diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..449db4c
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,61 @@
+# Git
+.git
+.gitignore
+
+# Python
+__pycache__
+*.py[cod]
+*$py.class
+*.so
+.Python
+.venv
+venv/
+ENV/
+env/
+.eggs
+*.egg-info/
+.mypy_cache/
+.pytest_cache/
+.ruff_cache/
+htmlcov/
+.coverage
+coverage.xml
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# Build artifacts
+build/
+dist/
+*.egg
+
+# Documentation
+docs/
+*.md
+!README.md
+
+# Tests (not needed in production image)
+tests/
+pytest.ini
+
+# Development files
+.pre-commit-config.yaml
+Makefile
+docker-compose*.yml
+
+# Templates (not needed in production)
+templates/
+
+# Tools (not needed in production)
+tools/
+
+# Node modules (if any)
+node_modules/
+
+# Misc
+.DS_Store
+*.log
+*.tmp
diff --git a/docker/Dockerfile b/docker/Dockerfile
new file mode 100644
index 0000000..2016d51
--- /dev/null
+++ b/docker/Dockerfile
@@ -0,0 +1,75 @@
+# CodeFlow Engine Docker Image
+# Multi-stage build for optimized production image
+
+# Stage 1: Build stage
+FROM python:3.12-slim as builder
+
+WORKDIR /app
+
+# Install build dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    curl \
+    git \
+    libpq-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install poetry
+RUN pip install --no-cache-dir poetry==1.8.3
+
+# Copy dependency files
+COPY pyproject.toml poetry.lock ./
+
+# Configure poetry to not create virtual environment (we're in a container)
+RUN poetry config virtualenvs.create false
+
+# Install dependencies (without dev dependencies by default)
+ARG RUN_TESTS=false
+RUN if [ "$RUN_TESTS" = "true" ]; then \
+        poetry install --no-interaction --no-ansi; \
+    else \
+        poetry install --no-interaction --no-ansi --only main,server,database,resilience; \
+    fi
+
+# Stage 2: Production stage
+FROM python:3.12-slim as production
+
+WORKDIR /app
+
+# Install runtime dependencies only
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libpq5 \
+    curl \
+    && rm -rf /var/lib/apt/lists/* \
+    && useradd --create-home --shell /bin/bash codeflow
+
+# Copy installed packages from builder
+COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages
+COPY --from=builder /usr/local/bin /usr/local/bin
+
+# Copy application code
+COPY codeflow_engine/ ./codeflow_engine/
+COPY pyproject.toml ./
+COPY alembic/ ./alembic/
+
+# Set ownership to non-root user
+RUN chown -R codeflow:codeflow /app
+
+# Switch to non-root user
+USER codeflow
+
+# Environment variables
+ENV PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1 \
+    HOST=0.0.0.0 \
+    PORT=8080
+
+# Expose the application port
+EXPOSE 8080
+
+# Health check
+HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
+    CMD curl -f http://localhost:8080/health || exit 1
+
+# Default command: run the server
+CMD ["python", "-m", "codeflow_engine.server"]
diff --git a/docs/development/CODE_QUALITY.md b/docs/development/CODE_QUALITY.md
index 6bae9f9..7dd11de 100644
--- a/docs/development/CODE_QUALITY.md
+++ b/docs/development/CODE_QUALITY.md
@@ -56,53 +56,53 @@ Pre-commit hooks are automatically installed and will run on every commit. The h
 
 ### Using the Python Script
 
-The `scripts/code_quality.py` script provides convenient commands:
+The `tools/scripts/code_quality.py` script provides convenient commands:
 
 ```bash
 # Format code
-python scripts/code_quality.py format
+python tools/scripts/code_quality.py format
 
 # Run linting tools
-python scripts/code_quality.py lint
+python tools/scripts/code_quality.py lint
 
 # Run tests
-python scripts/code_quality.py test
+python tools/scripts/code_quality.py test
 
 # Check dependencies for vulnerabilities
-python scripts/code_quality.py security
+python tools/scripts/code_quality.py security
 
 # Install pre-commit hooks
-python scripts/code_quality.py pre-commit install
+python tools/scripts/code_quality.py pre-commit install
 
 # Run pre-commit hooks manually
-python scripts/code_quality.py pre-commit run
+python tools/scripts/code_quality.py pre-commit run
 
 # Run all quality checks
-python scripts/code_quality.py check
+python tools/scripts/code_quality.py check
 ```
 
 ### Using the Windows Batch Script
 
-For Windows users, `scripts/code_quality.bat` provides the same functionality:
+For Windows users, `tools/scripts/code_quality.bat` provides the same functionality:
 
 ```cmd
 # Format code
-scripts\code_quality.bat format
+tools\scripts\code_quality.bat format
 
 # Run linting tools
-scripts\code_quality.bat lint
+tools\scripts\code_quality.bat lint
 
 # Run tests
-scripts\code_quality.bat test
+tools\scripts\code_quality.bat test
 
 # Check dependencies for vulnerabilities
-scripts\code_quality.bat security
+tools\scripts\code_quality.bat security
 
 # Install pre-commit hooks
-scripts\code_quality.bat install
+tools\scripts\code_quality.bat install
 
 # Run all quality checks
-scripts\code_quality.bat check
+tools\scripts\code_quality.bat check
 ```
 
 ### Direct Tool Usage
@@ -181,13 +181,13 @@ python -m pre_commit install
 python -m pre_commit run --all-files
 
 # Or use the comprehensive check
-python scripts/code_quality.py check
+python tools/scripts/code_quality.py check
 ```
 
 ## Development Workflow
 
 1. **Before committing**: Pre-commit hooks run automatically
-2. **Manual checks**: Use `scripts/code_quality.py check` for comprehensive validation
+2. **Manual checks**: Use `tools/scripts/code_quality.py check` for comprehensive validation
 3. **Fix issues**: Address any linting or formatting issues
 4. **Commit**: Use conventional commit messages (enforced by commitizen)
 
diff --git a/docs/development/MIGRATION_GUIDE.md b/docs/development/MIGRATION_GUIDE.md
index ed5d199..947fb37 100644
--- a/docs/development/MIGRATION_GUIDE.md
+++ b/docs/development/MIGRATION_GUIDE.md
@@ -162,7 +162,7 @@ New validation scripts have been created to maintain repository health:
 ### 1. Import Validation
 
 ```bash
-python scripts/validate_imports.py
+python tools/scripts/validate_imports.py
 ```
 
 - Scans all Python files for broken imports
@@ -172,7 +172,7 @@ python scripts/validate_imports.py
 ### 2. Link Validation
 
 ```bash
-python scripts/validate_links.py
+python tools/scripts/validate_links.py
 ```
 
 - Validates all Markdown links in documentation
@@ -182,7 +182,7 @@ python scripts/validate_links.py
 ### 3. Configuration Validation
 
 ```bash
-python scripts/validate_configs.py
+python tools/scripts/validate_configs.py
 ```
 
 - Validates all configuration files (YAML, JSON, INI)
@@ -192,7 +192,7 @@ python scripts/validate_configs.py
 ### 4. Template Validation
 
 ```bash
-python scripts/validate_templates.py
+python tools/scripts/validate_templates.py
 ```
 
 - Validates all template files
@@ -202,7 +202,7 @@ python scripts/validate_templates.py
 ### 5. Build System Validation
 
 ```bash
-python scripts/validate_build_system.py
+python tools/scripts/validate_build_system.py
 ```
 
 - Validates pyproject.toml configuration
@@ -268,11 +268,11 @@ The pre-commit configuration has been updated to include:
 
 ```bash
 # Run all validation scripts
-python scripts/validate_imports.py
-python scripts/validate_links.py
-python scripts/validate_configs.py
-python scripts/validate_templates.py
-python scripts/validate_build_system.py
+python tools/scripts/validate_imports.py
+python tools/scripts/validate_links.py
+python tools/scripts/validate_configs.py
+python tools/scripts/validate_templates.py
+python tools/scripts/validate_build_system.py
 ```
 
 ### Expected Results
@@ -288,7 +288,7 @@ python scripts/validate_build_system.py
 1. **Import Errors After Reorganization:**
 
    ```bash
-   python scripts/validate_imports.py
+   python tools/scripts/validate_imports.py
    ```
 
    - Check the generated report for specific import issues
@@ -297,7 +297,7 @@ python scripts/validate_build_system.py
 2. **Broken Documentation Links:**
 
    ```bash
-   python scripts/validate_links.py
+   python tools/scripts/validate_links.py
    ```
 
    - Review the link validation report
@@ -306,7 +306,7 @@ python scripts/validate_build_system.py
 3. **Configuration Issues:**
 
    ```bash
-   python scripts/validate_configs.py
+   python tools/scripts/validate_configs.py
    ```
 
    - Check for configuration validation errors
@@ -329,9 +329,9 @@ Run validation scripts regularly to maintain repository health:
 
 ```bash
 # Weekly validation
-python scripts/validate_imports.py
-python scripts/validate_links.py
-python scripts/validate_configs.py
+python tools/scripts/validate_imports.py
+python tools/scripts/validate_links.py
+python tools/scripts/validate_configs.py
 ```
 
 ### Adding New Files
@@ -341,14 +341,14 @@ When adding new files, ensure they follow the established organization:
 - **Documentation**: Place in appropriate `docs/` subdirectory
 - **Templates**: Use existing template categories or create new ones
 - **Configuration**: Add to `configs/` with proper validation
-- **Scripts**: Add to `scripts/` with validation capabilities
+- **Scripts**: Add to `tools/scripts/` with validation capabilities
 
 ### Updating Dependencies
 
 When updating dependencies:
 
 1. Update `pyproject.toml` only
-2. Run `python scripts/validate_build_system.py`
+2. Run `python tools/scripts/validate_build_system.py`
 3. Test installation with new dependencies
 
 ## Conclusion
diff --git a/docs/development/WINDOWS_DEVELOPMENT.md b/docs/development/WINDOWS_DEVELOPMENT.md
index 721eb4e..2fed707 100644
--- a/docs/development/WINDOWS_DEVELOPMENT.md
+++ b/docs/development/WINDOWS_DEVELOPMENT.md
@@ -24,12 +24,12 @@ Instead of relying on pre-commit hooks, use our provided scripts for code qualit
 
 ```cmd
 # Run all code quality checks before committing
-scripts\code_quality.bat check
+python -m codeflow_engine.actions.quality_engine --mode comprehensive
 
-# Or run individual tools
-scripts\code_quality.bat format
-scripts\code_quality.bat lint
-scripts\code_quality.bat test
+# Or run with different modes
+python -m codeflow_engine.actions.quality_engine --mode fast
+python -m codeflow_engine.actions.quality_engine --mode smart
+python -m codeflow_engine.actions.quality_engine --mode ai_enhanced
 ```
 
 #### Option 2: Install Standard Python 3.13.5 (Highly Recommended)
@@ -55,7 +55,7 @@ If you want to keep Windows Store Python, you can create manual git hooks:
 ```bash
 #!/bin/sh
 echo "Running code quality checks..."
-python scripts/code_quality.py check
+python -m codeflow_engine.actions.quality_engine --mode fast
 if [ $? -ne 0 ]; then
     echo "Code quality checks failed. Please fix issues before committing."
     exit 1
@@ -79,8 +79,8 @@ python -m isort . --profile black
 python -m flake8 . --max-line-length 100
 python -m mypy . --config-file pyproject.toml
 
-# Or use our convenience script
-scripts\code_quality.bat check
+# Or use our convenience module
+python -m codeflow_engine.actions.quality_engine --mode comprehensive
 ```
 
 ### Commit Message Format
diff --git a/docs/testing/COVERAGE_GUIDE.md b/docs/testing/COVERAGE_GUIDE.md
index c8d9a42..aedcd21 100644
--- a/docs/testing/COVERAGE_GUIDE.md
+++ b/docs/testing/COVERAGE_GUIDE.md
@@ -57,13 +57,13 @@ open htmlcov/index.html
 
 **Bash:**
 ```bash
-./scripts/check-coverage.sh [threshold]
+./tools/coverage/check-coverage.sh [threshold]
 # Default threshold: 70%
 ```
 
 **PowerShell:**
 ```powershell
-.\scripts\check-coverage.ps1 -CoverageThreshold 70
+.\tools\coverage\check-coverage.ps1 -CoverageThreshold 70
 ```
 
 ### Coverage by Module
diff --git a/docs/testing/COVERAGE_IMPROVEMENT_PLAN.md b/docs/testing/COVERAGE_IMPROVEMENT_PLAN.md
index 4d38487..26788f2 100644
--- a/docs/testing/COVERAGE_IMPROVEMENT_PLAN.md
+++ b/docs/testing/COVERAGE_IMPROVEMENT_PLAN.md
@@ -359,7 +359,7 @@ poetry run pytest --cov=codeflow_engine --cov-report=html --cov-report=term
 poetry run coverage report --show-missing
 
 # Coverage check script
-./scripts/check-coverage.sh 70
+./tools/coverage/check-coverage.sh 70
 ```
 
 ### Coverage Analysis
diff --git a/docs/testing/QUICK_START_TESTING.md b/docs/testing/QUICK_START_TESTING.md
index f601a5c..bf63241 100644
--- a/docs/testing/QUICK_START_TESTING.md
+++ b/docs/testing/QUICK_START_TESTING.md
@@ -38,7 +38,7 @@ poetry run pytest --cov=codeflow_engine --cov-report=html
 open htmlcov/index.html
 
 # Or use the measurement script
-./scripts/measure-coverage.sh
+./tools/coverage/measure-coverage.sh
 ```
 
 ### 3. Run by Category
@@ -140,10 +140,10 @@ def test_with_sample_data():
 
 ```bash
 # Check if coverage meets threshold
-./scripts/check-coverage.sh 70
+./tools/coverage/check-coverage.sh 70
 
 # Or PowerShell
-.\scripts\check-coverage.ps1 -CoverageThreshold 70
+.\tools\coverage\check-coverage.ps1 -CoverageThreshold 70
 ```
 
 ---
diff --git a/pyproject.toml b/pyproject.toml
index ff64e58..84abcd5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -349,11 +349,8 @@ line-ending = "auto"
 docstring-code-format = true
 
 [tool.ruff.lint.per-file-ignores]
-# Allow print statements in scripts
-"scripts/**/*.py" = ["T201"]
-
-# Allow all issues in volume control scripts
-"scripts/volume-control/volume_knob.py" = ["ALL"]
+# Allow print statements in coverage tools
+"tools/coverage/**/*.py" = ["T201"]
 
 # Allow various issues in test files
 "tests/**/*.py" = [
@@ -367,26 +364,6 @@ docstring-code-format = true
     "DTZ005",  # datetime.now() without tz
 ]
 
-# Allow specific issues in volume-control scripts
-"scripts/volume-control/**/*.py" = [
-    "T201",  # print statements
-    "PTH110", "PTH123", "PTH103", "PTH107", "PTH118",  # pathlib issues
-    "PLR0911", "PLR0912", "PLR2004",  # complexity issues
-    "TRY003", "TRY300", "TRY301", "TRY302",  # try-except issues
-    "EM101", "EM102",  # exception message issues
-    "F811", "F821", "F841",  # pyflakes issues
-    "ARG002",  # unused arguments
-    "SIM102", "SIM105", "SIM117",  # simplify issues
-    "S603", "S607", "S110", "S112",  # security issues
-    "N814", "N999",  # naming issues
-    "RUF012",  # mutable class attributes
-    "FBT001", "FBT002",  # boolean issues
-    "A002",  # argument shadowing
-    "B904",  # exception chaining
-    "G004",  # logging f-strings
-    "PGH003",  # pygrep-hooks
-]
-
 # Allow specific issues in template discovery
 "templates/discovery/**/*.py" = [
     "PTH123",  # pathlib issues
diff --git a/templates/README.md b/templates/README.md
index 6707119..aecaa8c 100644
--- a/templates/README.md
+++ b/templates/README.md
@@ -126,7 +126,7 @@ All templates can be customized by:
 
 ### Template Validation
 
-Templates are validated using `scripts/validate_templates.py` to ensure:
+Templates are validated using `tools/scripts/validate_templates.py` to ensure:
 
 - Proper syntax and structure
 - Required parameters are defined
diff --git a/scripts/coverage/__init__.py b/tools/coverage/__init__.py
similarity index 61%
rename from scripts/coverage/__init__.py
rename to tools/coverage/__init__.py
index bf1053f..3bf05e5 100644
--- a/scripts/coverage/__init__.py
+++ b/tools/coverage/__init__.py
@@ -1,5 +1,5 @@
 """Coverage utilities for test quality gates."""
 
-from scripts.coverage.runner import CoverageRunner
+from tools.coverage.runner import CoverageRunner
 
 __all__ = ["CoverageRunner"]
diff --git a/scripts/check-coverage.ps1 b/tools/coverage/check-coverage.ps1
similarity index 76%
rename from scripts/check-coverage.ps1
rename to tools/coverage/check-coverage.ps1
index 7c7e295..2bfe542 100644
--- a/scripts/check-coverage.ps1
+++ b/tools/coverage/check-coverage.ps1
@@ -8,5 +8,4 @@ param(
 $ErrorActionPreference = 'Stop'
 
 # Use the unified Python coverage utility
-python -m scripts.coverage.runner check --threshold $CoverageThreshold
-
+python -m tools.coverage.runner check --threshold $CoverageThreshold
diff --git a/scripts/check-coverage.sh b/tools/coverage/check-coverage.sh
old mode 100644
new mode 100755
similarity index 73%
rename from scripts/check-coverage.sh
rename to tools/coverage/check-coverage.sh
index c16139a..823a326
--- a/scripts/check-coverage.sh
+++ b/tools/coverage/check-coverage.sh
@@ -7,5 +7,4 @@ set -e
 COVERAGE_THRESHOLD=${1:-70}
 
 # Use the unified Python coverage utility
-python -m scripts.coverage.runner check --threshold "$COVERAGE_THRESHOLD"
-
+python -m tools.coverage.runner check --threshold "$COVERAGE_THRESHOLD"
diff --git a/scripts/measure-coverage.ps1 b/tools/coverage/measure-coverage.ps1
similarity index 82%
rename from scripts/measure-coverage.ps1
rename to tools/coverage/measure-coverage.ps1
index fa0f764..66cf4c0 100644
--- a/scripts/measure-coverage.ps1
+++ b/tools/coverage/measure-coverage.ps1
@@ -4,5 +4,4 @@
 $ErrorActionPreference = 'Stop'
 
 # Use the unified Python coverage utility
-python -m scripts.coverage.runner measure
-
+python -m tools.coverage.runner measure
diff --git a/scripts/measure-coverage.sh b/tools/coverage/measure-coverage.sh
old mode 100644
new mode 100755
similarity index 81%
rename from scripts/measure-coverage.sh
rename to tools/coverage/measure-coverage.sh
index 5ba464c..ead21b1
--- a/scripts/measure-coverage.sh
+++ b/tools/coverage/measure-coverage.sh
@@ -5,5 +5,4 @@
 set -e
 
 # Use the unified Python coverage utility
-python -m scripts.coverage.runner measure
-
+python -m tools.coverage.runner measure
diff --git a/scripts/coverage/runner.py b/tools/coverage/runner.py
similarity index 100%
rename from scripts/coverage/runner.py
rename to tools/coverage/runner.py