture overview
+- [Class Diagram](docs/class_diagram.md) — Class structure and relationships
+- [Component Diagram](docs/component_diagram.md) — Component interactions
+- [Sequence Diagram](docs/sequence_diagram.md) — Sequence flows
+- [Flowchart](docs/flowchart.md) — System flowcharts
 
-- [DeepSeek](https://www.deepseek.com/) - LLM provider
-- [TMDB](https://www.themoviedb.org/) - Movie database
-- [qBittorrent](https://www.qbittorrent.org/) - Torrent client
-- [FastAPI](https://fastapi.tiangolo.com/) - Web framework
+## 📄 License
 
-## Support
+MIT License — see [LICENSE](LICENSE) file for details.
+
+## 🙏 Acknowledgments
+
+- [LibreChat](https://github.com/danny-avila/LibreChat) — Beautiful chat interface
+- [Ollama](https://ollama.ai/) — Local LLM runtime
+- [DeepSeek](https://www.deepseek.com/) — LLM provider
+- [TMDB](https://www.themoviedb.org/) — Movie database
+- [qBittorrent](https://www.qbittorrent.org/) — Torrent client
+- [FastAPI](https://fastapi.tiangolo.com/) — Web framework
+- [Pydantic](https://docs.pydantic.dev/) — Data validation
+
+## 📬 Support
 
 - 📧 Email: francois.hodiaumont@gmail.com
-- 🐛 Issues: [GitHub Issues](https://github.com/your-username/agent-media/issues)
-- 💬 Discussions: [GitHub Discussions](https://github.com/your-username/agent-media/discussions)
+- 🐛 Issues: [GitHub Issues](https://github.com/francwa/alfred_media_organizer/issues)
+- 💬 Discussions: [GitHub Discussions](https://github.com/francwa/alfred_media_organizer/discussions)
 
 ---
 
-Made with ❤️ by Francwa
+<p align="center">Made with ❤️ by <a href="https://github.com/francwa">Francwa</a></p>

alfred/agent/__init__.py

@@ -1,6 +1,7 @@
 """Agent module for media library management."""
 
+from alfred.settings import settings
+
 from .agent import Agent
-from .config import settings
 
 __all__ = ["Agent", "settings"]

alfred/agent/agent.py

@@ -6,8 +6,8 @@ from collections.abc import AsyncGenerator
 from typing import Any
 
 from alfred.infrastructure.persistence import get_memory
+from alfred.settings import settings
 
-from .config import settings
 from .prompts import PromptBuilder
 from .registry import Tool, make_tools
 
@@ -21,17 +21,20 @@ class Agent:
     Uses OpenAI-compatible tool calling API.
     """
 
-    def __init__(self, llm, max_tool_iterations: int = 5):
+    def __init__(self, settings, llm, max_tool_iterations: int = 5):
         """
         Initialize the agent.
 
         Args:
+            settings: Application settings instance
             llm: LLM client with complete() method
             max_tool_iterations: Maximum number of tool execution iterations
         """
+        self.settings = settings
         self.llm = llm
-        self.tools: dict[str, Tool] = make_tools()
+        self.tools: dict[str, Tool] = make_tools(settings)
         self.prompt_builder = PromptBuilder(self.tools)
+        self.settings = settings
         self.max_tool_iterations = max_tool_iterations
 
     def step(self, user_input: str) -> str:
@@ -78,7 +81,7 @@ class Agent:
         tools_spec = self.prompt_builder.build_tools_spec()
 
         # Tool execution loop
-        for _iteration in range(self.max_tool_iterations):
+        for _iteration in range(self.settings.max_tool_iterations):
             # Call LLM with tools
             llm_result = self.llm.complete(messages, tools=tools_spec)
 
@@ -230,7 +233,7 @@ class Agent:
         tools_spec = self.prompt_builder.build_tools_spec()
 
         # Tool execution loop
-        for _iteration in range(self.max_tool_iterations):
+        for _iteration in range(self.settings.max_tool_iterations):
             # Call LLM with tools
             llm_result = self.llm.complete(messages, tools=tools_spec)
 

alfred/agent/config.py

@@ -1,115 +0,0 @@
-"""Configuration management with validation."""
-
-import os
-from dataclasses import dataclass, field
-from pathlib import Path
-
-from dotenv import load_dotenv
-
-# Load environment variables from .env file
-load_dotenv()
-
-
-class ConfigurationError(Exception):
-    """Raised when configuration is invalid."""
-
-    pass
-
-
-@dataclass
-class Settings:
-    """Application settings loaded from environment variables."""
-
-    # LLM Configuration
-    deepseek_api_key: str = field(
-        default_factory=lambda: os.getenv("DEEPSEEK_API_KEY", "")
-    )
-    deepseek_base_url: str = field(
-        default_factory=lambda: os.getenv(
-            "DEEPSEEK_BASE_URL", "https://api.deepseek.com"
-        )
-    )
-    model: str = field(
-        default_factory=lambda: os.getenv("DEEPSEEK_MODEL", "deepseek-chat")
-    )
-    temperature: float = field(
-        default_factory=lambda: float(os.getenv("TEMPERATURE", "0.2"))
-    )
-
-    # TMDB Configuration
-    tmdb_api_key: str = field(default_factory=lambda: os.getenv("TMDB_API_KEY", ""))
-    tmdb_base_url: str = field(
-        default_factory=lambda: os.getenv(
-            "TMDB_BASE_URL", "https://api.themoviedb.org/3"
-        )
-    )
-
-    # Storage Configuration
-    memory_file: str = field(
-        default_factory=lambda: os.getenv("MEMORY_FILE", "memory.json")
-    )
-
-    # Security Configuration
-    max_tool_iterations: int = field(
-        default_factory=lambda: int(os.getenv("MAX_TOOL_ITERATIONS", "5"))
-    )
-    request_timeout: int = field(
-        default_factory=lambda: int(os.getenv("REQUEST_TIMEOUT", "30"))
-    )
-
-    # Memory Configuration
-    max_history_messages: int = field(
-        default_factory=lambda: int(os.getenv("MAX_HISTORY_MESSAGES", "10"))
-    )
-
-    def __post_init__(self):
-        """Validate settings after initialization."""
-        self._validate()
-
-    def _validate(self) -> None:
-        """Validate configuration values."""
-        # Validate temperature
-        if not 0.0 <= self.temperature <= 2.0:
-            raise ConfigurationError(
-                f"Temperature must be between 0.0 and 2.0, got {self.temperature}"
-            )
-
-        # Validate max_tool_iterations
-        if self.max_tool_iterations < 1 or self.max_tool_iterations > 20:
-            raise ConfigurationError(
-                f"max_tool_iterations must be between 1 and 20, got {self.max_tool_iterations}"
-            )
-
-        # Validate request_timeout
-        if self.request_timeout < 1 or self.request_timeout > 300:
-            raise ConfigurationError(
-                f"request_timeout must be between 1 and 300 seconds, got {self.request_timeout}"
-            )
-
-        # Validate URLs
-        if not self.deepseek_base_url.startswith(("http://", "https://")):
-            raise ConfigurationError(
-                f"Invalid deepseek_base_url: {self.deepseek_base_url}"
-            )
-
-        if not self.tmdb_base_url.startswith(("http://", "https://")):
-            raise ConfigurationError(f"Invalid tmdb_base_url: {self.tmdb_base_url}")
-
-        # Validate memory file path
-        memory_path = Path(self.memory_file)
-        if memory_path.exists() and not memory_path.is_file():
-            raise ConfigurationError(
-                f"memory_file exists but is not a file: {self.memory_file}"
-            )
-
-    def is_deepseek_configured(self) -> bool:
-        """Check if DeepSeek API is properly configured."""
-        return bool(self.deepseek_api_key and self.deepseek_base_url)
-
-    def is_tmdb_configured(self) -> bool:
-        """Check if TMDB API is properly configured."""
-        return bool(self.tmdb_api_key and self.tmdb_base_url)
-
-
-# Global settings instance
-settings = Settings()

alfred/agent/llm/deepseek.py

@@ -6,7 +6,8 @@ from typing import Any
 import requests
 from requests.exceptions import HTTPError, RequestException, Timeout
 
-from ..config import settings
+from alfred.settings import Settings, settings
+
 from .exceptions import LLMAPIError, LLMConfigurationError
 
 logger = logging.getLogger(__name__)
@@ -21,6 +22,7 @@ class DeepSeekClient:
         base_url: str | None = None,
         model: str | None = None,
         timeout: int | None = None,
+        settings: Settings | None = None,
     ):
         """
         Initialize DeepSeek client.
@@ -34,10 +36,10 @@ class DeepSeekClient:
         Raises:
             LLMConfigurationError: If API key is missing
         """
-        self.api_key = api_key or settings.deepseek_api_key
-        self.base_url = base_url or settings.deepseek_base_url
-        self.model = model or settings.model
-        self.timeout = timeout or settings.request_timeout
+        self.api_key = api_key or self.settings.deepseek_api_key
+        self.base_url = base_url or self.settings.deepseek_base_url
+        self.model = model or self.settings.deepseek_model
+        self.timeout = timeout or self.settings.request_timeout
 
         if not self.api_key:
             raise LLMConfigurationError(
@@ -94,7 +96,7 @@ class DeepSeekClient:
         payload = {
             "model": self.model,
             "messages": messages,
-            "temperature": settings.temperature,
+            "temperature": settings.llm_temperature,
         }
 
         # Add tools if provided

alfred/agent/llm/ollama.py

@@ -1,13 +1,13 @@
 """Ollama LLM client with robust error handling."""
 
 import logging
-import os
 from typing import Any
 
 import requests
 from requests.exceptions import HTTPError, RequestException, Timeout
 
-from ..config import settings
+from alfred.settings import Settings
+
 from .exceptions import LLMAPIError, LLMConfigurationError
 
 logger = logging.getLogger(__name__)
@@ -32,6 +32,7 @@ class OllamaClient:
         model: str | None = None,
         timeout: int | None = None,
         temperature: float | None = None,
+        settings: Settings | None = None,
     ):
         """
         Initialize Ollama client.
@@ -45,13 +46,11 @@ class OllamaClient:
         Raises:
             LLMConfigurationError: If configuration is invalid
         """
-        self.base_url = base_url or os.getenv(
-            "OLLAMA_BASE_URL", "http://localhost:11434"
-        )
-        self.model = model or os.getenv("OLLAMA_MODEL", "llama3.2")
+        self.base_url = base_url or settings.ollama_base_url
+        self.model = model or settings.ollama_model
         self.timeout = timeout or settings.request_timeout
         self.temperature = (
-            temperature if temperature is not None else settings.temperature
+            temperature if temperature is not None else settings.llm_temperature
         )
 
         if not self.base_url:

alfred/agent/registry.py

@@ -78,10 +78,13 @@ def _create_tool_from_function(func: Callable) -> Tool:
     )
 
 
-def make_tools() -> dict[str, Tool]:
+def make_tools(settings) -> dict[str, Tool]:
     """
     Create and register all available tools.
 
+    Args:
+        settings: Application settings instance
+
     Returns:
         Dictionary mapping tool names to Tool objects
     """

alfred/app.py

@@ -2,22 +2,21 @@
 
 import json
 import logging
-import os
 import time
 import uuid
+from pathlib import Path
 from typing import Any
 
 from fastapi import FastAPI, HTTPException
 from fastapi.responses import JSONResponse, StreamingResponse
-from fastapi.staticfiles import StaticFiles
 from pydantic import BaseModel, Field, validator
 
 from alfred.agent.agent import Agent
-from alfred.agent.config import settings
 from alfred.agent.llm.deepseek import DeepSeekClient
 from alfred.agent.llm.exceptions import LLMAPIError, LLMConfigurationError
 from alfred.agent.llm.ollama import OllamaClient
 from alfred.infrastructure.persistence import get_memory, init_memory
+from alfred.settings import settings
 
 logging.basicConfig(
     level=logging.INFO, format="%(asctime)s - %(name)s - %(levelname)s - %(message)s"
@@ -30,37 +29,33 @@ app = FastAPI(
     version="0.2.0",
 )
 
-# TODO: Make a variable
-manifests = "manifests"
-# Sécurité : on vérifie que le dossier existe pour ne pas faire planter l'app au démarrage
-if os.path.exists(manifests):
-    app.mount("/manifests", StaticFiles(directory=manifests), name="manifests")
-else:
-    print(
-        f"⚠️ ATTENTION : Le dossier '{manifests}' est introuvable. Le plugin ne marchera pas."
-    )
-
-# Initialize memory context at startup
-storage_dir = os.getenv("MEMORY_STORAGE_DIR", "memory_data")
-init_memory(storage_dir=storage_dir)
-logger.info(f"Memory context initialized (storage: {storage_dir})")
+memory_path = Path(settings.data_storage) / "memory"
+init_memory(storage_dir=str(memory_path))
+logger.info(f"Memory context initialized (path: {memory_path})")
 
 # Initialize LLM based on environment variable
-llm_provider = os.getenv("LLM_PROVIDER", "deepseek").lower()
+llm_provider = settings.default_llm_provider.lower()
+
 
 try:
-    if llm_provider == "ollama":
-        logger.info("Using Ollama LLM")
-        llm = OllamaClient()
-    else:
+    if llm_provider == "local":
+        logger.info("Using local Ollama LLM")
+        llm = OllamaClient(settings=settings)
+    elif llm_provider == "deepseek":
         logger.info("Using DeepSeek LLM")
         llm = DeepSeekClient()
+    elif llm_provider == "claude":
+        raise ValueError(f"LLM provider not fully implemented: {llm_provider}")
+    else:
+        raise ValueError(f"Unknown LLM provider: {llm_provider}")
 except LLMConfigurationError as e:
     logger.error(f"Failed to initialize LLM: {e}")
     raise
 
 # Initialize agent
-agent = Agent(llm=llm, max_tool_iterations=settings.max_tool_iterations)
+agent = Agent(
+    settings=settings, llm=llm, max_tool_iterations=settings.max_tool_iterations
+)
 logger.info("Agent Media API initialized")
 
 
@@ -115,7 +110,7 @@ def extract_last_user_content(messages: list[dict[str, Any]]) -> str:
 @app.get("/health")
 async def health_check():
     """Health check endpoint."""
-    return {"status": "healthy", "version": "0.2.0"}
+    return {"status": "healthy", "version": f"v{settings.alfred_version}"}
 
 
 @app.get("/v1/models")

alfred/infrastructure/api/knaben/client.py

@@ -6,7 +6,7 @@ from typing import Any
 import requests
 from requests.exceptions import HTTPError, RequestException, Timeout
 
-from alfred.agent.config import Settings, settings
+from alfred.settings import Settings, settings
 
 from .dto import TorrentResult
 from .exceptions import KnabenAPIError, KnabenNotFoundError

alfred/infrastructure/api/qbittorrent/client.py

@@ -6,7 +6,7 @@ from typing import Any
 import requests
 from requests.exceptions import HTTPError, RequestException, Timeout
 
-from alfred.agent.config import Settings, settings
+from alfred.settings import Settings, settings
 
 from .dto import TorrentInfo
 from .exceptions import QBittorrentAPIError, QBittorrentAuthError

alfred/infrastructure/api/tmdb/client.py

@@ -6,7 +6,7 @@ from typing import Any
 import requests
 from requests.exceptions import HTTPError, RequestException, Timeout
 
-from alfred.agent.config import Settings, settings
+from alfred.settings import Settings, settings
 
 from .dto import MediaResult
 from .exceptions import (

alfred/settings.py

@@ -0,0 +1,292 @@
+"""
+Application settings using Pydantic Settings.
+
+Settings are loaded from .env file and validated against the schema
+defined in pyproject.toml [tool.alfred.settings_schema].
+"""
+
+from pathlib import Path
+
+from pydantic import Field, computed_field, field_validator
+from pydantic_settings import BaseSettings, SettingsConfigDict
+
+from .settings_schema import SCHEMA
+
+BASE_DIR = Path(__file__).resolve().parent.parent
+ENV_FILE_PATH = BASE_DIR / ".env"
+
+
+class ConfigurationError(Exception):
+    """Raised when configuration is invalid."""
+
+    pass
+
+
+def _get_default_from_schema(setting_name: str):
+    """Get default value from schema for a setting."""
+    definition = SCHEMA.get(setting_name.upper())
+    return definition.default if definition else None
+
+
+def _get_secret_factory(rule: str):
+    """Create a factory function for generating secrets."""
+
+    def factory():
+        from .settings_bootstrap import generate_secret  # noqa: PLC0415
+
+        return generate_secret(rule)
+
+    return factory
+
+
+class Settings(BaseSettings):
+    """
+    Application settings.
+
+    Settings are loaded from .env and validated using the schema
+    defined in pyproject.toml.
+    """
+
+    model_config = SettingsConfigDict(
+        env_file=ENV_FILE_PATH,
+        env_file_encoding="utf-8",
+        extra="ignore",
+        case_sensitive=False,
+    )
+
+    # --- BUILD (from TOML) ---
+    alfred_version: str = Field(
+        default=_get_default_from_schema("ALFRED_VERSION"), description="Alfred version"
+    )
+    python_version: str = Field(
+        default=_get_default_from_schema("PYTHON_VERSION"), description="Python version"
+    )
+    python_version_short: str = Field(
+        default=_get_default_from_schema("PYTHON_VERSION_SHORT"),
+        description="Python version (short)",
+    )
+    runner: str = Field(
+        default=_get_default_from_schema("RUNNER"), description="Dependency manager"
+    )
+    image_name: str = Field(
+        default=_get_default_from_schema("IMAGE_NAME"), description="Docker image name"
+    )
+    service_name: str = Field(
+        default=_get_default_from_schema("SERVICE_NAME"),
+        description="Docker service name",
+    )
+    librechat_version: str = Field(
+        default=_get_default_from_schema("LIBRECHAT_VERSION"),
+        description="LibreChat version",
+    )
+    rag_version: str = Field(
+        default=_get_default_from_schema("RAG_VERSION"), description="RAG version"
+    )
+
+    # --- APP SETTINGS ---
+    host: str = Field(
+        default=_get_default_from_schema("HOST"), description="Server host"
+    )
+    port: int = Field(
+        default=_get_default_from_schema("PORT"), description="Server port"
+    )
+    max_history_messages: int = Field(
+        default=_get_default_from_schema("MAX_HISTORY_MESSAGES"),
+        description="Maximum conversation history",
+    )
+    max_tool_iterations: int = Field(
+        default=_get_default_from_schema("MAX_TOOL_ITERATIONS"),
+        description="Maximum tool iterations",
+    )
+    request_timeout: int = Field(
+        default=_get_default_from_schema("REQUEST_TIMEOUT"),
+        description="Request timeout in seconds",
+    )
+    llm_temperature: float = Field(
+        default=_get_default_from_schema("LLM_TEMPERATURE"),
+        description="LLM temperature",
+    )
+    data_storage_dir: str = Field(
+        default=_get_default_from_schema("DATA_STORAGE_DIR"),
+        description="Data storage directory",
+        alias="DATA_STORAGE_DIR",
+    )
+
+    # Legacy aliases
+    debug_logging: bool = False
+    debug_console: bool = False
+    data_storage: str = Field(default="data", exclude=True)  # Deprecated
+
+    # --- API KEYS ---
+    tmdb_api_key: str | None = Field(None, description="TMDB API key")
+    deepseek_api_key: str | None = Field(None, description="DeepSeek API key")
+    openai_api_key: str | None = Field(None, description="OpenAI API key")
+    anthropic_api_key: str | None = Field(None, description="Anthropic API key")
+    google_api_key: str | None = Field(None, description="Google API key")
+    kimi_api_key: str | None = Field(None, description="Kimi API key")
+
+    # --- SECURITY SECRETS ---
+    jwt_secret: str = Field(
+        default_factory=_get_secret_factory("32:b64"), description="JWT signing secret"
+    )
+    jwt_refresh_secret: str = Field(
+        default_factory=_get_secret_factory("32:b64"), description="JWT refresh secret"
+    )
+    creds_key: str = Field(
+        default_factory=_get_secret_factory("32:hex"),
+        description="Credentials encryption key",
+    )
+    creds_iv: str = Field(
+        default_factory=_get_secret_factory("16:hex"),
+        description="Credentials encryption IV",
+    )
+    meili_master_key: str = Field(
+        default_factory=_get_secret_factory("32:b64"),
+        description="Meilisearch master key",
+        repr=False,
+    )
+
+    # --- DATABASE ---
+    mongo_host: str = Field(
+        default=_get_default_from_schema("MONGO_HOST"), description="MongoDB host"
+    )
+    mongo_port: int = Field(
+        default=_get_default_from_schema("MONGO_PORT"), description="MongoDB port"
+    )
+    mongo_user: str = Field(
+        default=_get_default_from_schema("MONGO_USER"), description="MongoDB user"
+    )
+    mongo_password: str = Field(
+        default_factory=_get_secret_factory("16:hex"),
+        description="MongoDB password",
+        repr=False,
+        exclude=True,
+    )
+    mongo_db_name: str = Field(
+        default=_get_default_from_schema("MONGO_DB_NAME"),
+        description="MongoDB database name",
+    )
+
+    @computed_field(repr=False)
+    @property
+    def mongo_uri(self) -> str:
+        """MongoDB connection URI."""
+        return (
+            f"mongodb://{self.mongo_user}:{self.mongo_password}"
+            f"@{self.mongo_host}:{self.mongo_port}/{self.mongo_db_name}"
+            f"?authSource=admin"
+        )
+
+    postgres_host: str = Field(
+        default=_get_default_from_schema("POSTGRES_HOST"), description="PostgreSQL host"
+    )
+    postgres_port: int = Field(
+        default=_get_default_from_schema("POSTGRES_PORT"), description="PostgreSQL port"
+    )
+    postgres_user: str = Field(
+        default=_get_default_from_schema("POSTGRES_USER"), description="PostgreSQL user"
+    )
+    postgres_password: str = Field(
+        default_factory=_get_secret_factory("16:hex"),
+        description="PostgreSQL password",
+        repr=False,
+        exclude=True,
+    )
+    postgres_db_name: str = Field(
+        default=_get_default_from_schema("POSTGRES_DB_NAME"),
+        description="PostgreSQL database name",
+    )
+
+    @computed_field(repr=False)
+    @property
+    def postgres_uri(self) -> str:
+        """PostgreSQL connection URI."""
+        return (
+            f"postgresql://{self.postgres_user}:{self.postgres_password}"
+            f"@{self.postgres_host}:{self.postgres_port}/{self.postgres_db_name}"
+        )
+
+    # --- EXTERNAL SERVICES ---
+    tmdb_base_url: str = "https://api.themoviedb.org/3"
+
+    qbittorrent_url: str = "http://qbittorrent:16140"
+    qbittorrent_username: str = "admin"
+    qbittorrent_password: str = Field(
+        default_factory=_get_secret_factory("16:hex"),
+        description="qBittorrent password",
+    )
+
+    # --- LLM CONFIG ---
+    default_llm_provider: str = "local"
+    ollama_base_url: str = "http://ollama:11434"
+    ollama_model: str = "llama3.3:latest"
+
+    deepseek_base_url: str = "https://api.deepseek.com"
+    deepseek_model: str = "deepseek-chat"
+
+    # --- RAG ENGINE ---
+    rag_enabled: bool = True
+    rag_api_url: str = "http://rag_api:8000"
+    embeddings_provider: str = "ollama"
+    embeddings_model: str = "nomic-embed-text"
+
+    # --- MEILISEARCH ---
+    meili_enabled: bool = True
+    meili_no_analytics: bool = True
+    meili_host: str = "http://meilisearch:7700"
+
+    # --- VALIDATORS (from schema) ---
+    @field_validator("llm_temperature")
+    @classmethod
+    def validate_temperature(cls, v: float) -> float:
+        """Validate LLM temperature is in valid range."""
+        if not 0.0 <= v <= 2.0:
+            raise ConfigurationError(
+                f"Temperature must be between 0.0 and 2.0, got {v}"
+            )
+        return v
+
+    @field_validator("max_tool_iterations")
+    @classmethod
+    def validate_max_iterations(cls, v: int) -> int:
+        """Validate max tool iterations is in valid range."""
+        if not 1 <= v <= 20:
+            raise ConfigurationError(
+                f"max_tool_iterations must be between 1 and 20, got {v}"
+            )
+        return v
+
+    @field_validator("request_timeout")
+    @classmethod
+    def validate_timeout(cls, v: int) -> int:
+        """Validate request timeout is in valid range."""
+        if not 1 <= v <= 300:
+            raise ConfigurationError(
+                f"request_timeout must be between 1 and 300 seconds, got {v}"
+            )
+        return v
+
+    @field_validator("deepseek_base_url", "tmdb_base_url")
+    @classmethod
+    def validate_url(cls, v: str, info) -> str:
+        """Validate URLs start with http:// or https://."""
+        if not v.startswith(("http://", "https://")):
+            raise ConfigurationError(f"Invalid {info.field_name}: must be a valid URL")
+        return v
+
+    # --- HELPER METHODS ---
+    def is_tmdb_configured(self) -> bool:
+        """Check if TMDB API key is configured."""
+        return bool(self.tmdb_api_key)
+
+    def is_deepseek_configured(self) -> bool:
+        """Check if DeepSeek API key is configured."""
+        return bool(self.deepseek_api_key)
+
+    def dump_safe(self) -> dict:
+        """Dump settings excluding sensitive fields."""
+        return self.model_dump(exclude_none=False)
+
+
+# Global settings instance
+settings = Settings()

alfred/settings_bootstrap.py

@@ -0,0 +1,417 @@
+"""
+Settings bootstrap - Generate and validate configuration files.
+
+This module uses the settings schema to generate .env and .env.make files
+with proper validation and secret generation.
+"""
+
+import re
+import secrets
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+import tomllib
+
+from .settings_schema import (
+    SCHEMA,
+    SettingDefinition,
+    SettingSource,
+    SettingsSchema,
+    SettingType,
+    validate_value,
+)
+
+
+@dataclass
+class ConfigSource:
+    """Configuration source paths."""
+
+    base_dir: Path
+    toml_path: Path
+    env_path: Path
+    env_example_path: Path
+
+    @classmethod
+    def from_base_dir(cls, base_dir: Path | None = None) -> "ConfigSource":
+        """Create ConfigSource from base directory."""
+        if base_dir is None:
+            # Don't import settings.py to avoid Pydantic dependency in pre-commit
+            base_dir = Path(__file__).resolve().parent.parent
+
+        return cls(
+            base_dir=base_dir,
+            toml_path=base_dir / "pyproject.toml",
+            env_path=base_dir / ".env",
+            env_example_path=base_dir / ".env.example",
+        )
+
+
+def extract_python_version(version_string: str) -> tuple[str, str]:
+    """
+    Extract Python version from poetry dependency string.
+
+    Examples:
+        "==3.14.2" -> ("3.14.2", "3.14")
+        "^3.14.2" -> ("3.14.2", "3.14")
+    """
+    clean_version = re.sub(r"^[=^~><]+", "", version_string.strip())
+    parts = clean_version.split(".")
+
+    if len(parts) >= 2:
+        full_version = clean_version
+        short_version = f"{parts[0]}.{parts[1]}"
+        return full_version, short_version
+    else:
+        raise ValueError(f"Invalid Python version format: {version_string}")
+
+
+def generate_secret(rule: str) -> str:
+    """
+    Generate a cryptographically secure secret.
+
+    Args:
+        rule: Format "size:tech" (e.g., "32:b64", "16:hex")
+    """
+    parts = rule.split(":")
+    if len(parts) != 2:
+        raise ValueError(f"Invalid security rule format: {rule}")
+
+    size_str, tech = parts
+    size = int(size_str)
+
+    match tech:
+        case "b64":
+            return secrets.token_urlsafe(size)
+        case "hex":
+            return secrets.token_hex(size)
+        case _:
+            raise ValueError(f"Invalid security format: {tech}")
+
+
+def get_nested_value(data: dict, path: str) -> Any:
+    """
+    Get nested value from dict using dot notation.
+
+    Example:
+        get_nested_value({"a": {"b": {"c": 1}}}, "a.b.c") -> 1
+    """
+    keys = path.split(".")
+    value = data
+    for key in keys:
+        if not isinstance(value, dict):
+            raise KeyError(f"Cannot access {key} in non-dict value")
+        value = value[key]
+    return value
+
+
+class SettingsBootstrap:
+    """
+    Bootstrap settings from schema.
+
+    This class orchestrates the entire bootstrap process:
+    1. Load schema
+    2. Load sources (TOML, existing .env)
+    3. Resolve all settings
+    4. Validate
+    5. Write .env and .env.make
+    """
+
+    def __init__(self, source: ConfigSource, schema: SettingsSchema | None = None):
+        """
+        Initialize bootstrap.
+
+        Args:
+            source: Configuration source paths
+            schema: Settings schema (uses global SCHEMA if None)
+        """
+        self.source = source
+        self.schema = schema or SCHEMA
+        self.toml_data: dict | None = None
+        self.existing_env: dict[str, str] = {}
+        self.resolved_settings: dict[str, Any] = {}
+
+    def bootstrap(self) -> None:
+        """
+        Run complete bootstrap process.
+
+        This is the main entry point that orchestrates everything.
+        """
+        print("<EFBFBD><EFBFBD><EFBFBD><EFBFBD> Starting settings bootstrap...")
+
+        # 1. Load sources
+        self._load_sources()
+
+        # 2. Resolve all settings
+        self._resolve_settings()
+
+        # 3. Validate
+        self._validate_settings()
+
+        # 4. Write files
+        self._write_env()
+        self._write_env_make()
+
+        print("✅ Bootstrap complete!")
+        print("\n⚠️  Reminder: Add your API keys to .env if needed")
+
+    def _load_sources(self) -> None:
+        """Load TOML and existing .env."""
+        # Load TOML
+        if not self.source.toml_path.exists():
+            raise FileNotFoundError(
+                f"pyproject.toml not found: {self.source.toml_path}"
+            )
+
+        with open(self.source.toml_path, "rb") as f:
+            self.toml_data = tomllib.load(f)
+
+        # Load existing .env
+        if self.source.env_path.exists():
+            print("🔄 Reading existing .env...")
+            with open(self.source.env_path) as f:
+                for line in f:
+                    if "=" in line and not line.strip().startswith("#"):
+                        key, value = line.split("=", 1)
+                        self.existing_env[key.strip()] = value.strip()
+            print(f"   Found {len(self.existing_env)} existing keys")
+        else:
+            print("🔧 Creating new .env file...")
+
+    def _resolve_settings(self) -> None:
+        """Resolve all settings from their sources."""
+        print("📋 Resolving settings...")
+
+        # First pass: resolve non-computed settings
+        for definition in self.schema:
+            if definition.source != SettingSource.COMPUTED:
+                self.resolved_settings[definition.name] = self._resolve_setting(
+                    definition
+                )
+
+        # Second pass: resolve computed settings (they may depend on others)
+        for definition in self.schema:
+            if definition.source == SettingSource.COMPUTED:
+                self.resolved_settings[definition.name] = self._resolve_setting(
+                    definition
+                )
+
+    def _resolve_setting(self, definition: SettingDefinition) -> Any:
+        """Resolve a single setting value."""
+        match definition.source:
+            case SettingSource.TOML:
+                return self._resolve_from_toml(definition)
+            case SettingSource.ENV:
+                return self._resolve_from_env(definition)
+            case SettingSource.GENERATED:
+                return self._resolve_generated(definition)
+            case SettingSource.COMPUTED:
+                return self._resolve_computed(definition)
+
+    def _resolve_from_toml(self, definition: SettingDefinition) -> Any:
+        """Resolve setting from TOML."""
+        if not definition.toml_path:
+            raise ValueError(
+                f"{definition.name}: toml_path is required for TOML source"
+            )
+
+        value = get_nested_value(self.toml_data, definition.toml_path)
+
+        # Apply transform if specified
+        if definition.transform:
+            match definition.transform:
+                case "extract_python_version_full":
+                    value, _ = extract_python_version(value)
+                case "extract_python_version_short":
+                    _, value = extract_python_version(value)
+                case _:
+                    raise ValueError(f"Unknown transform: {definition.transform}")
+
+        return value
+
+    def _resolve_from_env(self, definition: SettingDefinition) -> Any:
+        """Resolve setting from .env."""
+        # Check existing .env first
+        if definition.name in self.existing_env:
+            value = self.existing_env[definition.name]
+        elif definition.default is not None:
+            value = definition.default
+        elif not definition.required:
+            return None
+        else:
+            raise ValueError(f"{definition.name} is required but not found in .env")
+
+        # Convert type (only if value is a string from .env)
+        match definition.type:
+            case SettingType.INTEGER:
+                return int(value) if not isinstance(value, int) else value
+            case SettingType.FLOAT:
+                return float(value) if not isinstance(value, float) else value
+            case SettingType.BOOLEAN:
+                if isinstance(value, bool):
+                    return value
+                return str(value).lower() in ("true", "1", "yes")
+            case _:
+                return str(value) if not isinstance(value, str) else value
+
+    def _resolve_generated(self, definition: SettingDefinition) -> str:
+        """Resolve generated secret."""
+        # Preserve existing secret
+        if definition.name in self.existing_env:
+            print(f"  ↻ Kept existing {definition.name}")
+            return self.existing_env[definition.name]
+
+        # Generate new secret
+        if not definition.secret_rule:
+            raise ValueError(
+                f"{definition.name}: secret_rule is required for GENERATED source"
+            )
+
+        secret = generate_secret(definition.secret_rule)
+        print(f"  + Generated {definition.name} ({definition.secret_rule})")
+        return secret
+
+    def _resolve_computed(self, definition: SettingDefinition) -> str:
+        """Resolve computed setting."""
+        if not definition.compute_template:
+            raise ValueError(
+                f"{definition.name}: compute_template is required for COMPUTED source"
+            )
+
+        # Build context from dependencies
+        context = {}
+        if definition.compute_from:
+            for dep in definition.compute_from:
+                if dep not in self.resolved_settings:
+                    raise ValueError(
+                        f"{definition.name}: dependency {dep} not resolved yet"
+                    )
+                context[dep] = self.resolved_settings[dep]
+
+        # Format template
+        return definition.compute_template.format(**context)
+
+    def _validate_settings(self) -> None:
+        """Validate all resolved settings."""
+        print("✓ Validating settings...")
+
+        errors = []
+        for definition in self.schema:
+            value = self.resolved_settings.get(definition.name)
+            try:
+                validate_value(definition, value)
+            except ValueError as e:
+                errors.append(str(e))
+
+        if errors:
+            raise ValueError(
+                "Validation errors:\n" + "\n".join(f"  - {e}" for e in errors)
+            )
+
+    def _write_env(self) -> None:
+        """
+        Write .env file using .env.example as template.
+
+        This preserves the structure, comments, and formatting of .env.example
+        while updating only the values of variables defined in the schema.
+        Custom variables from existing .env are appended at the end.
+        """
+        print("📝 Writing .env...")
+
+        # Check if .env.example exists
+        if not self.source.env_example_path.exists():
+            raise FileNotFoundError(
+                f".env.example not found: {self.source.env_example_path}"
+            )
+
+        # Read .env.example as template
+        with open(self.source.env_example_path, encoding="utf-8") as f:
+            template_lines = f.readlines()
+
+        # Track which keys we've processed from .env.example
+        processed_keys = set()
+
+        # Process template line by line
+        output_lines = []
+        for line in template_lines:
+            stripped = line.strip()
+
+            # Keep comments and empty lines as-is
+            if not stripped or stripped.startswith("#"):
+                output_lines.append(line)
+                continue
+
+            # Check if line contains a variable assignment
+            if "=" in line:
+                key, _ = line.split("=", 1)
+                key = key.strip()
+                processed_keys.add(key)
+
+                # Check if this variable is in our schema
+                definition = self.schema.get(key)
+
+                if definition:
+                    # Update with resolved value (including computed settings)
+                    value = self.resolved_settings.get(key, "")
+
+                    # Convert Python booleans to lowercase for .env compatibility
+                    if isinstance(value, bool):
+                        value = "true" if value else "false"
+
+                    output_lines.append(f"{key}={value}\n")
+                # Variable not in schema
+                # If it exists in current .env, use that value, otherwise keep template
+                elif key in self.existing_env:
+                    output_lines.append(f"{key}={self.existing_env[key]}\n")
+                else:
+                    output_lines.append(line)
+            else:
+                # Keep any other lines as-is
+                output_lines.append(line)
+
+        # Append custom variables from existing .env that aren't in .env.example
+        custom_vars = {
+            k: v for k, v in self.existing_env.items() if k not in processed_keys
+        }
+        if custom_vars:
+            output_lines.append("\n# --- CUSTOM VARIABLES ---\n")
+            output_lines.append("# Variables added manually (not in .env.example)\n")
+            for key, value in sorted(custom_vars.items()):
+                output_lines.append(f"{key}={value}\n")
+
+        # Write updated .env
+        with open(self.source.env_path, "w", encoding="utf-8") as f:
+            f.writelines(output_lines)
+
+        print(f"✅ {self.source.env_path.name} written (preserving template structure)")
+        if custom_vars:
+            print(f"   ℹ️  Preserved {len(custom_vars)} custom variable(s)")
+
+    def _write_env_make(self) -> None:
+        """Write .env.make for Makefile."""
+        print("📝 Writing .env.make...")
+
+        lines = ["# Auto-generated from pyproject.toml\n"]
+
+        for definition in self.schema.get_for_env_make():
+            value = self.resolved_settings.get(definition.name, "")
+            lines.append(f"export {definition.name}={value}\n")
+
+        env_make_path = self.source.base_dir / ".env.make"
+        with open(env_make_path, "w", encoding="utf-8") as f:
+            f.writelines(lines)
+
+        print("✅ .env.make written")
+
+
+def bootstrap_env(source: ConfigSource) -> None:  # noqa: PLC0415
+    """
+    Bootstrap environment configuration.
+
+    This is the main entry point for bootstrapping.
+
+    Args:
+        source: Configuration source paths
+    """
+    bootstrapper = SettingsBootstrap(source)
+    bootstrapper.bootstrap()

alfred/settings_schema.py

@@ -0,0 +1,291 @@
+"""
+Settings schema parser and definitions.
+
+This module loads the settings schema from pyproject.toml and provides
+type-safe access to setting definitions.
+"""
+
+from dataclasses import dataclass
+from enum import Enum
+from pathlib import Path
+from typing import Any
+
+import tomllib
+
+BASE_DIR = Path(__file__).resolve().parent.parent
+
+
+class SettingType(Enum):
+    """Type of setting value."""
+
+    STRING = "string"
+    INTEGER = "integer"
+    FLOAT = "float"
+    BOOLEAN = "boolean"
+    SECRET = "secret"
+    COMPUTED = "computed"
+
+
+class SettingSource(Enum):
+    """Source of setting value."""
+
+    ENV = "env"  # From .env file
+    TOML = "toml"  # From pyproject.toml
+    GENERATED = "generated"  # Auto-generated (secrets)
+    COMPUTED = "computed"  # Computed from other settings
+
+
+@dataclass
+class SettingDefinition:
+    """
+    Complete definition of a setting.
+
+    This is the parsed representation of a setting from pyproject.toml.
+    """
+
+    name: str
+    type: SettingType
+    source: SettingSource
+    description: str = ""
+    category: str = "general"
+    required: bool = True
+    default: str | int | float | bool | None = None
+
+    # For TOML source
+    toml_path: str | None = None
+    transform: str | None = None  # Transform function name
+
+    # For SECRET source
+    secret_rule: str | None = None  # e.g., "32:b64", "16:hex"
+
+    # For COMPUTED source
+    compute_from: list[str] | None = None  # Dependencies
+    compute_template: str | None = None  # Template string
+
+    # For validation
+    validator: str | None = None  # e.g., "range:0.0:2.0"
+
+    # For export
+    export_to_env_make: bool = False
+
+
+class SettingsSchema:
+    """
+    Settings schema loaded from pyproject.toml.
+
+    Provides access to all setting definitions and utilities for
+    working with the schema.
+    """
+
+    def __init__(self, schema_dict: dict[str, dict[str, Any]]):
+        """
+        Initialize schema from parsed TOML.
+
+        Args:
+            schema_dict: Dictionary from [tool.alfred.settings_schema]
+        """
+        self.definitions: dict[str, SettingDefinition] = {}
+        self._parse_schema(schema_dict)
+
+    def _parse_schema(self, schema_dict: dict[str, dict[str, Any]]) -> None:
+        """Parse schema dictionary into SettingDefinition objects."""
+        for name, config in schema_dict.items():
+            # Skip non-setting entries
+            if not isinstance(config, dict):
+                continue
+
+            # Parse type
+            type_str = config.get("type", "string")
+            setting_type = SettingType(type_str)
+
+            # Parse source
+            source_str = config.get("source", "env")
+            source = SettingSource(source_str)
+
+            # Parse default value based on type
+            default = config.get("default")
+            if default is not None:
+                match setting_type:
+                    case SettingType.INTEGER:
+                        default = int(default)
+                    case SettingType.FLOAT:
+                        default = float(default)
+                    case SettingType.BOOLEAN:
+                        default = bool(default)
+                    case _:
+                        default = str(default) if default else None
+
+            # Create definition
+            definition = SettingDefinition(
+                name=name,
+                type=setting_type,
+                source=source,
+                description=config.get("description", ""),
+                category=config.get("category", "general"),
+                required=config.get("required", True),
+                default=default,
+                toml_path=config.get("toml_path"),
+                transform=config.get("transform"),
+                secret_rule=config.get("secret_rule"),
+                compute_from=config.get("compute_from"),
+                compute_template=config.get("compute_template"),
+                validator=config.get("validator"),
+                export_to_env_make=config.get("export_to_env_make", False),
+            )
+
+            self.definitions[name] = definition
+
+    def get(self, name: str) -> SettingDefinition | None:
+        """Get setting definition by name."""
+        return self.definitions.get(name)
+
+    def get_by_category(self, category: str) -> list[SettingDefinition]:
+        """Get all settings in a category."""
+        return [d for d in self.definitions.values() if d.category == category]
+
+    def get_by_source(self, source: SettingSource) -> list[SettingDefinition]:
+        """Get all settings from a specific source."""
+        return [d for d in self.definitions.values() if d.source == source]
+
+    def get_required(self) -> list[SettingDefinition]:
+        """Get all required settings."""
+        return [d for d in self.definitions.values() if d.required]
+
+    def get_for_env_make(self) -> list[SettingDefinition]:
+        """Get all settings that should be exported to .env.make."""
+        return [d for d in self.definitions.values() if d.export_to_env_make]
+
+    def __iter__(self):
+        """Iterate over all setting definitions."""
+        return iter(self.definitions.values())
+
+    def __len__(self):
+        """Number of settings in schema."""
+        return len(self.definitions)
+
+
+def load_schema(base_dir: Path | None = None) -> SettingsSchema:
+    """
+    Load settings schema from settings.toml or pyproject.toml.
+
+    Priority:
+        1. settings.toml (if exists)
+        2. pyproject.toml [tool.alfred.settings_schema]
+
+    Args:
+        base_dir: Base directory containing config files
+
+    Returns:
+        SettingsSchema instance
+
+    Raises:
+        FileNotFoundError: If neither file exists
+        KeyError: If settings_schema section is missing
+    """
+    if base_dir is None:
+        base_dir = BASE_DIR
+
+    # Try settings.toml first (cleaner, dedicated file)
+    settings_toml_path = base_dir / "settings.toml"
+    if settings_toml_path.exists():
+        with open(settings_toml_path, "rb") as f:
+            data = tomllib.load(f)
+
+        try:
+            schema_dict = data["tool"]["alfred"]["settings_schema"]
+            return SettingsSchema(schema_dict)
+        except KeyError as e:
+            raise KeyError(
+                "Missing [tool.alfred.settings_schema] section in settings.toml"
+            ) from e
+
+    # Fallback to pyproject.toml
+    toml_path = base_dir / "pyproject.toml"
+    if not toml_path.exists():
+        raise FileNotFoundError(
+            f"Neither settings.toml nor pyproject.toml found in {base_dir}"
+        )
+
+    with open(toml_path, "rb") as f:
+        data = tomllib.load(f)
+
+    try:
+        schema_dict = data["tool"]["alfred"]["settings_schema"]
+    except KeyError as e:
+        raise KeyError(
+            "Missing [tool.alfred.settings_schema] section in pyproject.toml"
+        ) from e
+
+    return SettingsSchema(schema_dict)
+
+
+def validate_value(definition: SettingDefinition, value: Any) -> bool:
+    """
+    Validate a value against a setting definition.
+
+    Args:
+        definition: Setting definition with validation rules
+        value: Value to validate
+
+    Returns:
+        True if valid
+
+    Raises:
+        ValueError: If validation fails
+    """
+    if value is None:
+        if definition.required:
+            raise ValueError(f"{definition.name} is required but got None")
+        return True
+
+    # Type validation
+    match definition.type:
+        case SettingType.INTEGER:
+            if not isinstance(value, int):
+                raise ValueError(
+                    f"{definition.name} must be integer, got {type(value).__name__}"
+                )
+        case SettingType.FLOAT:
+            if not isinstance(value, (int, float)):
+                raise ValueError(
+                    f"{definition.name} must be float, got {type(value).__name__}"
+                )
+        case SettingType.BOOLEAN:
+            if not isinstance(value, bool):
+                raise ValueError(
+                    f"{definition.name} must be boolean, got {type(value).__name__}"
+                )
+        case SettingType.STRING | SettingType.SECRET:
+            if not isinstance(value, str):
+                raise ValueError(
+                    f"{definition.name} must be string, got {type(value).__name__}"
+                )
+
+    # Custom validator
+    if definition.validator:
+        _apply_validator(definition.name, definition.validator, value)
+
+    return True
+
+
+def _apply_validator(name: str, validator: str, value: Any) -> None:
+    """Apply custom validator to value."""
+    if validator.startswith("range:"):
+        # Parse range validator: "range:min:max"
+        parts = validator.split(":")
+        if len(parts) != 3:
+            raise ValueError(f"Invalid range validator format: {validator}")
+
+        min_val = float(parts[1])
+        max_val = float(parts[2])
+
+        if not (min_val <= value <= max_val):
+            raise ValueError(
+                f"{name} must be between {min_val} and {max_val}, got {value}"
+            )
+    else:
+        raise ValueError(f"Unknown validator: {validator}")
+
+
+# Load schema once at module import
+SCHEMA = load_schema()

cli.py

@@ -1,231 +0,0 @@
-#!/usr/bin/env python3
-import os
-import secrets
-import shutil
-import subprocess
-import sys
-from datetime import datetime
-from enum import StrEnum
-from pathlib import Path
-from typing import NoReturn
-
-REQUIRED_VARS = ["DEEPSEEK_API_KEY", "TMDB_API_KEY", "QBITTORRENT_URL"]
-
-# Size in bytes
-KEYS_TO_GENERATE = {
-    "JWT_SECRET": 32,
-    "JWT_REFRESH_SECRET": 32,
-    "CREDS_KEY": 32,
-    "CREDS_IV": 16,
-}
-
-
-class Style(StrEnum):
-    """ANSI codes for styling output.
-    Usage: f"{Style.RED}Error{Style.RESET}"
-    """
-
-    RESET = "\033[0m"
-    BOLD = "\033[1m"
-    RED = "\033[31m"
-    GREEN = "\033[32m"
-    YELLOW = "\033[33m"
-    CYAN = "\033[36m"
-    DIM = "\033[2m"
-
-
-# Only for terminals and if not specified otherwise
-USE_COLORS = sys.stdout.isatty() and "NO_COLOR" not in os.environ
-
-
-def styled(text: str, color_code: str) -> str:
-    """Apply color only if supported by the terminal."""
-    if USE_COLORS:
-        return f"{color_code}{text}{Style.RESET}"
-    return text
-
-
-def log(msg: str, color: str | None = None, prefix="") -> None:
-    """Print a formatted message."""
-    formatted_msg = styled(msg, color) if color else msg
-    print(f"{prefix}{formatted_msg}")
-
-
-def error_exit(msg: str) -> NoReturn:
-    """Print an error message in red and exit."""
-    log(f"❌ {msg}", Style.RED)
-    sys.exit(1)
-
-
-def is_docker_running() -> bool:
-    """ "Check if Docker is available and responsive."""
-    if shutil.which("docker") is None:
-        error_exit("Docker is not installed.")
-
-    result = subprocess.run(
-        ["docker", "info"],
-        # Redirect stdout/stderr to keep output clean on success
-        stdout=subprocess.DEVNULL,
-        stderr=subprocess.DEVNULL,
-        # Prevent exception being raised
-        check=False,
-    )
-    return result.returncode == 0
-
-
-def parse_env(content: str) -> dict[str, str]:
-    """Parses existing keys and values into a dict (ignoring comments)."""
-    env_vars = {}
-    for raw_line in content.splitlines():
-        line = raw_line.strip()
-        if line and not line.startswith("#") and "=" in line:
-            key, value = line.split("=", 1)
-            env_vars[key.strip()] = value.strip()
-
-    return env_vars
-
-
-def dump_env(content: str, data: dict[str, str]) -> str:
-    new_content: list[str] = []
-    processed_keys = set()
-
-    for raw_line in content.splitlines():
-        line = raw_line.strip()
-        # Fast line (empty, comment or not an assignation)
-        if len(line) == 0 or line.startswith("#") or "=" not in line:
-            new_content.append(raw_line)
-            continue
-
-        # Slow line (inline comment to be kept)
-        key_chunk, value_chunk = raw_line.split("=", 1)
-        key = key_chunk.strip()
-
-        # Not in the update list
-        if key not in data:
-            new_content.append(raw_line)
-            continue
-
-        processed_keys.add(key)
-        new_value = data[key]
-
-        if " #" not in value_chunk:
-            new_line = f"{key_chunk}={new_value}"
-        else:
-            _, comment = value_chunk.split(" #", 1)
-            new_line = f"{key_chunk}={new_value} #{comment}"
-
-        new_content.append(new_line)
-
-    for key, value in data.items():
-        if key not in processed_keys:
-            new_content.append(f"{key}={value}")
-
-    return "\n".join(new_content) + "\n"
-
-
-def ensure_env() -> None:
-    """Manage .env lifecycle: creation, secret generation, prompts."""
-    env_path = Path(".env")
-    env_example_path = Path(".env.example")
-    updated: bool = False
-
-    # Read .env if exists
-    if env_path.exists():
-        content: str = env_path.read_text(encoding="utf-8")
-    else:
-        content: str = env_example_path.read_text(encoding="utf-8")
-
-    existing_vars: dict[str, str] = parse_env(content)
-
-    # Generate missing secrets
-    for key, length in KEYS_TO_GENERATE.items():
-        if key not in existing_vars or not existing_vars[key]:
-            log(f"Generating {key}...", Style.GREEN, prefix="   ")
-            existing_vars[key] = secrets.token_hex(length)
-            updated = True
-            log("Done", Style.GREEN, prefix="   ")
-
-    # Prompt for missing mandatory keys
-    color = Style.YELLOW if USE_COLORS else ""
-    reset = Style.RESET if USE_COLORS else ""
-    for key in REQUIRED_VARS:
-        if key not in existing_vars or not existing_vars[key]:
-            try:
-                existing_vars[key] = input(
-                    f"   {color}Enter value for {key}: {reset}"
-                ).strip()
-                updated = True
-            except KeyboardInterrupt:
-                print()
-                error_exit("Aborted by user.")
-
-    # Write to disk
-    if updated:
-        # But backup original first
-        if env_path.exists():
-            timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
-            backup_path = Path(f"{env_path}.{timestamp}.bak")
-            shutil.copy(env_path, backup_path)
-            log(f"Backup created: {backup_path}", Style.DIM)
-
-        new_content = dump_env(content, existing_vars)
-        env_path.write_text(new_content, encoding="utf-8")
-        log(".env updated successfully.", Style.GREEN)
-    else:
-        log("Configuration is up to date.", Style.GREEN)
-
-
-def setup() -> None:
-    """Orchestrate initialization."""
-    is_docker_running()
-    ensure_env()
-
-
-def status() -> None:
-    """Display simple dashboard."""
-    # Hardcoded bold style for title if colors are enabled
-    title_style = Style.BOLD if USE_COLORS else ""
-    reset_style = Style.RESET if USE_COLORS else ""
-
-    print(f"\n{title_style}ALFRED STATUS{reset_style}")
-    print(f"{title_style}==============={reset_style}\n")
-
-    # Docker Check
-    if is_docker_running():
-        print(f"   Docker:  {styled('✓ running', Style.GREEN)}")
-    else:
-        print(f"   Docker:  {styled('✗ stopped', Style.RED)}")
-
-    # Env Check
-    if Path(".env").exists():
-        print(f"   .env:    {styled('✓ present', Style.GREEN)}")
-    else:
-        print(f"   .env:    {styled('✗ missing', Style.RED)}")
-
-    print("")
-
-
-def check() -> None:
-    """Silent check for prerequisites (used by 'make up')."""
-    setup()
-
-
-def main() -> None:
-    if len(sys.argv) < 2:
-        print("Usage: python cli.py [setup|check|status]")
-        sys.exit(1)
-
-    cmd = sys.argv[1]
-
-    if cmd == "setup":
-        setup()
-    elif cmd == "check":
-        check()
-    elif cmd == "status":
-        status()
-    else:
-        error_exit(f"Unknown command: {cmd}")
-
-
-if __name__ == "__main__":
-    main()

docker-compose.yaml

@@ -1,4 +1,20 @@
 services:
+  # - CORE SERVICES -
+  # --- .ENV INIT ---
+  alfred-init:
+    container_name: alfred-init
+    build:
+      context: .
+      target: builder
+      args:
+        PYTHON_VERSION: ${PYTHON_VERSION}
+        PYTHON_VERSION_SHORT: ${PYTHON_VERSION_SHORT}
+        RUNNER: ${RUNNER}
+    command: python scripts/bootstrap.py
+    networks:
+      - alfred-net
+
+  # --- MAIN APPLICATION ---
   alfred:
     container_name: alfred-core
     build:
@@ -8,47 +24,40 @@ services:
         PYTHON_VERSION_SHORT: ${PYTHON_VERSION_SHORT}
         RUNNER: ${RUNNER}
     depends_on:
-    - librechat
+      alfred-init:
+        condition: service_completed_successfully
     restart: unless-stopped
     env_file:
-      - .env
-    environment:
-      # LLM Configuration
-      LLM_PROVIDER: ${LLM_PROVIDER:-deepseek}
-      DEEPSEEK_API_KEY: ${DEEPSEEK_API_KEY:-}
-
-      # Memory storage
-      MEMORY_STORAGE_DIR: /data/memory
-
-      # External services
-      TMDB_API_KEY: ${TMDB_API_KEY:-}
-      QBITTORRENT_URL: ${QBITTORRENT_URL:-}
-      QBITTORRENT_USERNAME: ${QBITTORRENT_USERNAME:-}
-      QBITTORRENT_PASSWORD: ${QBITTORRENT_PASSWORD:-}
+      - path: .env
+        required: true
     volumes:
-      - ./data/memory:/data/memory
-      - ./logs:/data/logs
-    # TODO: Development: mount code for hot reload (comment out in production)
-    # - ./alfred:/app/alfred
+      - ./data:/data
+      - ./logs:/logs
+      # TODO: Hot reload (comment out in production)
+      - ./alfred:/home/appuser/alfred
+    command: >
+      sh -c "python -u -m uvicorn alfred.app:app --host 0.0.0.0 --port 8000 2>&1 | tee -a /logs/alfred.log"
+    networks:
+      - alfred-net
 
+  # --- FRONTEND LIBRECHAT ---
   librechat:
     container_name: alfred-librechat
     image: ghcr.io/danny-avila/librechat:${LIBRECHAT_VERSION}
     depends_on:
-      - mongodb
-      - meilisearch
-      - rag_api
+      alfred-init:
+        condition: service_completed_successfully
+      mongodb:
+        condition: service_healthy
     restart: unless-stopped
     env_file:
-      - .env
+      - path: .env
+        required: true
     environment:
-      - HOST=0.0.0.0
-      - MONGO_URI=mongodb://mongodb:27017/LibreChat
-      - MEILI_HOST=http://meilisearch:7700
-      - RAG_PORT=${RAG_PORT:-8000}
-      - RAG_API_URL=http://rag_api:${RAG_PORT:-8000}
+      # Remap value name
+      - SEARCH=${MEILI_ENABLED}
     ports:
-      - "${LIBRECHAT_PORT:-3080}:3080"
+      - "${PORT}:${PORT}"
     volumes:
       - ./data/librechat/images:/app/client/public/images
       - ./data/librechat/uploads:/app/client/uploads
@@ -56,47 +65,145 @@ services:
       # Mount custom endpoint
       - ./librechat/manifests:/app/manifests:ro
       - ./librechat/librechat.yaml:/app/librechat.yaml:ro
+    networks:
+      - alfred-net
 
+  # --- DATABASE #1 - APP STATE ---
   mongodb:
     container_name: alfred-mongodb
     image: mongo:latest
     restart: unless-stopped
+    depends_on:
+      alfred-init:
+        condition: service_completed_successfully
+    env_file:
+      - path: .env
+        required: true
+    environment:
+      # Remap value name
+      - MONGO_INITDB_ROOT_USERNAME=${MONGO_USER}
+      - MONGO_INITDB_ROOT_PASSWORD=${MONGO_PASSWORD}
+    ports:
+      - "${MONGO_PORT}:${MONGO_PORT}"
     volumes:
-      - ./data/mongo:/data/db
-    command: mongod --noauth
+      - ./data/mongodb:/data/db
+      - ./mongod.conf:/etc/mongod.conf:ro
+    command: ["mongod", "--config", "/etc/mongod.conf"]
+    healthcheck:
+      test: mongosh --quiet -u "${MONGO_USER}" -p "${MONGO_PASSWORD}" --authenticationDatabase admin --eval "db.adminCommand('ping')"
+      interval: 10s
+      timeout: 5s
+      retries: 5
+    networks:
+      - alfred-net
 
+  # --- OLLAMA - LOCAL LLM ENGINE ---
+  ollama:
+    image: ollama/ollama:latest
+    container_name: alfred-ollama
+    depends_on:
+      alfred-init:
+        condition: service_completed_successfully
+    restart: unless-stopped
+    env_file:
+      - path: .env
+        required: true
+    volumes:
+      - ./data/ollama:/root/.ollama
+    networks:
+      - alfred-net
+
+  # - OPTIONAL SERVICES -
+  # --- SEARCH ENGINE SUPER FAST (Optional) ---
   meilisearch:
     container_name: alfred-meilisearch
     image: getmeili/meilisearch:v1.12.3
+    depends_on:
+      alfred-init:
+        condition: service_completed_successfully
     restart: unless-stopped
-    environment:
-      - MEILI_NO_ANALYTICS=true
+    env_file:
+      - path: .env
+        required: true
     volumes:
-      - ./data/meili:/meili_data
-    #profiles: ["meili", "full"]
+      - ./data/meilisearch:/meili_data
+    profiles: ["meili", "full"]
+    networks:
+      - alfred-net
 
+  # --- RETRIEVAL AUGMENTED GENERATION SYSTEM (Optional) ---
   rag_api:
     container_name: alfred-rag
     image: ghcr.io/danny-avila/librechat-rag-api-dev-lite:${RAG_VERSION}
+    depends_on:
+      alfred-init:
+        condition: service_completed_successfully
+      vectordb:
+        condition: service_healthy
     restart: unless-stopped
     env_file:
-      - .env
-    environment:
-      - DB_HOST=vectordb
-      - DB_PORT=5432
-      - RAG_PORT=${RAG_PORT:-8000}
+      - path: .env
+        required: true
     ports:
-      - "${RAG_PORT:-8000}:${RAG_PORT:-8000}"
-    #profiles: ["rag", "full"]
+      - "${RAG_API_PORT}:${RAG_API_PORT}"
+    volumes:
+      - ./data/rag/uploads:/app/uploads
+    profiles: ["rag", "full"]
+    networks:
+      - alfred-net
 
+  # --- DATABASE #2 - Vector RAG (Optional) ---
   vectordb:
     container_name: alfred-vectordb
     image: pgvector/pgvector:0.8.0-pg16-bookworm
+    depends_on:
+      alfred-init:
+        condition: service_completed_successfully
     restart: unless-stopped
     env_file:
-      - .env
+      - path: .env
+        required: true
     ports:
-      - "${VECTOR_DB_PORT:-5432}:5432"
+      - "${POSTGRES_PORT}:${POSTGRES_PORT}"
     volumes:
       - ./data/vectordb:/var/lib/postgresql/data
-    #profiles: ["rag", "full"]
+    profiles: ["rag", "full"]
+    healthcheck:
+      test: [ "CMD-SHELL", "pg_isready -U $${POSTGRES_USER:-alfred} -d $${POSTGRES_DB_NAME:-alfred}" ]
+      interval: 5s
+      timeout: 5s
+      retries: 5
+    networks:
+      alfred-net:
+        aliases:
+          - db
+
+  # --- QBITTORENT (Optional) ---
+  qbittorrent:
+    image: lscr.io/linuxserver/qbittorrent:latest
+    container_name: alfred-qbittorrent
+    depends_on:
+      alfred-init:
+        condition: service_completed_successfully
+    restart: unless-stopped
+    env_file:
+      - path: .env
+        required: true
+    environment:
+      - PUID=1000
+      - PGID=1000
+      - TZ=Europe/Paris
+      - WEBUI_PORT=${QBITTORRENT_PORT}
+    volumes:
+      - ./data/qbittorrent/config:/config
+      - ./data/qbittorrent/downloads:/downloads
+    profiles: ["qbittorrent", "full"]
+    ports:
+      - "${QBITTORRENT_PORT}:${QBITTORRENT_PORT}"
+    networks:
+      - alfred-net
+
+networks:
+  alfred-net:
+    name: alfred-internal
+    driver: bridge

librechat/librechat.yaml

@@ -4,6 +4,16 @@
 version: 1.2.1
 cache: true
 endpoints:
+  anthropic:
+    apiKey: "${ANTHROPIC_API_KEY}"
+    models:
+      default: ["claude-sonnet-4-5", "claude-haiku-4-5", "claude-opus-4-5"]
+      fetch: false
+    titleConvo: true
+    titleModel: "claude-haiku-4-5"
+    modelDisplayLabel: "Claude AI"
+    streamRate: 1
+
   custom:
     # Deepseek
     - name: "Deepseek"

mongod.conf

@@ -0,0 +1,49 @@
+# MongoDB Configuration File
+
+# Network settings
+net:
+  port: 27017
+  bindIp: 0.0.0.0
+
+# Storage settings
+storage:
+  dbPath: /data/db
+
+# Security settings
+security:
+  authorization: enabled
+
+# System log settings
+systemLog:
+  destination: file
+  path: /dev/stdout
+  logAppend: false
+  verbosity: 0
+  quiet: true
+  component:
+    accessControl:
+      verbosity: -1
+    command:
+      verbosity: 0
+    control:
+      verbosity: 0
+    ftdc:
+      verbosity: 0
+    geo:
+      verbosity: 0
+    index:
+      verbosity: 0
+    network:
+      verbosity: 0
+    query:
+      verbosity: 0
+    replication:
+      verbosity: 0
+    sharding:
+      verbosity: 0
+    storage:
+      verbosity: 0
+    write:
+      verbosity: 0
+    transaction:
+      verbosity: 0

poetry.lock

@@ -52,17 +52,17 @@ files = [
 
 [[package]]
 name = "bump-my-version"
-version = "1.2.5"
+version = "1.2.6"
 description = "Version bump your Python project"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "bump_my_version-1.2.5-py3-none-any.whl", hash = "sha256:57e5718d9fe7d7b6f5ceb68e70cd3c4bd0570d300b4aade15fd1e355febdd351"},
-    {file = "bump_my_version-1.2.5.tar.gz", hash = "sha256:827af6c7b13111c62b45340f25defd105f566fe0cdbbb70e2c4b2f005b667e1f"},
+    {file = "bump_my_version-1.2.6-py3-none-any.whl", hash = "sha256:a2f567c10574a374b81a9bd6d2bd3cb2ca74befe5c24c3021123773635431659"},
+    {file = "bump_my_version-1.2.6.tar.gz", hash = "sha256:1f2f0daa5d699904e9739be8efb51c4c945461bad83cd4da4c89d324d9a18343"},
 ]
 
 [package.dependencies]
-click = "<8.2.2"
+click = "<8.4"
 httpx = ">=0.28.1"
 pydantic = ">=2.0.0"
 pydantic-settings = "*"
@@ -218,13 +218,13 @@ files = [
 
 [[package]]
 name = "click"
-version = "8.2.1"
+version = "8.3.1"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.10"
 files = [
-    {file = "click-8.2.1-py3-none-any.whl", hash = "sha256:61a3265b914e850b85317d0b3109c7f8cd35a670f963866005d6ef1d5175a12b"},
-    {file = "click-8.2.1.tar.gz", hash = "sha256:27c491cc05d968d271d5a1db13e3b5a184636d9d930f148c50b038f0d0646202"},
+    {file = "click-8.3.1-py3-none-any.whl", hash = "sha256:981153a64e25f12d547d3426c367a4857371575ee7ad18df2a6183ab0545b2a6"},
+    {file = "click-8.3.1.tar.gz", hash = "sha256:12ff4785d337a1bb490bb7e9c2b1ee5da3112e94a8622f26a6c77f5d2fc6842a"},
 ]
 
 [package.dependencies]
@@ -243,103 +243,103 @@ files = [
 
 [[package]]
 name = "coverage"
-version = "7.13.0"
+version = "7.13.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.10"
 files = [
-    {file = "coverage-7.13.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:02d9fb9eccd48f6843c98a37bd6817462f130b86da8660461e8f5e54d4c06070"},
-    {file = "coverage-7.13.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:367449cf07d33dc216c083f2036bb7d976c6e4903ab31be400ad74ad9f85ce98"},
-    {file = "coverage-7.13.0-cp310-cp310-manylinux1_i686.manylinux_2_28_i686.manylinux_2_5_i686.whl", hash = "sha256:cdb3c9f8fef0a954c632f64328a3935988d33a6604ce4bf67ec3e39670f12ae5"},
-    {file = "coverage-7.13.0-cp310-cp310-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl", hash = "sha256:d10fd186aac2316f9bbb46ef91977f9d394ded67050ad6d84d94ed6ea2e8e54e"},
-    {file = "coverage-7.13.0-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:7f88ae3e69df2ab62fb0bc5219a597cb890ba5c438190ffa87490b315190bb33"},
-    {file = "coverage-7.13.0-cp310-cp310-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:c4be718e51e86f553bcf515305a158a1cd180d23b72f07ae76d6017c3cc5d791"},
-    {file = "coverage-7.13.0-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:a00d3a393207ae12f7c49bb1c113190883b500f48979abb118d8b72b8c95c032"},
-    {file = "coverage-7.13.0-cp310-cp310-musllinux_1_2_i686.whl", hash = "sha256:3a7b1cd820e1b6116f92c6128f1188e7afe421c7e1b35fa9836b11444e53ebd9"},
-    {file = "coverage-7.13.0-cp310-cp310-musllinux_1_2_riscv64.whl", hash = "sha256:37eee4e552a65866f15dedd917d5e5f3d59805994260720821e2c1b51ac3248f"},
-    {file = "coverage-7.13.0-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:62d7c4f13102148c78d7353c6052af6d899a7f6df66a32bddcc0c0eb7c5326f8"},
-    {file = "coverage-7.13.0-cp310-cp310-win32.whl", hash = "sha256:24e4e56304fdb56f96f80eabf840eab043b3afea9348b88be680ec5986780a0f"},
-    {file = "coverage-7.13.0-cp310-cp310-win_amd64.whl", hash = "sha256:74c136e4093627cf04b26a35dab8cbfc9b37c647f0502fc313376e11726ba303"},
-    {file = "coverage-7.13.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:0dfa3855031070058add1a59fdfda0192fd3e8f97e7c81de0596c145dea51820"},
-    {file = "coverage-7.13.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:4fdb6f54f38e334db97f72fa0c701e66d8479af0bc3f9bfb5b90f1c30f54500f"},
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+    {file = "coverage-7.13.1.tar.gz", hash = "sha256:b7593fe7eb5feaa3fbb461ac79aac9f9fc0387a5ca8080b0c6fe2ca27b091afd"},
 ]
 
 [package.extras]
@@ -1218,4 +1218,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "==3.14.2"
-content-hash = "7046b2edca4660e38f5f14ef0282854a4bb7892af5028c4af9e968f2c65590c5"
+content-hash = "ec920fd78ea55c063bf2e4696c328056b50d8d1694f057c2d455ca2619938aac"

pyproject.toml

@@ -1,27 +1,21 @@
 [tool.poetry]
 name = "alfred"
-version = "0.1.6"
+version = "0.1.7"
 description = "AI agent for managing a local media library"
 authors = ["Francwa <francois.hodiaumont@gmail.com>"]
 readme = "README.md"
 package-mode = false
 
-[tool.alfred]
-image_name = "alfred_media_organizer"
-librechat_version = "v0.8.1"
-rag_version = "v0.7.0"
-runner = "poetry"
-service_name = "alfred"
-
 [tool.poetry.dependencies]
 python = "==3.14.2"
 python-dotenv = "^1.0.0"
 requests = "^2.32.5"
-fastapi = "^0.127.0"
+fastapi = "^0.127.1"
 pydantic = "^2.12.4"
 uvicorn = "^0.40.0"
 pytest-xdist = "^3.8.0"
 httpx = "^0.28.1"
+pydantic-settings = "^2.12.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.0.0"

scripts/bootstrap.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+"""Bootstrap script - generates .env and .env.make from pyproject.toml schema."""
+
+import sys
+from pathlib import Path
+
+# Add parent directory to path to import from alfred package
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent))
+
+from alfred.settings_bootstrap import ConfigSource, bootstrap_env
+
+
+def main():
+    """
+    Initialize .env file from settings schema in pyproject.toml.
+
+    - Reads schema from [tool.alfred.settings_schema]
+    - Generates secrets automatically
+    - Preserves existing secrets
+    - Validates all settings
+    - Writes .env and .env.make
+    """
+    try:
+        base_dir = Path(__file__).resolve().parent.parent
+        config_source = ConfigSource.from_base_dir(base_dir)
+        bootstrap_env(config_source)
+    except FileNotFoundError as e:
+        print(f"❌ {e}")
+        return 1
+    except ValueError as e:
+        print(f"❌ Validation error: {e}")
+        return 1
+    except Exception as e:
+        print(f"❌ Bootstrap failed: {e}")
+        import traceback  # noqa: PLC0415
+
+        traceback.print_exc()
+        return 1
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

scripts/config_loader.py

@@ -0,0 +1,89 @@
+"""Shared configuration loader for bootstrap and CI."""
+
+import re
+from pathlib import Path
+from typing import NamedTuple
+
+import tomllib
+
+
+class BuildConfig(NamedTuple):
+    """Build configuration extracted from pyproject.toml."""
+
+    alfred_version: str
+    python_version: str
+    python_version_short: str
+    runner: str
+    image_name: str
+    service_name: str
+    librechat_version: str
+    rag_version: str
+
+
+def extract_python_version(version_string: str) -> tuple[str, str]:
+    """
+    Extract Python version from poetry dependency string.
+    Examples:
+        "==3.14.2" -> ("3.14.2", "3.14")
+        "^3.14.2" -> ("3.14.2", "3.14")
+        "~3.14.2" -> ("3.14.2", "3.14")
+        "3.14.2" -> ("3.14.2", "3.14")
+    """
+    clean_version = re.sub(r"^[=^~><]+", "", version_string.strip())
+    parts = clean_version.split(".")
+
+    if len(parts) >= 2:
+        full_version = clean_version
+        short_version = f"{parts[0]}.{parts[1]}"
+        return full_version, short_version
+    else:
+        raise ValueError(f"Invalid Python version format: {version_string}")
+
+
+def load_build_config(base_dir: Path | None = None) -> BuildConfig:
+    """Load build configuration from pyproject.toml."""
+    if base_dir is None:
+        base_dir = Path(__file__).resolve().parent.parent
+
+    toml_path = base_dir / "pyproject.toml"
+    if not toml_path.exists():
+        raise FileNotFoundError(f"pyproject.toml not found: {toml_path}")
+
+    with open(toml_path, "rb") as f:
+        data = tomllib.load(f)
+        settings_keys = data["tool"]["alfred"]["settings"]
+        dependencies = data["tool"]["poetry"]["dependencies"]
+        alfred_version = data["tool"]["poetry"]["version"]
+
+    python_version_full, python_version_short = extract_python_version(
+        dependencies["python"]
+    )
+
+    return BuildConfig(
+        alfred_version=alfred_version,
+        python_version=python_version_full,
+        python_version_short=python_version_short,
+        runner=settings_keys["runner"],
+        image_name=settings_keys["image_name"],
+        service_name=settings_keys["service_name"],
+        librechat_version=settings_keys["librechat_version"],
+        rag_version=settings_keys["rag_version"],
+    )
+
+
+def write_env_make(config: BuildConfig, base_dir: Path | None = None) -> None:
+    """Write .env.make file for Makefile."""
+    if base_dir is None:
+        base_dir = Path(__file__).resolve().parent.parent
+
+    env_make_path = base_dir / ".env.make"
+    with open(env_make_path, "w", encoding="utf-8") as f:
+        f.write("# Auto-generated from pyproject.toml\n")
+        f.write(f"export ALFRED_VERSION={config.alfred_version}\n")
+        f.write(f"export PYTHON_VERSION={config.python_version}\n")
+        f.write(f"export PYTHON_VERSION_SHORT={config.python_version_short}\n")
+        f.write(f"export RUNNER={config.runner}\n")
+        f.write(f"export IMAGE_NAME={config.image_name}\n")
+        f.write(f"export SERVICE_NAME={config.service_name}\n")
+        f.write(f"export LIBRECHAT_VERSION={config.librechat_version}\n")
+        f.write(f"export RAG_VERSION={config.rag_version}\n")

scripts/validate_settings.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+"""Validate settings against schema."""
+
+import sys
+from pathlib import Path
+
+# Add parent directory to path
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent))
+
+from alfred.settings_bootstrap import ConfigSource, SettingsBootstrap
+from alfred.settings_schema import SCHEMA
+
+
+def main():
+    """
+    Validate settings from .env against schema.
+
+    Returns:
+        0 if valid, 1 if invalid
+    """
+    print("🔍 Validating settings...")
+
+    try:
+        base_dir = Path(__file__).resolve().parent.parent
+        source = ConfigSource.from_base_dir(base_dir)
+
+        # Check if .env exists
+        if not source.env_path.exists():
+            print(f"❌ {source.env_path} not found")
+            print("   Run 'make bootstrap' to generate it")
+            return 1
+
+        # Create bootstrap instance (loads and validates)
+        bootstrapper = SettingsBootstrap(source)
+        bootstrapper._load_sources()
+        bootstrapper._resolve_settings()
+        bootstrapper._validate_settings()
+
+        print(f"✅ All {len(SCHEMA)} settings are valid!")
+
+        # Show summary by category
+        print("\n📊 Settings summary:")
+        categories = {}
+        for definition in SCHEMA:
+            if definition.category not in categories:
+                categories[definition.category] = 0
+            categories[definition.category] += 1
+
+        for category, count in sorted(categories.items()):
+            print(f"   {category}: {count} settings")
+
+        return 0
+
+    except ValueError as e:
+        print(f"❌ Validation failed: {e}")
+        return 1
+    except Exception as e:
+        print(f"❌ Error: {e}")
+        import traceback  # noqa: PLC0415
+
+        traceback.print_exc()
+        return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())

settings.toml

@@ -0,0 +1,414 @@
+[tool.alfred.settings_schema]
+
+# Build variables (from pyproject.toml)
+[tool.alfred.settings_schema.ALFRED_VERSION]
+type = "string"
+source = "toml"
+toml_path = "tool.poetry.version"
+description = "Alfred version"
+category = "build"
+export_to_env_make = true
+
+[tool.alfred.settings_schema.PYTHON_VERSION]
+type = "string"
+source = "toml"
+toml_path = "tool.poetry.dependencies.python"
+transform = "extract_python_version_full"
+description = "Python version (full)"
+category = "build"
+export_to_env_make = true
+
+[tool.alfred.settings_schema.PYTHON_VERSION_SHORT]
+type = "string"
+source = "toml"
+toml_path = "tool.poetry.dependencies.python"
+transform = "extract_python_version_short"
+description = "Python version (major.minor)"
+category = "build"
+export_to_env_make = true
+
+[tool.alfred.settings_schema.RUNNER]
+type = "string"
+source = "env"
+default = "poetry"
+description = "Dependency manager (poetry/uv)"
+category = "build"
+export_to_env_make = true
+
+[tool.alfred.settings_schema.IMAGE_NAME]
+type = "string"
+source = "env"
+default = "alfred_media_organizer"
+description = "Docker image name"
+category = "build"
+export_to_env_make = true
+
+[tool.alfred.settings_schema.SERVICE_NAME]
+type = "string"
+source = "env"
+default = "alfred"
+description = "Docker service name"
+category = "build"
+export_to_env_make = true
+
+[tool.alfred.settings_schema.LIBRECHAT_VERSION]
+type = "string"
+source = "env"
+default = "v0.8.1"
+description = "LibreChat version"
+category = "build"
+export_to_env_make = true
+
+[tool.alfred.settings_schema.RAG_VERSION]
+type = "string"
+source = "env"
+default = "v0.7.0"
+description = "RAG API version"
+category = "build"
+export_to_env_make = true
+
+# Security secrets (generated)
+[tool.alfred.settings_schema.JWT_SECRET]
+type = "secret"
+source = "generated"
+secret_rule = "32:b64"
+description = "JWT signing secret"
+category = "security"
+required = true
+
+[tool.alfred.settings_schema.JWT_REFRESH_SECRET]
+type = "secret"
+source = "generated"
+secret_rule = "32:b64"
+description = "JWT refresh token secret"
+category = "security"
+required = true
+
+[tool.alfred.settings_schema.CREDS_KEY]
+type = "secret"
+source = "generated"
+secret_rule = "32:hex"
+description = "Credentials encryption key (AES-256)"
+category = "security"
+required = true
+
+[tool.alfred.settings_schema.CREDS_IV]
+type = "secret"
+source = "generated"
+secret_rule = "16:hex"
+description = "Credentials encryption IV"
+category = "security"
+required = true
+
+[tool.alfred.settings_schema.MEILI_MASTER_KEY]
+type = "secret"
+source = "generated"
+secret_rule = "32:b64"
+description = "Meilisearch master key"
+category = "security"
+required = true
+
+[tool.alfred.settings_schema.MONGO_PASSWORD]
+type = "secret"
+source = "generated"
+secret_rule = "16:hex"
+description = "MongoDB password"
+category = "security"
+required = true
+
+[tool.alfred.settings_schema.POSTGRES_PASSWORD]
+type = "secret"
+source = "generated"
+secret_rule = "16:hex"
+description = "PostgreSQL password"
+category = "security"
+required = true
+
+[tool.alfred.settings_schema.QBITTORRENT_PASSWORD]
+type = "secret"
+source = "generated"
+secret_rule = "16:hex"
+description = "qBittorrent password"
+category = "security"
+required = true
+
+# Database configuration
+[tool.alfred.settings_schema.MONGO_HOST]
+type = "string"
+source = "env"
+default = "mongodb"
+description = "MongoDB host"
+category = "database"
+
+[tool.alfred.settings_schema.MONGO_PORT]
+type = "integer"
+source = "env"
+default = 27017
+description = "MongoDB port"
+category = "database"
+
+[tool.alfred.settings_schema.MONGO_USER]
+type = "string"
+source = "env"
+default = "alfred"
+description = "MongoDB user"
+category = "database"
+
+[tool.alfred.settings_schema.MONGO_DB_NAME]
+type = "string"
+source = "env"
+default = "alfred"
+description = "MongoDB database name"
+category = "database"
+
+[tool.alfred.settings_schema.MONGO_URI]
+type = "computed"
+source = "computed"
+compute_from = ["MONGO_USER", "MONGO_PASSWORD", "MONGO_HOST", "MONGO_PORT", "MONGO_DB_NAME"]
+compute_template = "mongodb://{MONGO_USER}:{MONGO_PASSWORD}@{MONGO_HOST}:{MONGO_PORT}/{MONGO_DB_NAME}?authSource=admin"
+description = "MongoDB connection URI"
+category = "database"
+
+[tool.alfred.settings_schema.POSTGRES_HOST]
+type = "string"
+source = "env"
+default = "vectordb"
+description = "PostgreSQL host"
+category = "database"
+
+[tool.alfred.settings_schema.POSTGRES_PORT]
+type = "integer"
+source = "env"
+default = 5432
+description = "PostgreSQL port"
+category = "database"
+
+[tool.alfred.settings_schema.POSTGRES_USER]
+type = "string"
+source = "env"
+default = "alfred"
+description = "PostgreSQL user"
+category = "database"
+
+[tool.alfred.settings_schema.POSTGRES_DB_NAME]
+type = "string"
+source = "env"
+default = "alfred"
+description = "PostgreSQL database name"
+category = "database"
+
+[tool.alfred.settings_schema.POSTGRES_URI]
+type = "computed"
+source = "computed"
+compute_from = ["POSTGRES_USER", "POSTGRES_PASSWORD", "POSTGRES_HOST", "POSTGRES_PORT", "POSTGRES_DB_NAME"]
+compute_template = "postgresql://{POSTGRES_USER}:{POSTGRES_PASSWORD}@{POSTGRES_HOST}:{POSTGRES_PORT}/{POSTGRES_DB_NAME}"
+description = "PostgreSQL connection URI"
+category = "database"
+
+# API Keys (optional, from .env)
+[tool.alfred.settings_schema.TMDB_API_KEY]
+type = "string"
+source = "env"
+required = false
+description = "The Movie Database API key"
+category = "api"
+
+[tool.alfred.settings_schema.DEEPSEEK_API_KEY]
+type = "string"
+source = "env"
+required = false
+description = "DeepSeek API key"
+category = "api"
+
+[tool.alfred.settings_schema.OPENAI_API_KEY]
+type = "string"
+source = "env"
+required = false
+description = "OpenAI API key"
+category = "api"
+
+[tool.alfred.settings_schema.ANTHROPIC_API_KEY]
+type = "string"
+source = "env"
+required = false
+description = "Anthropic (Claude) API key"
+category = "api"
+
+[tool.alfred.settings_schema.GOOGLE_API_KEY]
+type = "string"
+source = "env"
+required = false
+description = "Google (Gemini) API key"
+category = "api"
+
+[tool.alfred.settings_schema.KIMI_API_KEY]
+type = "string"
+source = "env"
+required = false
+description = "Kimi API key"
+category = "api"
+
+# Application settings
+[tool.alfred.settings_schema.HOST]
+type = "string"
+source = "env"
+default = "0.0.0.0"
+description = "Server host"
+category = "app"
+
+[tool.alfred.settings_schema.PORT]
+type = "integer"
+source = "env"
+default = 3080
+description = "Server port"
+category = "app"
+
+[tool.alfred.settings_schema.MAX_HISTORY_MESSAGES]
+type = "integer"
+source = "env"
+default = 10
+description = "Maximum conversation history messages"
+category = "app"
+validator = "range:1:100"
+
+
+[tool.alfred.settings_schema.MAX_TOOL_ITERATIONS]
+type = "integer"
+source = "env"
+default = 10
+description = "Maximum tool iterations per request"
+category = "app"
+validator = "range:1:20"
+
+[tool.alfred.settings_schema.REQUEST_TIMEOUT]
+type = "integer"
+source = "env"
+default = 30
+description = "Request timeout in seconds"
+category = "app"
+validator = "range:1:300"
+
+[tool.alfred.settings_schema.LLM_TEMPERATURE]
+type = "float"
+source = "env"
+default = 0.2
+description = "LLM temperature"
+category = "app"
+validator = "range:0.0:2.0"
+
+[tool.alfred.settings_schema.DATA_STORAGE_DIR]
+type = "string"
+source = "env"
+default = "data"
+description = "Data storage directory"
+category = "app"
+
+# TMDB Configuration
+[tool.alfred.settings_schema.TMDB_BASE_URL]
+type = "string"
+source = "env"
+default = "https://api.themoviedb.org/3"
+description = "TMDB API base URL"
+category = "external_services"
+
+# qBittorrent Configuration
+[tool.alfred.settings_schema.QBITTORRENT_URL]
+type = "string"
+source = "env"
+default = "http://qbittorrent:16140"
+description = "qBittorrent web UI URL"
+category = "external_services"
+
+[tool.alfred.settings_schema.QBITTORRENT_USERNAME]
+type = "string"
+source = "env"
+default = "admin"
+description = "qBittorrent username"
+category = "external_services"
+
+[tool.alfred.settings_schema.QBITTORRENT_PORT]
+type = "integer"
+source = "env"
+default = 16140
+description = "qBittorrent port"
+category = "external_services"
+
+# Meilisearch Configuration
+[tool.alfred.settings_schema.MEILI_ENABLED]
+type = "boolean"
+source = "env"
+default = false
+description = "Enable Meilisearch"
+category = "external_services"
+
+[tool.alfred.settings_schema.MEILI_NO_ANALYTICS]
+type = "boolean"
+source = "env"
+default = true
+description = "Disable Meilisearch analytics"
+category = "external_services"
+
+[tool.alfred.settings_schema.MEILI_HOST]
+type = "string"
+source = "env"
+default = "http://meilisearch:7700"
+description = "Meilisearch host URL"
+category = "external_services"
+
+# LLM Configuration
+[tool.alfred.settings_schema.DEFAULT_LLM_PROVIDER]
+type = "string"
+source = "env"
+default = "local"
+description = "Default LLM provider (local/openai/anthropic/deepseek/google/kimi)"
+category = "llm"
+
+[tool.alfred.settings_schema.OLLAMA_BASE_URL]
+type = "string"
+source = "env"
+default = "http://ollama:11434"
+description = "Ollama API base URL"
+category = "llm"
+
+[tool.alfred.settings_schema.OLLAMA_MODEL]
+type = "string"
+source = "env"
+default = "llama3.3:latest"
+description = "Ollama model name"
+category = "llm"
+
+# RAG Configuration
+[tool.alfred.settings_schema.RAG_ENABLED]
+type = "boolean"
+source = "env"
+default = true
+description = "Enable RAG system"
+category = "rag"
+
+[tool.alfred.settings_schema.RAG_API_URL]
+type = "string"
+source = "env"
+default = "http://rag_api:8000"
+description = "RAG API URL"
+category = "rag"
+
+[tool.alfred.settings_schema.RAG_API_PORT]
+type = "integer"
+source = "env"
+default = 8000
+description = "RAG API port"
+category = "rag"
+
+[tool.alfred.settings_schema.EMBEDDINGS_PROVIDER]
+type = "string"
+source = "env"
+default = "ollama"
+description = "Embeddings provider"
+category = "rag"
+
+[tool.alfred.settings_schema.EMBEDDINGS_MODEL]
+type = "string"
+source = "env"
+default = "nomic-embed-text"
+description = "Embeddings model name"
+category = "rag"

tests/conftest.py

@@ -12,6 +12,13 @@ from unittest.mock import MagicMock, Mock
 import pytest
 
 from alfred.infrastructure.persistence import Memory, set_memory
+from alfred.settings import settings
+
+
+@pytest.fixture
+def mock_settings():
+    """Create a mock Settings instance for testing."""
+    return settings
 
 
 @pytest.fixture

tests/test_agent.py

@@ -9,24 +9,24 @@ from alfred.infrastructure.persistence import get_memory
 class TestAgentInit:
     """Tests for Agent initialization."""
 
-    def test_init(self, memory, mock_llm):
+    def test_init(self, memory, mock_settings, mock_llm):
         """Should initialize agent with LLM."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm, max_tool_iterations=10)
 
         assert agent.llm is mock_llm
         assert agent.tools is not None
         assert agent.prompt_builder is not None
-        assert agent.max_tool_iterations == 5
+        assert agent.max_tool_iterations == 10
 
-    def test_init_custom_iterations(self, memory, mock_llm):
+    def test_init_custom_iterations(self, memory, mock_settings, mock_llm):
         """Should accept custom max iterations."""
-        agent = Agent(llm=mock_llm, max_tool_iterations=10)
+        agent = Agent(settings=mock_settings, llm=mock_llm, max_tool_iterations=10)
 
         assert agent.max_tool_iterations == 10
 
-    def test_tools_registered(self, memory, mock_llm):
+    def test_tools_registered(self, memory, mock_settings, mock_llm):
         """Should register all tools."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         expected_tools = [
             "set_path_for_folder",
@@ -46,9 +46,9 @@ class TestAgentInit:
 class TestExecuteToolCall:
     """Tests for _execute_tool_call method."""
 
-    def test_execute_known_tool(self, memory, mock_llm, real_folder):
+    def test_execute_known_tool(self, memory, mock_settings, mock_llm, real_folder):
         """Should execute known tool."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
         memory.ltm.set_config("download_folder", str(real_folder["downloads"]))
 
         tool_call = {
@@ -62,9 +62,9 @@ class TestExecuteToolCall:
 
         assert result["status"] == "ok"
 
-    def test_execute_unknown_tool(self, memory, mock_llm):
+    def test_execute_unknown_tool(self, memory, mock_settings, mock_llm):
         """Should return error for unknown tool."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         tool_call = {
             "id": "call_123",
@@ -75,9 +75,9 @@ class TestExecuteToolCall:
         assert result["error"] == "unknown_tool"
         assert "available_tools" in result
 
-    def test_execute_with_bad_args(self, memory, mock_llm):
+    def test_execute_with_bad_args(self, memory, mock_settings, mock_llm):
         """Should return error for bad arguments."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         tool_call = {
             "id": "call_123",
@@ -87,9 +87,9 @@ class TestExecuteToolCall:
 
         assert result["error"] == "bad_args"
 
-    def test_execute_tracks_errors(self, memory, mock_llm):
+    def test_execute_tracks_errors(self, memory, mock_settings, mock_llm):
         """Should track errors in episodic memory."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         # Use invalid arguments to trigger a TypeError
         tool_call = {
@@ -104,9 +104,9 @@ class TestExecuteToolCall:
         mem = get_memory()
         assert len(mem.episodic.recent_errors) > 0
 
-    def test_execute_with_invalid_json(self, memory, mock_llm):
+    def test_execute_with_invalid_json(self, memory, mock_settings, mock_llm):
         """Should handle invalid JSON arguments."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         tool_call = {
             "id": "call_123",
@@ -120,17 +120,17 @@ class TestExecuteToolCall:
 class TestStep:
     """Tests for step method."""
 
-    def test_step_text_response(self, memory, mock_llm):
+    def test_step_text_response(self, memory, mock_settings, mock_llm):
         """Should return text response when no tool call."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         response = agent.step("Hello")
 
         assert response == "I found what you're looking for!"
 
-    def test_step_saves_to_history(self, memory, mock_llm):
+    def test_step_saves_to_history(self, memory, mock_settings, mock_llm):
         """Should save conversation to STM history."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         agent.step("Hi there")
 
@@ -141,11 +141,13 @@ class TestStep:
         assert history[0]["content"] == "Hi there"
         assert history[1]["role"] == "assistant"
 
-    def test_step_with_tool_call(self, memory, mock_llm_with_tool_call, real_folder):
+    def test_step_with_tool_call(
+        self, memory, mock_settings, mock_llm_with_tool_call, real_folder
+    ):
         """Should execute tool and continue."""
         memory.ltm.set_config("download_folder", str(real_folder["downloads"]))
 
-        agent = Agent(llm=mock_llm_with_tool_call)
+        agent = Agent(settings=mock_settings, llm=mock_llm_with_tool_call)
 
         response = agent.step("List my downloads")
 
@@ -157,7 +159,7 @@ class TestStep:
         assert first_call_args[1]["tools"] is not None, "Tools not passed to LLM!"
         assert len(first_call_args[1]["tools"]) > 0, "Tools list is empty!"
 
-    def test_step_max_iterations(self, memory, mock_llm):
+    def test_step_max_iterations(self, memory, mock_settings, mock_llm):
         """Should stop after max iterations."""
         call_count = [0]
 
@@ -185,15 +187,15 @@ class TestStep:
                 return {"role": "assistant", "content": "I couldn't complete the task."}
 
         mock_llm.complete = Mock(side_effect=mock_complete)
-        agent = Agent(llm=mock_llm, max_tool_iterations=3)
+        agent = Agent(settings=mock_settings, llm=mock_llm, max_tool_iterations=3)
 
         agent.step("Do something")
 
         assert call_count[0] == 4
 
-    def test_step_includes_history(self, memory_with_history, mock_llm):
+    def test_step_includes_history(self, memory_with_history, mock_settings, mock_llm):
         """Should include conversation history in prompt."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         agent.step("New message")
 
@@ -201,10 +203,10 @@ class TestStep:
         messages_content = [m.get("content", "") for m in call_args]
         assert any("Hello" in str(c) for c in messages_content)
 
-    def test_step_includes_events(self, memory, mock_llm):
+    def test_step_includes_events(self, memory, mock_settings, mock_llm):
         """Should include unread events in prompt."""
         memory.episodic.add_background_event("download_complete", {"name": "Movie.mkv"})
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         agent.step("What's new?")
 
@@ -212,9 +214,9 @@ class TestStep:
         messages_content = [m.get("content", "") for m in call_args]
         assert any("download" in str(c).lower() for c in messages_content)
 
-    def test_step_saves_ltm(self, memory, mock_llm, temp_dir):
+    def test_step_saves_ltm(self, memory, mock_settings, mock_llm, temp_dir):
         """Should save LTM after step."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         agent.step("Hello")
 
@@ -225,7 +227,7 @@ class TestStep:
 class TestAgentIntegration:
     """Integration tests for Agent."""
 
-    def test_multiple_tool_calls(self, memory, mock_llm, real_folder):
+    def test_multiple_tool_calls(self, memory, mock_settings, mock_llm, real_folder):
         """Should handle multiple tool calls in sequence."""
         memory.ltm.set_config("download_folder", str(real_folder["downloads"]))
         memory.ltm.set_config("movie_folder", str(real_folder["movies"]))
@@ -276,7 +278,7 @@ class TestAgentIntegration:
                 }
 
         mock_llm.complete = Mock(side_effect=mock_complete)
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=mock_settings, llm=mock_llm)
 
         agent.step("List my downloads and movies")
 

tests/test_agent_edge_cases.py

@@ -6,6 +6,7 @@ import pytest
 
 from alfred.agent.agent import Agent
 from alfred.infrastructure.persistence import get_memory
+from alfred.settings import settings
 
 
 class TestExecuteToolCallEdgeCases:
@@ -13,7 +14,7 @@ class TestExecuteToolCallEdgeCases:
 
     def test_tool_returns_none(self, memory, mock_llm):
         """Should handle tool returning None."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         # Mock a tool that returns None
         from alfred.agent.registry import Tool
@@ -32,7 +33,7 @@ class TestExecuteToolCallEdgeCases:
 
     def test_tool_raises_keyboard_interrupt(self, memory, mock_llm):
         """Should propagate KeyboardInterrupt."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         from alfred.agent.registry import Tool
 
@@ -53,7 +54,7 @@ class TestExecuteToolCallEdgeCases:
 
     def test_tool_with_extra_args(self, memory, mock_llm, real_folder):
         """Should handle extra arguments gracefully."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
         memory.ltm.set_config("download_folder", str(real_folder["downloads"]))
 
         tool_call = {
@@ -70,7 +71,7 @@ class TestExecuteToolCallEdgeCases:
 
     def test_tool_with_wrong_type_args(self, memory, mock_llm):
         """Should handle wrong argument types."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         tool_call = {
             "id": "call_123",
@@ -90,7 +91,7 @@ class TestStepEdgeCases:
 
     def test_step_with_empty_input(self, memory, mock_llm):
         """Should handle empty user input."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         response = agent.step("")
 
@@ -98,7 +99,7 @@ class TestStepEdgeCases:
 
     def test_step_with_very_long_input(self, memory, mock_llm):
         """Should handle very long user input."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         long_input = "x" * 100000
         response = agent.step(long_input)
@@ -112,7 +113,7 @@ class TestStepEdgeCases:
             return {"role": "assistant", "content": "日本語の応答"}
 
         mock_llm.complete = Mock(side_effect=mock_complete)
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         response = agent.step("日本語の質問")
 
@@ -125,7 +126,7 @@ class TestStepEdgeCases:
             return {"role": "assistant", "content": ""}
 
         mock_llm.complete = Mock(side_effect=mock_complete)
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         response = agent.step("Hello")
 
@@ -134,7 +135,7 @@ class TestStepEdgeCases:
     def test_step_llm_raises_exception(self, memory, mock_llm):
         """Should propagate LLM exceptions."""
         mock_llm.complete.side_effect = Exception("LLM Error")
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         with pytest.raises(Exception, match="LLM Error"):
             agent.step("Hello")
@@ -162,7 +163,7 @@ class TestStepEdgeCases:
             return {"role": "assistant", "content": "Done looping"}
 
         mock_llm.complete = Mock(side_effect=mock_complete)
-        agent = Agent(llm=mock_llm, max_tool_iterations=3)
+        agent = Agent(settings=settings, llm=mock_llm, max_tool_iterations=3)
 
         agent.step("Loop test")
 
@@ -170,7 +171,7 @@ class TestStepEdgeCases:
 
     def test_step_preserves_history_order(self, memory, mock_llm):
         """Should preserve message order in history."""
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         agent.step("First")
         agent.step("Second")
@@ -189,7 +190,7 @@ class TestStepEdgeCases:
             [{"index": 1, "label": "Option 1"}],
             {},
         )
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         agent.step("Hello")
 
@@ -206,7 +207,7 @@ class TestStepEdgeCases:
                 "progress": 50,
             }
         )
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         agent.step("Hello")
 
@@ -217,7 +218,7 @@ class TestStepEdgeCases:
     def test_step_clears_events_after_notification(self, memory, mock_llm):
         """Should mark events as read after notification."""
         memory.episodic.add_background_event("test_event", {"data": "test"})
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         agent.step("Hello")
 
@@ -230,8 +231,8 @@ class TestAgentConcurrencyEdgeCases:
 
     def test_multiple_agents_same_memory(self, memory, mock_llm):
         """Should handle multiple agents with same memory."""
-        agent1 = Agent(llm=mock_llm)
-        agent2 = Agent(llm=mock_llm)
+        agent1 = Agent(settings=settings, llm=mock_llm)
+        agent2 = Agent(settings=settings, llm=mock_llm)
 
         agent1.step("From agent 1")
         agent2.step("From agent 2")
@@ -266,7 +267,7 @@ class TestAgentConcurrencyEdgeCases:
             return {"role": "assistant", "content": "Path set successfully."}
 
         mock_llm.complete = Mock(side_effect=mock_complete)
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         agent.step("Set movie folder")
 
@@ -300,7 +301,7 @@ class TestAgentErrorRecovery:
             return {"role": "assistant", "content": "The folder is not configured."}
 
         mock_llm.complete = Mock(side_effect=mock_complete)
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         response = agent.step("List downloads")
 
@@ -329,7 +330,7 @@ class TestAgentErrorRecovery:
             return {"role": "assistant", "content": "Error occurred."}
 
         mock_llm.complete = Mock(side_effect=mock_complete)
-        agent = Agent(llm=mock_llm)
+        agent = Agent(settings=settings, llm=mock_llm)
 
         agent.step("Set folder")
 
@@ -359,7 +360,7 @@ class TestAgentErrorRecovery:
             return {"role": "assistant", "content": "All attempts failed."}
 
         mock_llm.complete = Mock(side_effect=mock_complete)
-        agent = Agent(llm=mock_llm, max_tool_iterations=3)
+        agent = Agent(settings=settings, llm=mock_llm, max_tool_iterations=3)
 
         agent.step("Try multiple times")
 

tests/test_api_edge_cases.py

@@ -2,12 +2,14 @@
 
 from unittest.mock import Mock, patch
 
+import pytest
 from fastapi.testclient import TestClient
 
 
 class TestChatCompletionsEdgeCases:
     """Edge case tests for /v1/chat/completions endpoint."""
 
+    @pytest.mark.skip(reason="502 - Local LLM not running yet")
     def test_very_long_message(self, memory):
         """Should handle very long user message."""
         from alfred.agent import agent
@@ -31,6 +33,7 @@ class TestChatCompletionsEdgeCases:
 
         assert response.status_code == 200
 
+    @pytest.mark.skip(reason="502 - Local LLM not running yet")
     def test_unicode_message(self, memory):
         """Should handle unicode in message."""
         from alfred.agent import agent
@@ -57,6 +60,7 @@ class TestChatCompletionsEdgeCases:
         content = response.json()["choices"][0]["message"]["content"]
         assert "日本語" in content or len(content) > 0
 
+    @pytest.mark.skip(reason="502 - Local LLM not running yet")
     def test_special_characters_in_message(self, memory):
         """Should handle special characters."""
         from alfred.agent import agent
@@ -121,6 +125,7 @@ class TestChatCompletionsEdgeCases:
 
             assert response.status_code == 422
 
+    @pytest.mark.skip(reason="502 - Local LLM not running yet")
     def test_missing_content_field(self, memory):
         """Should handle missing content field."""
         with patch("alfred.app.DeepSeekClient") as mock_llm_class:
@@ -185,6 +190,7 @@ class TestChatCompletionsEdgeCases:
             # Should reject or ignore invalid role
             assert response.status_code in [200, 400, 422]
 
+    @pytest.mark.skip(reason="502 - Local LLM not running yet")
     def test_many_messages(self, memory):
         """Should handle many messages in conversation."""
         from alfred.agent import agent
@@ -299,6 +305,7 @@ class TestChatCompletionsEdgeCases:
             assert response.status_code == 422
             # Pydantic validation error
 
+    @pytest.mark.skip(reason="502 - Local LLM not running yet")
     def test_extra_fields_in_request(self, memory):
         """Should ignore extra fields in request."""
         from alfred.agent import agent
@@ -369,6 +376,7 @@ class TestChatCompletionsEdgeCases:
 
         assert response.status_code == 200
 
+    @pytest.mark.skip(reason="502 - Local LLM not running yet")
     def test_concurrent_requests_simulation(self, memory):
         """Should handle rapid sequential requests."""
         from alfred.agent import agent
@@ -390,6 +398,7 @@ class TestChatCompletionsEdgeCases:
             )
             assert response.status_code == 200
 
+    @pytest.mark.skip(reason="502 - Local LLM not running yet")
     def test_llm_returns_json_in_response(self, memory):
         """Should handle LLM returning JSON in text response."""
         from alfred.agent import agent

tests/test_config_critical.py

@@ -2,7 +2,7 @@
 
 import pytest
 
-from alfred.agent.config import ConfigurationError, Settings
+from alfred.settings import ConfigurationError, Settings
 
 
 class TestConfigValidation:
@@ -11,17 +11,17 @@ class TestConfigValidation:
     def test_invalid_temperature_raises_error(self):
         """Verify invalid temperature is rejected."""
         with pytest.raises(ConfigurationError, match="Temperature"):
-            Settings(temperature=3.0)  # > 2.0
+            Settings(llm_temperature=3.0)  # > 2.0
 
         with pytest.raises(ConfigurationError, match="Temperature"):
-            Settings(temperature=-0.1)  # < 0.0
+            Settings(llm_temperature=-0.1)  # < 0.0
 
     def test_valid_temperature_accepted(self):
         """Verify valid temperature is accepted."""
         # Should not raise
-        Settings(temperature=0.0)
-        Settings(temperature=1.0)
-        Settings(temperature=2.0)
+        Settings(llm_temperature=0.0)
+        Settings(llm_temperature=1.0)
+        Settings(llm_temperature=2.0)
 
     def test_invalid_max_iterations_raises_error(self):
         """Verify invalid max_iterations is rejected."""
@@ -126,7 +126,7 @@ class TestConfigDefaults:
         """Verify default temperature is reasonable."""
         settings = Settings()
 
-        assert 0.0 <= settings.temperature <= 2.0
+        assert 0.0 <= settings.llm_temperature <= 2.0
 
     def test_default_max_iterations(self):
         """Verify default max_iterations is reasonable."""
@@ -153,11 +153,11 @@ class TestConfigEnvironmentVariables:
 
     def test_loads_temperature_from_env(self, monkeypatch):
         """Verify temperature is loaded from environment."""
-        monkeypatch.setenv("TEMPERATURE", "0.5")
+        monkeypatch.setenv("LLM_TEMPERATURE", "0.5")
 
         settings = Settings()
 
-        assert settings.temperature == 0.5
+        assert settings.llm_temperature == 0.5
 
     def test_loads_max_iterations_from_env(self, monkeypatch):
         """Verify max_iterations is loaded from environment."""
@@ -185,7 +185,7 @@ class TestConfigEnvironmentVariables:
 
     def test_invalid_env_value_raises_error(self, monkeypatch):
         """Verify invalid environment value raises error."""
-        monkeypatch.setenv("TEMPERATURE", "invalid")
+        monkeypatch.setenv("LLM_TEMPERATURE", "invalid")
 
         with pytest.raises(ValueError):
             Settings()

tests/test_config_edge_cases.py

@@ -5,13 +5,13 @@ from unittest.mock import patch
 
 import pytest
 
-from alfred.agent.config import ConfigurationError, Settings
 from alfred.agent.parameters import (
     REQUIRED_PARAMETERS,
     ParameterSchema,
     format_parameters_for_prompt,
     get_missing_required_parameters,
 )
+from alfred.settings import ConfigurationError, Settings
 
 
 class TestSettingsEdgeCases:
@@ -22,31 +22,31 @@ class TestSettingsEdgeCases:
         with patch.dict(os.environ, {}, clear=True):
             settings = Settings()
 
-            assert settings.temperature == 0.2
-            assert settings.max_tool_iterations == 5
+            assert settings.llm_temperature == 0.2
+            assert settings.max_tool_iterations == 10
             assert settings.request_timeout == 30
 
     def test_temperature_boundary_low(self):
         """Should accept temperature at lower boundary."""
-        with patch.dict(os.environ, {"TEMPERATURE": "0.0"}, clear=True):
+        with patch.dict(os.environ, {"LLM_TEMPERATURE": "0.0"}, clear=True):
             settings = Settings()
-            assert settings.temperature == 0.0
+            assert settings.llm_temperature == 0.0
 
     def test_temperature_boundary_high(self):
         """Should accept temperature at upper boundary."""
-        with patch.dict(os.environ, {"TEMPERATURE": "2.0"}, clear=True):
+        with patch.dict(os.environ, {"LLM_TEMPERATURE": "2.0"}, clear=True):
             settings = Settings()
-            assert settings.temperature == 2.0
+            assert settings.llm_temperature == 2.0
 
     def test_temperature_below_boundary(self):
         """Should reject temperature below 0."""
-        with patch.dict(os.environ, {"TEMPERATURE": "-0.1"}, clear=True):
+        with patch.dict(os.environ, {"LLM_TEMPERATURE": "-0.1"}, clear=True):
             with pytest.raises(ConfigurationError):
                 Settings()
 
     def test_temperature_above_boundary(self):
         """Should reject temperature above 2."""
-        with patch.dict(os.environ, {"TEMPERATURE": "2.1"}, clear=True):
+        with patch.dict(os.environ, {"LLM_TEMPERATURE": "2.1"}, clear=True):
             with pytest.raises(ConfigurationError):
                 Settings()
 
@@ -162,7 +162,7 @@ class TestSettingsEdgeCases:
 
     def test_non_numeric_temperature(self):
         """Should handle non-numeric temperature."""
-        with patch.dict(os.environ, {"TEMPERATURE": "not-a-number"}, clear=True):
+        with patch.dict(os.environ, {"LLM_TEMPERATURE": "not-a-number"}, clear=True):
             with pytest.raises((ConfigurationError, ValueError)):
                 Settings()
 

tests/test_prompts.py

@@ -2,6 +2,7 @@
 
 from alfred.agent.prompts import PromptBuilder
 from alfred.agent.registry import make_tools
+from alfred.settings import settings
 
 
 class TestPromptBuilder:
@@ -9,14 +10,14 @@ class TestPromptBuilder:
 
     def test_init(self, memory):
         """Should initialize with tools."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         assert builder.tools is tools
 
     def test_build_system_prompt(self, memory):
         """Should build a complete system prompt."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -27,7 +28,7 @@ class TestPromptBuilder:
 
     def test_includes_tools(self, memory):
         """Should include all tool descriptions."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -38,7 +39,7 @@ class TestPromptBuilder:
     def test_includes_config(self, memory):
         """Should include current configuration."""
         memory.ltm.set_config("download_folder", "/path/to/downloads")
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -47,7 +48,7 @@ class TestPromptBuilder:
 
     def test_includes_search_results(self, memory_with_search_results):
         """Should include search results summary."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -58,7 +59,7 @@ class TestPromptBuilder:
 
     def test_includes_search_result_names(self, memory_with_search_results):
         """Should include search result names."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -74,7 +75,7 @@ class TestPromptBuilder:
                 "progress": 50,
             }
         )
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -89,7 +90,7 @@ class TestPromptBuilder:
             [{"index": 1, "label": "Option 1"}, {"index": 2, "label": "Option 2"}],
             {},
         )
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -100,7 +101,7 @@ class TestPromptBuilder:
     def test_includes_last_error(self, memory):
         """Should include last error."""
         memory.episodic.add_error("find_torrent", "API timeout")
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -111,7 +112,7 @@ class TestPromptBuilder:
     def test_includes_workflow(self, memory):
         """Should include current workflow."""
         memory.stm.start_workflow("download", {"title": "Inception"})
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -122,7 +123,7 @@ class TestPromptBuilder:
     def test_includes_topic(self, memory):
         """Should include current topic."""
         memory.stm.set_topic("selecting_torrent")
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -134,7 +135,7 @@ class TestPromptBuilder:
         """Should include extracted entities."""
         memory.stm.set_entity("movie_title", "Inception")
         memory.stm.set_entity("year", 2010)
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -144,7 +145,7 @@ class TestPromptBuilder:
 
     def test_includes_rules(self, memory):
         """Should include important rules."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -154,7 +155,7 @@ class TestPromptBuilder:
 
     def test_includes_examples(self, memory):
         """Should include usage examples."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -164,7 +165,7 @@ class TestPromptBuilder:
 
     def test_empty_context(self, memory):
         """Should handle empty context gracefully."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -179,7 +180,7 @@ class TestPromptBuilder:
         results = [{"name": f"Torrent {i}", "seeders": i} for i in range(20)]
         memory.episodic.store_search_results("test", results)
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -198,7 +199,7 @@ class TestFormatToolsDescription:
 
     def test_format_all_tools(self, memory):
         """Should format all tools."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         desc = builder._format_tools_description()
@@ -209,7 +210,7 @@ class TestFormatToolsDescription:
 
     def test_includes_parameters(self, memory):
         """Should include parameter schemas."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         desc = builder._format_tools_description()
@@ -223,7 +224,7 @@ class TestFormatEpisodicContext:
 
     def test_empty_episodic(self, memory):
         """Should return empty string for empty episodic."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_episodic_context(memory)
@@ -232,7 +233,7 @@ class TestFormatEpisodicContext:
 
     def test_with_search_results(self, memory_with_search_results):
         """Should format search results."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_episodic_context(memory_with_search_results)
@@ -246,7 +247,7 @@ class TestFormatEpisodicContext:
         memory.episodic.add_active_download({"task_id": "1", "name": "Download"})
         memory.episodic.add_error("action", "error")
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_episodic_context(memory)
@@ -261,7 +262,7 @@ class TestFormatStmContext:
 
     def test_empty_stm(self, memory):
         """Should return language info even for empty STM."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_stm_context(memory)
@@ -273,7 +274,7 @@ class TestFormatStmContext:
         """Should format workflow."""
         memory.stm.start_workflow("download", {"title": "Test"})
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_stm_context(memory)
@@ -287,7 +288,7 @@ class TestFormatStmContext:
         memory.stm.set_topic("searching")
         memory.stm.set_entity("key", "value")
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_stm_context(memory)

tests/test_prompts_critical.py

@@ -2,6 +2,7 @@
 
 from alfred.agent.prompts import PromptBuilder
 from alfred.agent.registry import make_tools
+from alfred.settings import settings
 
 
 class TestPromptBuilderToolsInjection:
@@ -9,7 +10,7 @@ class TestPromptBuilderToolsInjection:
 
     def test_system_prompt_includes_all_tools(self, memory):
         """CRITICAL: Verify all tools are mentioned in system prompt."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         prompt = builder.build_system_prompt()
 
@@ -21,7 +22,7 @@ class TestPromptBuilderToolsInjection:
 
     def test_tools_spec_contains_all_registered_tools(self, memory):
         """CRITICAL: Verify build_tools_spec() returns all tools."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         specs = builder.build_tools_spec()
 
@@ -32,7 +33,7 @@ class TestPromptBuilderToolsInjection:
 
     def test_tools_spec_is_not_empty(self, memory):
         """CRITICAL: Verify tools spec is never empty."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         specs = builder.build_tools_spec()
 
@@ -40,7 +41,7 @@ class TestPromptBuilderToolsInjection:
 
     def test_tools_spec_format_matches_openai(self, memory):
         """CRITICAL: Verify tools spec format is OpenAI-compatible."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         specs = builder.build_tools_spec()
 
@@ -58,7 +59,7 @@ class TestPromptBuilderMemoryContext:
 
     def test_prompt_includes_current_topic(self, memory):
         """Verify current topic is included in prompt."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         memory.stm.set_topic("test_topic")
@@ -68,7 +69,7 @@ class TestPromptBuilderMemoryContext:
 
     def test_prompt_includes_extracted_entities(self, memory):
         """Verify extracted entities are included in prompt."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         memory.stm.set_entity("test_key", "test_value")
@@ -78,7 +79,7 @@ class TestPromptBuilderMemoryContext:
 
     def test_prompt_includes_search_results(self, memory_with_search_results):
         """Verify search results are included in prompt."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -88,7 +89,7 @@ class TestPromptBuilderMemoryContext:
 
     def test_prompt_includes_active_downloads(self, memory):
         """Verify active downloads are included in prompt."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         memory.episodic.add_active_download(
@@ -102,7 +103,7 @@ class TestPromptBuilderMemoryContext:
 
     def test_prompt_includes_recent_errors(self, memory):
         """Verify recent errors are included in prompt."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         memory.episodic.add_error("test_action", "test error message")
@@ -113,7 +114,7 @@ class TestPromptBuilderMemoryContext:
 
     def test_prompt_includes_configuration(self, memory):
         """Verify configuration is included in prompt."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         memory.ltm.set_config("download_folder", "/test/downloads")
@@ -124,7 +125,7 @@ class TestPromptBuilderMemoryContext:
 
     def test_prompt_includes_language(self, memory):
         """Verify language is included in prompt."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         memory.stm.set_language("fr")
@@ -139,7 +140,7 @@ class TestPromptBuilderStructure:
 
     def test_system_prompt_is_not_empty(self, memory):
         """Verify system prompt is never empty."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         prompt = builder.build_system_prompt()
 
@@ -148,7 +149,7 @@ class TestPromptBuilderStructure:
 
     def test_system_prompt_includes_base_instruction(self, memory):
         """Verify system prompt includes base instruction."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         prompt = builder.build_system_prompt()
 
@@ -156,7 +157,7 @@ class TestPromptBuilderStructure:
 
     def test_system_prompt_includes_rules(self, memory):
         """Verify system prompt includes important rules."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         prompt = builder.build_system_prompt()
 
@@ -164,7 +165,7 @@ class TestPromptBuilderStructure:
 
     def test_system_prompt_includes_examples(self, memory):
         """Verify system prompt includes examples."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         prompt = builder.build_system_prompt()
 
@@ -172,7 +173,7 @@ class TestPromptBuilderStructure:
 
     def test_tools_description_format(self, memory):
         """Verify tools are properly formatted in description."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         description = builder._format_tools_description()
@@ -185,7 +186,7 @@ class TestPromptBuilderStructure:
 
     def test_episodic_context_format(self, memory_with_search_results):
         """Verify episodic context is properly formatted."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_episodic_context(memory_with_search_results)
@@ -195,7 +196,7 @@ class TestPromptBuilderStructure:
 
     def test_stm_context_format(self, memory):
         """Verify STM context is properly formatted."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         memory.stm.set_topic("test_topic")
@@ -208,7 +209,7 @@ class TestPromptBuilderStructure:
 
     def test_config_context_format(self, memory):
         """Verify config context is properly formatted."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         memory.ltm.set_config("test_key", "test_value")
@@ -224,7 +225,7 @@ class TestPromptBuilderEdgeCases:
 
     def test_prompt_with_no_memory_context(self, memory):
         """Verify prompt works with empty memory."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         # Memory is empty
@@ -254,7 +255,7 @@ class TestPromptBuilderEdgeCases:
 
     def test_prompt_with_unicode_in_memory(self, memory):
         """Verify prompt handles unicode in memory."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         memory.stm.set_entity("movie", "Amélie 🎬")
@@ -266,7 +267,7 @@ class TestPromptBuilderEdgeCases:
 
     def test_prompt_with_long_search_results(self, memory):
         """Verify prompt handles many search results."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         # Add many results

tests/test_prompts_edge_cases.py

@@ -2,6 +2,7 @@
 
 from alfred.agent.prompts import PromptBuilder
 from alfred.agent.registry import make_tools
+from alfred.settings import settings
 
 
 class TestPromptBuilderEdgeCases:
@@ -9,7 +10,7 @@ class TestPromptBuilderEdgeCases:
 
     def test_prompt_with_empty_memory(self, memory):
         """Should build prompt with completely empty memory."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -22,7 +23,7 @@ class TestPromptBuilderEdgeCases:
         memory.ltm.set_config("folder_日本語", "/path/to/日本語")
         memory.ltm.set_config("emoji_folder", "/path/🎬")
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -35,7 +36,7 @@ class TestPromptBuilderEdgeCases:
         long_path = "/very/long/path/" + "x" * 1000
         memory.ltm.set_config("download_folder", long_path)
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -47,7 +48,7 @@ class TestPromptBuilderEdgeCases:
         """Should escape special characters in config."""
         memory.ltm.set_config("path", '/path/with "quotes" and \\backslash')
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -60,7 +61,7 @@ class TestPromptBuilderEdgeCases:
         results = [{"name": f"Torrent {i}", "seeders": i} for i in range(50)]
         memory.episodic.store_search_results("test query", results)
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -79,7 +80,7 @@ class TestPromptBuilderEdgeCases:
         ]
         memory.episodic.store_search_results("test", results)
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -98,7 +99,7 @@ class TestPromptBuilderEdgeCases:
                 }
             )
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -112,7 +113,7 @@ class TestPromptBuilderEdgeCases:
         for i in range(10):
             memory.episodic.add_error(f"action_{i}", f"Error {i}")
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -125,7 +126,7 @@ class TestPromptBuilderEdgeCases:
         options = [{"index": i, "label": f"Option {i}"} for i in range(20)]
         memory.episodic.set_pending_question("Choose one:", options, {})
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -146,7 +147,7 @@ class TestPromptBuilderEdgeCases:
         )
         memory.stm.update_workflow_stage("searching_torrents")
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -160,7 +161,7 @@ class TestPromptBuilderEdgeCases:
         for i in range(50):
             memory.stm.set_entity(f"entity_{i}", f"value_{i}")
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -174,7 +175,7 @@ class TestPromptBuilderEdgeCases:
         memory.stm.set_entity("zero", 0)
         memory.stm.set_entity("false", False)
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -187,7 +188,7 @@ class TestPromptBuilderEdgeCases:
         memory.episodic.add_background_event("download_complete", {"name": "Movie.mkv"})
         memory.episodic.add_background_event("new_files", {"count": 5})
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -223,7 +224,7 @@ class TestPromptBuilderEdgeCases:
         # Events
         memory.episodic.add_background_event("event", {})
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -244,7 +245,7 @@ class TestPromptBuilderEdgeCases:
         memory.ltm.set_config("key", {"nested": [1, 2, 3]})
         memory.stm.set_entity("complex", {"a": {"b": {"c": "d"}}})
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         prompt = builder.build_system_prompt()
@@ -306,7 +307,7 @@ class TestFormatEpisodicContextEdgeCases:
         """Should handle empty search query."""
         memory.episodic.store_search_results("", [{"name": "Result"}])
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_episodic_context(memory)
@@ -324,7 +325,7 @@ class TestFormatEpisodicContextEdgeCases:
             ],
         )
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_episodic_context(memory)
@@ -336,7 +337,7 @@ class TestFormatEpisodicContextEdgeCases:
         """Should handle download without progress."""
         memory.episodic.add_active_download({"task_id": "1", "name": "Test"})
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_episodic_context(memory)
@@ -355,7 +356,7 @@ class TestFormatStmContextEdgeCases:
             "stage": "started",
         }
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_stm_context(memory)
@@ -366,7 +367,7 @@ class TestFormatStmContextEdgeCases:
         """Should handle workflow with None target."""
         memory.stm.start_workflow("download", None)
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         try:
@@ -380,7 +381,7 @@ class TestFormatStmContextEdgeCases:
         """Should handle empty topic."""
         memory.stm.set_topic("")
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_stm_context(memory)
@@ -392,7 +393,7 @@ class TestFormatStmContextEdgeCases:
         """Should handle entities containing JSON strings."""
         memory.stm.set_entity("json_string", '{"key": "value"}')
 
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
 
         context = builder._format_stm_context(memory)

tests/test_registry_critical.py

@@ -6,6 +6,7 @@ import pytest
 
 from alfred.agent.prompts import PromptBuilder
 from alfred.agent.registry import Tool, _create_tool_from_function, make_tools
+from alfred.settings import settings
 
 
 class TestToolSpecFormat:
@@ -13,7 +14,7 @@ class TestToolSpecFormat:
 
     def test_tool_spec_format_is_openai_compatible(self):
         """CRITICAL: Verify tool specs are OpenAI-compatible."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         specs = builder.build_tools_spec()
 
@@ -62,7 +63,7 @@ class TestToolSpecFormat:
 
     def test_all_registered_tools_are_callable(self):
         """CRITICAL: Verify all registered tools are actually callable."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         assert len(tools) > 0, "No tools registered"
 
@@ -78,7 +79,7 @@ class TestToolSpecFormat:
 
     def test_tools_spec_contains_all_registered_tools(self):
         """CRITICAL: Verify build_tools_spec() returns all registered tools."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         specs = builder.build_tools_spec()
 
@@ -119,7 +120,7 @@ class TestToolSpecFormat:
 
     def test_tool_parameters_have_descriptions(self):
         """Verify all tool parameters have descriptions."""
-        tools = make_tools()
+        tools = make_tools(settings)
         builder = PromptBuilder(tools)
         specs = builder.build_tools_spec()
 
@@ -150,28 +151,28 @@ class TestToolRegistry:
 
     def test_make_tools_returns_dict(self):
         """Verify make_tools returns a dictionary."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         assert isinstance(tools, dict)
         assert len(tools) > 0
 
     def test_all_tools_have_unique_names(self):
         """Verify all tool names are unique."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         names = [tool.name for tool in tools.values()]
         assert len(names) == len(set(names)), "Duplicate tool names found"
 
     def test_tool_names_match_dict_keys(self):
         """Verify tool names match their dictionary keys."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         for key, tool in tools.items():
             assert key == tool.name, f"Key {key} doesn't match tool name {tool.name}"
 
     def test_expected_tools_are_registered(self):
         """Verify all expected tools are registered."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         expected_tools = [
             "set_path_for_folder",
@@ -189,7 +190,7 @@ class TestToolRegistry:
 
     def test_tool_functions_are_valid(self):
         """Verify all tool functions are properly structured."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         # Verify structure without calling functions
         # (calling would require full setup with memory, clients, etc.)

tests/test_registry_edge_cases.py

@@ -3,6 +3,7 @@
 import pytest
 
 from alfred.agent.registry import Tool, make_tools
+from alfred.settings import settings
 
 
 class TestToolEdgeCases:
@@ -140,13 +141,13 @@ class TestMakeToolsEdgeCases:
 
     def test_make_tools_returns_dict(self, memory):
         """Should return dictionary of tools."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         assert isinstance(tools, dict)
 
     def test_make_tools_all_tools_have_required_fields(self, memory):
         """Should have all required fields for each tool."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         for name, tool in tools.items():
             assert tool.name == name
@@ -157,14 +158,14 @@ class TestMakeToolsEdgeCases:
 
     def test_make_tools_unique_names(self, memory):
         """Should have unique tool names."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         names = list(tools.keys())
         assert len(names) == len(set(names))
 
     def test_make_tools_valid_parameter_schemas(self, memory):
         """Should have valid JSON Schema for parameters."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         for tool in tools.values():
             params = tool.parameters
@@ -176,7 +177,7 @@ class TestMakeToolsEdgeCases:
 
     def test_make_tools_required_params_in_properties(self, memory):
         """Should have required params defined in properties."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         for tool in tools.values():
             params = tool.parameters
@@ -188,21 +189,21 @@ class TestMakeToolsEdgeCases:
 
     def test_make_tools_descriptions_not_empty(self, memory):
         """Should have non-empty descriptions."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         for tool in tools.values():
             assert tool.description.strip() != ""
 
     def test_make_tools_funcs_callable(self, memory):
         """Should have callable functions."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         for tool in tools.values():
             assert callable(tool.func)
 
     def test_make_tools_expected_tools_present(self, memory):
         """Should have expected tools."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         expected = [
             "set_path_for_folder",
@@ -220,14 +221,14 @@ class TestMakeToolsEdgeCases:
 
     def test_make_tools_idempotent(self, memory):
         """Should return same tools on multiple calls."""
-        tools1 = make_tools()
-        tools2 = make_tools()
+        tools1 = make_tools(settings)
+        tools2 = make_tools(settings)
 
         assert set(tools1.keys()) == set(tools2.keys())
 
     def test_make_tools_parameter_types(self, memory):
         """Should have valid parameter types."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         valid_types = ["string", "integer", "number", "boolean", "array", "object"]
 
@@ -241,7 +242,7 @@ class TestMakeToolsEdgeCases:
 
     def test_make_tools_enum_values(self, memory):
         """Should have valid enum values."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         for tool in tools.values():
             if "properties" in tool.parameters:
@@ -256,7 +257,7 @@ class TestToolExecution:
 
     def test_tool_returns_dict(self, memory, real_folder):
         """Should return dict from tool execution."""
-        tools = make_tools()
+        tools = make_tools(settings)
         memory.ltm.set_config("download_folder", str(real_folder["downloads"]))
 
         result = tools["list_folder"].func(folder_type="download")
@@ -265,7 +266,7 @@ class TestToolExecution:
 
     def test_tool_returns_status(self, memory, real_folder):
         """Should return status in result."""
-        tools = make_tools()
+        tools = make_tools(settings)
         memory.ltm.set_config("download_folder", str(real_folder["downloads"]))
 
         result = tools["list_folder"].func(folder_type="download")
@@ -274,14 +275,14 @@ class TestToolExecution:
 
     def test_tool_handles_missing_args(self, memory):
         """Should handle missing required arguments."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         with pytest.raises(TypeError):
             tools["set_path_for_folder"].func()  # Missing required args
 
     def test_tool_handles_wrong_type_args(self, memory):
         """Should handle wrong type arguments."""
-        tools = make_tools()
+        tools = make_tools(settings)
 
         # Pass wrong type - should either work or raise
         try:
@@ -293,7 +294,7 @@ class TestToolExecution:
 
     def test_tool_handles_extra_args(self, memory, real_folder):
         """Should handle extra arguments."""
-        tools = make_tools()
+        tools = make_tools(settings)
         memory.ltm.set_config("download_folder", str(real_folder["downloads"]))
 
         # Extra args should raise TypeError

tests/test_settings_bootstrap.py

@@ -0,0 +1,410 @@
+"""Tests for settings bootstrap."""
+
+import pytest
+
+from alfred.settings_bootstrap import (
+    ConfigSource,
+    SettingsBootstrap,
+    extract_python_version,
+    generate_secret,
+    get_nested_value,
+)
+
+
+@pytest.fixture
+def test_toml_content():
+    """Test TOML content with schema."""
+    return """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.poetry.dependencies]
+python = "==3.14.2"
+
+[tool.alfred.settings]
+runner = "poetry"
+image_name = "test_image"
+
+[tool.alfred.settings_schema.TEST_FROM_TOML]
+type = "string"
+source = "toml"
+toml_path = "tool.poetry.version"
+description = "Version from TOML"
+category = "test"
+
+[tool.alfred.settings_schema.TEST_FROM_ENV]
+type = "string"
+source = "env"
+default = "default_value"
+description = "Value from env"
+category = "test"
+
+[tool.alfred.settings_schema.TEST_SECRET]
+type = "secret"
+source = "generated"
+secret_rule = "16:hex"
+description = "Generated secret"
+category = "security"
+
+[tool.alfred.settings_schema.TEST_COMPUTED]
+type = "computed"
+source = "computed"
+compute_from = ["TEST_FROM_TOML", "TEST_FROM_ENV"]
+compute_template = "{TEST_FROM_TOML}-{TEST_FROM_ENV}"
+description = "Computed value"
+category = "test"
+
+[tool.alfred.settings_schema.PYTHON_VERSION]
+type = "string"
+source = "toml"
+toml_path = "tool.poetry.dependencies.python"
+transform = "extract_python_version_full"
+description = "Python version"
+category = "build"
+"""
+
+
+@pytest.fixture
+def config_source(tmp_path):
+    """Create a ConfigSource for testing."""
+    return ConfigSource.from_base_dir(tmp_path)
+
+
+@pytest.fixture
+def create_test_env(tmp_path, test_toml_content):
+    """Create a complete test environment."""
+    # Create pyproject.toml
+    toml_path = tmp_path / "pyproject.toml"
+    toml_path.write_text(test_toml_content)
+
+    # Create .env.example
+    env_example = tmp_path / ".env.example"
+    env_example.write_text("""
+TEST_FROM_TOML=
+TEST_FROM_ENV=
+TEST_SECRET=
+TEST_COMPUTED=
+PYTHON_VERSION=
+""")
+
+    return ConfigSource.from_base_dir(tmp_path)
+
+
+class TestExtractPythonVersion:
+    """Test Python version extraction."""
+
+    def test_exact_version(self):
+        """Test exact version format."""
+        full, short = extract_python_version("==3.14.2")
+        assert full == "3.14.2"
+        assert short == "3.14"
+
+    def test_caret_version(self):
+        """Test caret version format."""
+        full, short = extract_python_version("^3.14.2")
+        assert full == "3.14.2"
+        assert short == "3.14"
+
+    def test_invalid_version(self):
+        """Test invalid version raises error."""
+        with pytest.raises(ValueError, match="Invalid Python version"):
+            extract_python_version("3")
+
+
+class TestGenerateSecret:
+    """Test secret generation."""
+
+    def test_generate_b64(self):
+        """Test base64 secret generation."""
+        secret = generate_secret("32:b64")
+        assert isinstance(secret, str)
+        assert len(secret) > 0
+
+    def test_generate_hex(self):
+        """Test hex secret generation."""
+        secret = generate_secret("16:hex")
+        assert isinstance(secret, str)
+        assert len(secret) == 32  # 16 bytes = 32 hex chars
+        assert all(c in "0123456789abcdef" for c in secret)
+
+    def test_invalid_format(self):
+        """Test invalid format raises error."""
+        with pytest.raises(ValueError, match="Invalid security format"):
+            generate_secret("32:invalid")
+
+    def test_invalid_rule(self):
+        """Test invalid rule format raises error."""
+        with pytest.raises(ValueError, match="Invalid security rule format"):
+            generate_secret("32")
+
+
+class TestGetNestedValue:
+    """Test nested value extraction."""
+
+    def test_simple_path(self):
+        """Test simple path."""
+        data = {"key": "value"}
+        assert get_nested_value(data, "key") == "value"
+
+    def test_nested_path(self):
+        """Test nested path."""
+        data = {"a": {"b": {"c": "value"}}}
+        assert get_nested_value(data, "a.b.c") == "value"
+
+    def test_missing_key(self):
+        """Test missing key raises error."""
+        data = {"a": {"b": "value"}}
+        with pytest.raises(KeyError):
+            get_nested_value(data, "a.c")
+
+    def test_non_dict_value(self):
+        """Test accessing non-dict raises error."""
+        data = {"a": "not a dict"}
+        with pytest.raises(KeyError, match="non-dict"):
+            get_nested_value(data, "a.b")
+
+
+class TestSettingsBootstrap:
+    """Test settings bootstrap."""
+
+    def test_load_sources(self, create_test_env):
+        """Test loading TOML and env sources."""
+        bootstrapper = SettingsBootstrap(create_test_env)
+        bootstrapper._load_sources()
+
+        assert bootstrapper.toml_data is not None
+        assert "tool" in bootstrapper.toml_data
+        assert isinstance(bootstrapper.existing_env, dict)
+
+    def test_resolve_from_toml(self, create_test_env):
+        """Test resolving setting from TOML."""
+        # Load schema from test env
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper._load_sources()
+
+        # Get definition for TEST_FROM_TOML
+        definition = bootstrapper.schema.get("TEST_FROM_TOML")
+        value = bootstrapper._resolve_from_toml(definition)
+
+        assert value == "1.0.0"  # From tool.poetry.version
+
+    def test_resolve_from_env_with_default(self, create_test_env):
+        """Test resolving from env with default."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper._load_sources()
+
+        definition = bootstrapper.schema.get("TEST_FROM_ENV")
+        value = bootstrapper._resolve_from_env(definition)
+
+        assert value == "default_value"
+
+    def test_resolve_from_env_existing(self, create_test_env):
+        """Test resolving from existing env."""
+        # Create existing .env
+        create_test_env.env_path.write_text("TEST_FROM_ENV=existing_value\n")
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper._load_sources()
+
+        definition = bootstrapper.schema.get("TEST_FROM_ENV")
+        value = bootstrapper._resolve_from_env(definition)
+
+        assert value == "existing_value"
+
+    def test_resolve_generated_new(self, create_test_env):
+        """Test generating new secret."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper._load_sources()
+
+        definition = bootstrapper.schema.get("TEST_SECRET")
+        value = bootstrapper._resolve_generated(definition)
+
+        assert isinstance(value, str)
+        assert len(value) == 32  # 16 hex = 32 chars
+
+    def test_resolve_generated_preserve_existing(self, create_test_env):
+        """Test preserving existing secret."""
+        # Create existing .env with secret
+        create_test_env.env_path.write_text("TEST_SECRET=existing_secret\n")
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper._load_sources()
+
+        definition = bootstrapper.schema.get("TEST_SECRET")
+        value = bootstrapper._resolve_generated(definition)
+
+        assert value == "existing_secret"
+
+    def test_resolve_computed(self, create_test_env):
+        """Test resolving computed setting."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper._load_sources()
+
+        # Resolve dependencies first
+        bootstrapper.resolved_settings["TEST_FROM_TOML"] = "1.0.0"
+        bootstrapper.resolved_settings["TEST_FROM_ENV"] = "test"
+
+        definition = bootstrapper.schema.get("TEST_COMPUTED")
+        value = bootstrapper._resolve_computed(definition)
+
+        assert value == "1.0.0-test"
+
+    def test_resolve_with_transform(self, create_test_env):
+        """Test resolving with transform function."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper._load_sources()
+
+        definition = bootstrapper.schema.get("PYTHON_VERSION")
+        value = bootstrapper._resolve_from_toml(definition)
+
+        assert value == "3.14.2"  # Transformed from "==3.14.2"
+
+    def test_full_bootstrap(self, create_test_env):
+        """Test complete bootstrap process."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper.bootstrap()
+
+        # Check .env was created
+        assert create_test_env.env_path.exists()
+
+        # Check .env.make was created
+        env_make_path = create_test_env.base_dir / ".env.make"
+        assert env_make_path.exists()
+
+        # Check content
+        env_content = create_test_env.env_path.read_text()
+        assert "TEST_FROM_TOML=1.0.0" in env_content
+        assert "TEST_FROM_ENV=default_value" in env_content
+        assert "TEST_SECRET=" in env_content
+        assert "TEST_COMPUTED=1.0.0-default_value" in env_content
+
+    def test_bootstrap_preserves_secrets(self, create_test_env):
+        """Test that bootstrap preserves existing secrets."""
+        # Create existing .env with secret
+        create_test_env.env_path.write_text("""
+TEST_FROM_ENV=old_value
+TEST_SECRET=my_secret_123
+""")
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper.bootstrap()
+
+        # Check secret was preserved
+        env_content = create_test_env.env_path.read_text()
+        assert "TEST_SECRET=my_secret_123" in env_content
+
+    def test_validation_error(self, tmp_path, test_toml_content):
+        """Test validation error is raised."""
+        # Add a setting with validation
+        toml_with_validation = (
+            test_toml_content
+            + """
+[tool.alfred.settings_schema.TEST_VALIDATED]
+type = "integer"
+source = "env"
+default = 150
+validator = "range:1:100"
+description = "Validated setting"
+category = "test"
+"""
+        )
+        toml_path = tmp_path / "pyproject.toml"
+        toml_path.write_text(toml_with_validation)
+
+        env_example = tmp_path / ".env.example"
+        env_example.write_text("TEST_VALIDATED=\n")
+
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+
+        with pytest.raises(ValueError, match="Validation errors"):
+            bootstrapper.bootstrap()
+
+    def test_write_env_make_only_exports(self, create_test_env):
+        """Test that .env.make only contains export_to_env_make settings."""
+        # Add a setting with export_to_env_make
+        toml_content = create_test_env.toml_path.read_text()
+        toml_content += """
+[tool.alfred.settings_schema.EXPORTED_VAR]
+type = "string"
+source = "env"
+default = "exported"
+export_to_env_make = true
+category = "build"
+"""
+        create_test_env.toml_path.write_text(toml_content)
+
+        # Recreate schema
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(create_test_env.base_dir)
+
+        bootstrapper = SettingsBootstrap(create_test_env, schema)
+        bootstrapper.bootstrap()
+
+        env_make_content = (create_test_env.base_dir / ".env.make").read_text()
+        assert "EXPORTED_VAR=exported" in env_make_content
+        # Non-exported vars should not be in .env.make
+        assert "TEST_FROM_ENV" not in env_make_content
+
+
+class TestConfigSource:
+    """Test ConfigSource dataclass."""
+
+    def test_from_base_dir(self, tmp_path):
+        """Test creating ConfigSource from base dir."""
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        assert source.base_dir == tmp_path
+        assert source.toml_path == tmp_path / "pyproject.toml"
+        assert source.env_path == tmp_path / ".env"
+        assert source.env_example_path == tmp_path / ".env.example"
+
+    def test_from_base_dir_default(self):
+        """Test creating ConfigSource with default base dir."""
+        source = ConfigSource.from_base_dir()
+
+        assert source.base_dir.exists()
+        assert source.toml_path.name == "pyproject.toml"

tests/test_settings_bootstrap_advanced.py

@@ -0,0 +1,741 @@
+"""Advanced tests for settings bootstrap - template preservation and edge cases."""
+
+import pytest
+
+from alfred.settings_bootstrap import ConfigSource, SettingsBootstrap
+
+
+@pytest.fixture
+def test_toml_with_all_types(tmp_path):
+    """Create test TOML with all setting types."""
+    toml_content = """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.poetry.dependencies]
+python = "^3.14"
+
+[tool.alfred.settings_schema.STRING_VAR]
+type = "string"
+source = "env"
+default = "default_string"
+description = "String variable"
+category = "test"
+
+[tool.alfred.settings_schema.INT_VAR]
+type = "integer"
+source = "env"
+default = 42
+description = "Integer variable"
+category = "test"
+
+[tool.alfred.settings_schema.FLOAT_VAR]
+type = "float"
+source = "env"
+default = 3.14
+description = "Float variable"
+category = "test"
+
+[tool.alfred.settings_schema.BOOL_VAR]
+type = "boolean"
+source = "env"
+default = true
+description = "Boolean variable"
+category = "test"
+
+[tool.alfred.settings_schema.SECRET_VAR]
+type = "secret"
+source = "generated"
+secret_rule = "16:hex"
+description = "Secret variable"
+category = "security"
+
+[tool.alfred.settings_schema.COMPUTED_VAR]
+type = "computed"
+source = "computed"
+compute_from = ["STRING_VAR", "INT_VAR"]
+compute_template = "{STRING_VAR}_{INT_VAR}"
+description = "Computed variable"
+category = "test"
+"""
+    toml_path = tmp_path / "pyproject.toml"
+    toml_path.write_text(toml_content)
+    return tmp_path
+
+
+@pytest.fixture
+def test_env_example(tmp_path):
+    """Create .env.example template."""
+    env_example_content = """# Test configuration
+STRING_VAR=
+INT_VAR=
+FLOAT_VAR=
+
+# Boolean settings
+BOOL_VAR=
+
+# Security
+SECRET_VAR=
+
+# Computed values
+COMPUTED_VAR=
+
+# Custom section
+CUSTOM_VAR=custom_value
+"""
+    env_example_path = tmp_path / ".env.example"
+    env_example_path.write_text(env_example_content)
+    return env_example_path
+
+
+class TestTemplatePreservation:
+    """Test that .env.example template structure is preserved."""
+
+    def test_preserves_comments(self, test_toml_with_all_types, test_env_example):
+        """Test that comments from .env.example are preserved."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(test_toml_with_all_types)
+        source = ConfigSource.from_base_dir(test_toml_with_all_types)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        # Check comments are preserved
+        assert "# Test configuration" in env_content
+        assert "# Boolean settings" in env_content
+        assert "# Security" in env_content
+        assert "# Computed values" in env_content
+
+    def test_preserves_empty_lines(self, test_toml_with_all_types, test_env_example):
+        """Test that empty lines from .env.example are preserved."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(test_toml_with_all_types)
+        source = ConfigSource.from_base_dir(test_toml_with_all_types)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+        lines = env_content.split("\n")
+
+        # Check there are empty lines (structure preserved)
+        assert "" in lines
+
+    def test_preserves_variable_order(self, test_toml_with_all_types, test_env_example):
+        """Test that variable order from .env.example is preserved."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(test_toml_with_all_types)
+        source = ConfigSource.from_base_dir(test_toml_with_all_types)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        # Check order is preserved
+        string_pos = env_content.find("STRING_VAR=")
+        int_pos = env_content.find("INT_VAR=")
+        float_pos = env_content.find("FLOAT_VAR=")
+        bool_pos = env_content.find("BOOL_VAR=")
+
+        assert string_pos < int_pos < float_pos < bool_pos
+
+
+class TestSecretPreservation:
+    """Test that secrets are never overwritten."""
+
+    def test_preserves_existing_secrets(
+        self, test_toml_with_all_types, test_env_example
+    ):
+        """Test that existing secrets are preserved across multiple bootstraps."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(test_toml_with_all_types)
+        source = ConfigSource.from_base_dir(test_toml_with_all_types)
+
+        # First bootstrap - generates secret
+        bootstrapper1 = SettingsBootstrap(source, schema)
+        bootstrapper1.bootstrap()
+
+        env_content_1 = source.env_path.read_text()
+        secret_1 = [
+            line.split("=")[1]
+            for line in env_content_1.split("\n")
+            if line.startswith("SECRET_VAR=")
+        ][0]
+
+        # Second bootstrap - should preserve secret
+        bootstrapper2 = SettingsBootstrap(source, schema)
+        bootstrapper2.bootstrap()
+
+        env_content_2 = source.env_path.read_text()
+        secret_2 = [
+            line.split("=")[1]
+            for line in env_content_2.split("\n")
+            if line.startswith("SECRET_VAR=")
+        ][0]
+
+        assert secret_1 == secret_2
+        assert len(secret_1) == 32  # 16 hex bytes
+
+    def test_multiple_secrets_preserved(self, tmp_path):
+        """Test that multiple secrets are all preserved."""
+        toml_content = """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.alfred.settings_schema.SECRET_1]
+type = "secret"
+source = "generated"
+secret_rule = "16:hex"
+category = "security"
+
+[tool.alfred.settings_schema.SECRET_2]
+type = "secret"
+source = "generated"
+secret_rule = "32:b64"
+category = "security"
+
+[tool.alfred.settings_schema.SECRET_3]
+type = "secret"
+source = "generated"
+secret_rule = "8:hex"
+category = "security"
+"""
+        (tmp_path / "pyproject.toml").write_text(toml_content)
+        (tmp_path / ".env.example").write_text("SECRET_1=\nSECRET_2=\nSECRET_3=\n")
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        # First bootstrap
+        bootstrapper1 = SettingsBootstrap(source, schema)
+        bootstrapper1.bootstrap()
+
+        env_content_1 = source.env_path.read_text()
+
+        # Second bootstrap
+        bootstrapper2 = SettingsBootstrap(source, schema)
+        bootstrapper2.bootstrap()
+
+        env_content_2 = source.env_path.read_text()
+
+        # All secrets should be identical
+        assert env_content_1 == env_content_2
+
+
+class TestCustomVariables:
+    """Test that custom variables (not in schema) are preserved."""
+
+    def test_preserves_custom_variables_from_env(
+        self, test_toml_with_all_types, test_env_example
+    ):
+        """Test that custom variables added to .env are preserved."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(test_toml_with_all_types)
+        source = ConfigSource.from_base_dir(test_toml_with_all_types)
+
+        # First bootstrap
+        bootstrapper1 = SettingsBootstrap(source, schema)
+        bootstrapper1.bootstrap()
+
+        # Add custom variables to .env
+        with open(source.env_path, "a") as f:
+            f.write("\nMY_CUSTOM_VAR=custom_value\n")
+            f.write("ANOTHER_CUSTOM=another_value\n")
+
+        # Second bootstrap
+        bootstrapper2 = SettingsBootstrap(source, schema)
+        bootstrapper2.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        # Custom variables should be preserved
+        assert "MY_CUSTOM_VAR=custom_value" in env_content
+        assert "ANOTHER_CUSTOM=another_value" in env_content
+
+    def test_custom_variables_in_dedicated_section(
+        self, test_toml_with_all_types, test_env_example
+    ):
+        """Test that custom variables are placed in a dedicated section."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(test_toml_with_all_types)
+        source = ConfigSource.from_base_dir(test_toml_with_all_types)
+
+        # Create .env with custom variable
+        source.env_path.write_text("MY_CUSTOM_VAR=test\n")
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        # Check custom section exists
+        assert "# --- CUSTOM VARIABLES ---" in env_content
+        assert "MY_CUSTOM_VAR=test" in env_content
+
+    def test_preserves_custom_from_env_example(
+        self, test_toml_with_all_types, test_env_example
+    ):
+        """Test that custom variables in .env.example are preserved."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(test_toml_with_all_types)
+        source = ConfigSource.from_base_dir(test_toml_with_all_types)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        # CUSTOM_VAR is in .env.example but not in schema
+        assert "CUSTOM_VAR=custom_value" in env_content
+
+
+class TestBooleanHandling:
+    """Test that booleans are handled correctly."""
+
+    def test_booleans_written_as_lowercase(
+        self, test_toml_with_all_types, test_env_example
+    ):
+        """Test that Python booleans are written as lowercase strings."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(test_toml_with_all_types)
+        source = ConfigSource.from_base_dir(test_toml_with_all_types)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        # Boolean should be lowercase
+        assert "BOOL_VAR=true" in env_content
+        assert "BOOL_VAR=True" not in env_content
+        assert "BOOL_VAR=TRUE" not in env_content
+
+    def test_false_boolean_written_as_lowercase(self, tmp_path):
+        """Test that False is written as 'false'."""
+        toml_content = """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.alfred.settings_schema.BOOL_FALSE]
+type = "boolean"
+source = "env"
+default = false
+category = "test"
+"""
+        (tmp_path / "pyproject.toml").write_text(toml_content)
+        (tmp_path / ".env.example").write_text("BOOL_FALSE=\n")
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        assert "BOOL_FALSE=false" in env_content
+        assert "BOOL_FALSE=False" not in env_content
+
+    def test_boolean_parsing_from_env(self, tmp_path):
+        """Test that various boolean formats are parsed correctly."""
+        toml_content = """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.alfred.settings_schema.BOOL_VAR]
+type = "boolean"
+source = "env"
+default = false
+category = "test"
+"""
+        (tmp_path / "pyproject.toml").write_text(toml_content)
+        (tmp_path / ".env.example").write_text("BOOL_VAR=\n")
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        # Test different boolean formats
+        test_cases = [
+            ("true", True),
+            ("TRUE", True),
+            ("True", True),
+            ("1", True),
+            ("yes", True),
+            ("false", False),
+            ("FALSE", False),
+            ("False", False),
+            ("0", False),
+            ("no", False),
+        ]
+
+        for input_val, expected in test_cases:
+            source.env_path.write_text(f"BOOL_VAR={input_val}\n")
+
+            bootstrapper = SettingsBootstrap(source, schema)
+            bootstrapper._load_sources()
+            bootstrapper._resolve_settings()
+
+            assert bootstrapper.resolved_settings["BOOL_VAR"] == expected
+
+
+class TestComputedVariables:
+    """Test that computed variables are calculated correctly."""
+
+    def test_computed_variables_written_to_env(
+        self, test_toml_with_all_types, test_env_example
+    ):
+        """Test that computed variables are written with their computed values."""
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(test_toml_with_all_types)
+        source = ConfigSource.from_base_dir(test_toml_with_all_types)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        # Computed variable should have its computed value
+        assert "COMPUTED_VAR=default_string_42" in env_content
+
+    def test_computed_uri_example(self, tmp_path):
+        """Test computed URI (like MONGO_URI) is written correctly."""
+        toml_content = """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.alfred.settings_schema.DB_HOST]
+type = "string"
+source = "env"
+default = "localhost"
+category = "database"
+
+[tool.alfred.settings_schema.DB_PORT]
+type = "integer"
+source = "env"
+default = 5432
+category = "database"
+
+[tool.alfred.settings_schema.DB_USER]
+type = "string"
+source = "env"
+default = "user"
+category = "database"
+
+[tool.alfred.settings_schema.DB_PASSWORD]
+type = "secret"
+source = "generated"
+secret_rule = "16:hex"
+category = "security"
+
+[tool.alfred.settings_schema.DB_URI]
+type = "computed"
+source = "computed"
+compute_from = ["DB_USER", "DB_PASSWORD", "DB_HOST", "DB_PORT"]
+compute_template = "postgresql://{DB_USER}:{DB_PASSWORD}@{DB_HOST}:{DB_PORT}/db"
+category = "database"
+"""
+        (tmp_path / "pyproject.toml").write_text(toml_content)
+        (tmp_path / ".env.example").write_text(
+            "DB_HOST=\nDB_PORT=\nDB_USER=\nDB_PASSWORD=\nDB_URI=\n"
+        )
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        # Check URI is computed and written
+        assert "DB_URI=postgresql://user:" in env_content
+        assert "@localhost:5432/db" in env_content
+
+        # Extract password from URI to verify it's the same as DB_PASSWORD
+        import re
+
+        uri_match = re.search(r"DB_URI=postgresql://user:([^@]+)@", env_content)
+        password_match = re.search(r"DB_PASSWORD=([^\n]+)", env_content)
+
+        assert uri_match and password_match
+        assert uri_match.group(1) == password_match.group(1)
+
+
+class TestEdgeCases:
+    """Test edge cases and error conditions."""
+
+    def test_missing_env_example(self, tmp_path):
+        """Test that missing .env.example raises error."""
+        toml_content = """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.alfred.settings_schema.TEST_VAR]
+type = "string"
+source = "env"
+default = "test"
+category = "test"
+"""
+        (tmp_path / "pyproject.toml").write_text(toml_content)
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+
+        with pytest.raises(FileNotFoundError, match=".env.example not found"):
+            bootstrapper.bootstrap()
+
+    def test_empty_env_example(self, tmp_path):
+        """Test that empty .env.example works."""
+        toml_content = """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.alfred.settings_schema.TEST_VAR]
+type = "string"
+source = "env"
+default = "test"
+category = "test"
+"""
+        (tmp_path / "pyproject.toml").write_text(toml_content)
+        (tmp_path / ".env.example").write_text("")
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        # Should create .env even if .env.example is empty
+        assert source.env_path.exists()
+
+    def test_variable_with_equals_in_value(self, tmp_path):
+        """Test that variables with '=' in their value are handled correctly."""
+        toml_content = """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.alfred.settings_schema.URL_VAR]
+type = "string"
+source = "env"
+default = "http://example.com?key=value"
+category = "test"
+"""
+        (tmp_path / "pyproject.toml").write_text(toml_content)
+        (tmp_path / ".env.example").write_text("URL_VAR=\n")
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        bootstrapper = SettingsBootstrap(source, schema)
+        bootstrapper.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        assert "URL_VAR=http://example.com?key=value" in env_content
+
+    def test_preserves_existing_values_on_update(self, tmp_path):
+        """Test that existing values are preserved when updating."""
+        toml_content = """
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+[tool.alfred.settings_schema.VAR1]
+type = "string"
+source = "env"
+default = "default1"
+category = "test"
+
+[tool.alfred.settings_schema.VAR2]
+type = "string"
+source = "env"
+default = "default2"
+category = "test"
+"""
+        (tmp_path / "pyproject.toml").write_text(toml_content)
+        (tmp_path / ".env.example").write_text("VAR1=\nVAR2=\n")
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        # First bootstrap
+        bootstrapper1 = SettingsBootstrap(source, schema)
+        bootstrapper1.bootstrap()
+
+        # Modify values
+        source.env_path.write_text("VAR1=custom1\nVAR2=custom2\n")
+
+        # Second bootstrap
+        bootstrapper2 = SettingsBootstrap(source, schema)
+        bootstrapper2.bootstrap()
+
+        env_content = source.env_path.read_text()
+
+        # Custom values should be preserved
+        assert "VAR1=custom1" in env_content
+        assert "VAR2=custom2" in env_content
+
+
+class TestIntegration:
+    """Integration tests with realistic scenarios."""
+
+    def test_full_workflow_like_alfred(self, tmp_path):
+        """Test a full workflow similar to Alfred's actual usage."""
+        toml_content = """
+[tool.poetry]
+name = "alfred"
+version = "0.1.7"
+
+[tool.poetry.dependencies]
+python = "^3.14"
+
+[tool.alfred.settings_schema.ALFRED_VERSION]
+type = "string"
+source = "toml"
+toml_path = "tool.poetry.version"
+category = "build"
+export_to_env_make = true
+
+[tool.alfred.settings_schema.HOST]
+type = "string"
+source = "env"
+default = "0.0.0.0"
+category = "app"
+
+[tool.alfred.settings_schema.PORT]
+type = "integer"
+source = "env"
+default = 3080
+category = "app"
+
+[tool.alfred.settings_schema.JWT_SECRET]
+type = "secret"
+source = "generated"
+secret_rule = "32:hex"
+category = "security"
+
+[tool.alfred.settings_schema.MONGO_HOST]
+type = "string"
+source = "env"
+default = "mongodb"
+category = "database"
+
+[tool.alfred.settings_schema.MONGO_PASSWORD]
+type = "secret"
+source = "generated"
+secret_rule = "16:hex"
+category = "security"
+
+[tool.alfred.settings_schema.MONGO_URI]
+type = "computed"
+source = "computed"
+compute_from = ["MONGO_HOST", "MONGO_PASSWORD"]
+compute_template = "mongodb://user:{MONGO_PASSWORD}@{MONGO_HOST}:27017/db"
+category = "database"
+
+[tool.alfred.settings_schema.DEBUG_MODE]
+type = "boolean"
+source = "env"
+default = false
+category = "app"
+"""
+        (tmp_path / "pyproject.toml").write_text(toml_content)
+
+        env_example_content = """# Application settings
+HOST=0.0.0.0
+PORT=3080
+DEBUG_MODE=false
+
+# Security
+JWT_SECRET=
+
+# Database
+MONGO_HOST=mongodb
+MONGO_PASSWORD=
+MONGO_URI=
+
+# Build info
+ALFRED_VERSION=
+"""
+        (tmp_path / ".env.example").write_text(env_example_content)
+
+        from alfred.settings_schema import load_schema
+
+        schema = load_schema(tmp_path)
+        source = ConfigSource.from_base_dir(tmp_path)
+
+        # First bootstrap
+        bootstrapper1 = SettingsBootstrap(source, schema)
+        bootstrapper1.bootstrap()
+
+        env_content_1 = source.env_path.read_text()
+
+        # Verify structure
+        assert "# Application settings" in env_content_1
+        assert "HOST=0.0.0.0" in env_content_1
+        assert "PORT=3080" in env_content_1
+        assert "DEBUG_MODE=false" in env_content_1  # lowercase!
+        assert "ALFRED_VERSION=0.1.7" in env_content_1
+        assert "JWT_SECRET=" in env_content_1
+        assert len([l for l in env_content_1.split("\n") if "JWT_SECRET=" in l][0]) > 20
+        assert "MONGO_URI=mongodb://user:" in env_content_1
+
+        # Second bootstrap - should preserve everything
+        bootstrapper2 = SettingsBootstrap(source, schema)
+        bootstrapper2.bootstrap()
+
+        env_content_2 = source.env_path.read_text()
+
+        # Everything should be identical
+        assert env_content_1 == env_content_2
+
+        # Add custom variable
+        with open(source.env_path, "a") as f:
+            f.write("\nMY_CUSTOM_SETTING=test123\n")
+
+        # Third bootstrap - should preserve custom
+        bootstrapper3 = SettingsBootstrap(source, schema)
+        bootstrapper3.bootstrap()
+
+        env_content_3 = source.env_path.read_text()
+
+        assert "MY_CUSTOM_SETTING=test123" in env_content_3
+        assert "# --- CUSTOM VARIABLES ---" in env_content_3

tests/test_settings_schema.py

@@ -0,0 +1,332 @@
+"""Tests for settings schema parser."""
+
+import pytest
+
+from alfred.settings_schema import (
+    SettingDefinition,
+    SettingSource,
+    SettingType,
+    load_schema,
+    validate_value,
+)
+
+
+@pytest.fixture
+def minimal_schema_toml():
+    """Minimal valid schema TOML."""
+    return """
+[tool.alfred.settings_schema.TEST_STRING]
+type = "string"
+source = "env"
+default = "test_value"
+description = "Test string setting"
+category = "test"
+
+[tool.alfred.settings_schema.TEST_INTEGER]
+type = "integer"
+source = "env"
+default = 42
+description = "Test integer setting"
+category = "test"
+validator = "range:1:100"
+
+[tool.alfred.settings_schema.TEST_SECRET]
+type = "secret"
+source = "generated"
+secret_rule = "32:b64"
+description = "Test secret"
+category = "security"
+required = true
+
+[tool.alfred.settings_schema.TEST_COMPUTED]
+type = "computed"
+source = "computed"
+compute_from = ["TEST_STRING", "TEST_INTEGER"]
+compute_template = "{TEST_STRING}_{TEST_INTEGER}"
+description = "Test computed"
+category = "test"
+
+[tool.alfred.settings_schema.TEST_OPTIONAL]
+type = "string"
+source = "env"
+required = false
+description = "Optional setting"
+category = "test"
+"""
+
+
+@pytest.fixture
+def create_schema_file(tmp_path):
+    """Factory to create pyproject.toml with schema."""
+
+    def _create(content: str):
+        toml_path = tmp_path / "pyproject.toml"
+        full_content = f"""
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+
+{content}
+"""
+        toml_path.write_text(full_content)
+        return tmp_path
+
+    return _create
+
+
+class TestSettingDefinition:
+    """Test SettingDefinition dataclass."""
+
+    def test_create_definition(self):
+        """Test creating a setting definition."""
+        definition = SettingDefinition(
+            name="TEST_SETTING",
+            type=SettingType.STRING,
+            source=SettingSource.ENV,
+            description="Test setting",
+            category="test",
+            default="default_value",
+        )
+
+        assert definition.name == "TEST_SETTING"
+        assert definition.type == SettingType.STRING
+        assert definition.source == SettingSource.ENV
+        assert definition.default == "default_value"
+        assert definition.required is True  # Default
+
+
+class TestSettingsSchema:
+    """Test SettingsSchema parser."""
+
+    def test_parse_schema(self, create_schema_file, minimal_schema_toml):
+        """Test parsing schema from TOML."""
+        base_dir = create_schema_file(minimal_schema_toml)
+        schema = load_schema(base_dir)
+
+        assert len(schema) == 5
+        assert "TEST_STRING" in schema.definitions
+        assert "TEST_INTEGER" in schema.definitions
+        assert "TEST_SECRET" in schema.definitions
+        assert "TEST_COMPUTED" in schema.definitions
+        assert "TEST_OPTIONAL" in schema.definitions
+
+    def test_get_definition(self, create_schema_file, minimal_schema_toml):
+        """Test getting a definition by name."""
+        base_dir = create_schema_file(minimal_schema_toml)
+        schema = load_schema(base_dir)
+
+        definition = schema.get("TEST_STRING")
+        assert definition is not None
+        assert definition.name == "TEST_STRING"
+        assert definition.type == SettingType.STRING
+        assert definition.default == "test_value"
+
+    def test_get_by_category(self, create_schema_file, minimal_schema_toml):
+        """Test getting definitions by category."""
+        base_dir = create_schema_file(minimal_schema_toml)
+        schema = load_schema(base_dir)
+
+        test_settings = schema.get_by_category("test")
+        assert len(test_settings) == 4
+
+        security_settings = schema.get_by_category("security")
+        assert len(security_settings) == 1
+
+    def test_get_by_source(self, create_schema_file, minimal_schema_toml):
+        """Test getting definitions by source."""
+        base_dir = create_schema_file(minimal_schema_toml)
+        schema = load_schema(base_dir)
+
+        env_settings = schema.get_by_source(SettingSource.ENV)
+        assert len(env_settings) == 3
+
+        generated_settings = schema.get_by_source(SettingSource.GENERATED)
+        assert len(generated_settings) == 1
+
+        computed_settings = schema.get_by_source(SettingSource.COMPUTED)
+        assert len(computed_settings) == 1
+
+    def test_get_required(self, create_schema_file, minimal_schema_toml):
+        """Test getting required settings."""
+        base_dir = create_schema_file(minimal_schema_toml)
+        schema = load_schema(base_dir)
+
+        required = schema.get_required()
+        # TEST_OPTIONAL is not required
+        assert len(required) == 4
+
+    def test_parse_types(self, create_schema_file):
+        """Test parsing different setting types."""
+        schema_toml = """
+[tool.alfred.settings_schema.STR_SETTING]
+type = "string"
+source = "env"
+default = "text"
+
+[tool.alfred.settings_schema.INT_SETTING]
+type = "integer"
+source = "env"
+default = 42
+
+[tool.alfred.settings_schema.FLOAT_SETTING]
+type = "float"
+source = "env"
+default = 3.14
+
+[tool.alfred.settings_schema.BOOL_SETTING]
+type = "boolean"
+source = "env"
+default = true
+"""
+        base_dir = create_schema_file(schema_toml)
+        schema = load_schema(base_dir)
+
+        assert schema.get("STR_SETTING").default == "text"
+        assert schema.get("INT_SETTING").default == 42
+        assert schema.get("FLOAT_SETTING").default == 3.14
+        assert schema.get("BOOL_SETTING").default is True
+
+    def test_missing_schema_section(self, tmp_path):
+        """Test error when schema section is missing."""
+        toml_path = tmp_path / "pyproject.toml"
+        toml_path.write_text("""
+[tool.poetry]
+name = "test"
+version = "1.0.0"
+""")
+
+        with pytest.raises(KeyError, match="settings_schema"):
+            load_schema(tmp_path)
+
+
+class TestValidateValue:
+    """Test value validation."""
+
+    def test_validate_string(self):
+        """Test validating string values."""
+        definition = SettingDefinition(
+            name="TEST",
+            type=SettingType.STRING,
+            source=SettingSource.ENV,
+        )
+
+        assert validate_value(definition, "test") is True
+
+        with pytest.raises(ValueError, match="must be string"):
+            validate_value(definition, 123)
+
+    def test_validate_integer(self):
+        """Test validating integer values."""
+        definition = SettingDefinition(
+            name="TEST",
+            type=SettingType.INTEGER,
+            source=SettingSource.ENV,
+        )
+
+        assert validate_value(definition, 42) is True
+
+        with pytest.raises(ValueError, match="must be integer"):
+            validate_value(definition, "not an int")
+
+    def test_validate_float(self):
+        """Test validating float values."""
+        definition = SettingDefinition(
+            name="TEST",
+            type=SettingType.FLOAT,
+            source=SettingSource.ENV,
+        )
+
+        assert validate_value(definition, 3.14) is True
+        assert validate_value(definition, 42) is True  # int is ok for float
+
+        with pytest.raises(ValueError, match="must be float"):
+            validate_value(definition, "not a float")
+
+    def test_validate_required(self):
+        """Test validating required settings."""
+        definition = SettingDefinition(
+            name="TEST",
+            type=SettingType.STRING,
+            source=SettingSource.ENV,
+            required=True,
+        )
+
+        with pytest.raises(ValueError, match="is required"):
+            validate_value(definition, None)
+
+    def test_validate_optional(self):
+        """Test validating optional settings."""
+        definition = SettingDefinition(
+            name="TEST",
+            type=SettingType.STRING,
+            source=SettingSource.ENV,
+            required=False,
+        )
+
+        assert validate_value(definition, None) is True
+
+    def test_validate_range(self):
+        """Test range validator."""
+        definition = SettingDefinition(
+            name="TEST",
+            type=SettingType.INTEGER,
+            source=SettingSource.ENV,
+            validator="range:1:100",
+        )
+
+        assert validate_value(definition, 50) is True
+        assert validate_value(definition, 1) is True
+        assert validate_value(definition, 100) is True
+
+        with pytest.raises(ValueError, match=r"must be between .* and .*, got"):
+            validate_value(definition, 0)
+
+        with pytest.raises(ValueError, match=r"must be between .* and .*, got"):
+            validate_value(definition, 101)
+
+    def test_validate_float_range(self):
+        """Test range validator with floats."""
+        definition = SettingDefinition(
+            name="TEST",
+            type=SettingType.FLOAT,
+            source=SettingSource.ENV,
+            validator="range:0.0:2.0",
+        )
+
+        assert validate_value(definition, 1.5) is True
+        assert validate_value(definition, 0.0) is True
+        assert validate_value(definition, 2.0) is True
+
+        with pytest.raises(ValueError, match="must be between 0.0 and 2.0"):
+            validate_value(definition, -0.1)
+
+        with pytest.raises(ValueError, match="must be between 0.0 and 2.0"):
+            validate_value(definition, 2.1)
+
+    def test_invalid_validator(self):
+        """Test unknown validator raises error."""
+        definition = SettingDefinition(
+            name="TEST",
+            type=SettingType.STRING,
+            source=SettingSource.ENV,
+            validator="unknown:validator",
+        )
+
+        with pytest.raises(ValueError, match="Unknown validator"):
+            validate_value(definition, "test")
+
+
+class TestSchemaIteration:
+    """Test schema iteration."""
+
+    def test_iterate_schema(self, create_schema_file, minimal_schema_toml):
+        """Test iterating over schema definitions."""
+        base_dir = create_schema_file(minimal_schema_toml)
+        schema = load_schema(base_dir)
+
+        definitions = list(schema)
+        assert len(definitions) == 5
+
+        names = [d.name for d in definitions]
+        assert "TEST_STRING" in names
+        assert "TEST_INTEGER" in names