diff --git a/.github/workflows/automation.yml b/.github/workflows/automation.yml
index 12d4e197..faadc048 100644
--- a/.github/workflows/automation.yml
+++ b/.github/workflows/automation.yml
@@ -28,9 +28,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -e .
-        pip install pytest pytest-cov pytest-mock pytest-asyncio pytest-timeout
+        pip install -e ".[dev]"
 
     - name: Run tests
       env:
@@ -97,5 +95,5 @@ jobs:
 
     - name: Check dependencies with safety
       run: |
-        pip install -r requirements.txt
+        pip install -e ".[dev]"
         safety check --full-report || echo "::warning::Vulnerable dependencies found."
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c7b63636..b2fe27bb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -60,7 +60,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('requirements*.txt') }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-pip-${{ matrix.python-version }}-
             ${{ runner.os }}-pip-
@@ -68,10 +68,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install -U pip
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
-          pip install -e .
-          pip install pytest pytest-cov pytest-timeout pytest-asyncio pytest-mock
+          pip install -e ".[dev]"
 
       - name: Run tests with coverage
         env:
diff --git a/AGENTS.md b/AGENTS.md
index 9f86e362..95100f68 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -37,8 +37,7 @@ cortex install nginx --dry-run
 ```bash
 python3 -m venv venv
 source venv/bin/activate
-pip install -e .
-pip install -r requirements-dev.txt
+pip install -e ".[dev]"
 pytest tests/ -v
 ```
 
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index a2edaebf..3048d5dc 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -123,24 +123,19 @@ git remote add upstream https://github.com/cortexlinux/cortex.git
 python3 -m venv venv
 source venv/bin/activate  # On Windows: venv\Scripts\activate
 
-# Install dependencies
-pip install -r requirements.txt
-pip install -r requirements-dev.txt
-
-# Install in development mode
-pip install -e .
+# Install in development mode (includes all dependencies)
+pip install -e ".[dev]"
 
 # Run tests to verify setup
 pytest tests/ -v
 ```
 
-### Requirements Files
-
-If `requirements-dev.txt` doesn't exist, install these manually:
+### Dependencies
 
-```bash
-pip install pytest pytest-cov pytest-mock black pylint mypy bandit
-```
+All dependencies are defined in `pyproject.toml`. To install:
+- **Core dependencies**: `pip install -e .`
+- **With dev tools**: `pip install -e ".[dev]"`
+- **All extras**: `pip install -e ".[all]"`
 
 ### IDE Setup
 
diff --git a/Makefile b/Makefile
index 35aab6c9..0074bdd5 100644
--- a/Makefile
+++ b/Makefile
@@ -18,8 +18,7 @@ help:
 
 dev:
 	$(PYTHON) -m pip install -U pip
-	$(PYTHON) -m pip install -e .
-	$(PYTHON) -m pip install -r requirements-dev.txt
+	$(PYTHON) -m pip install -e ".[dev]"
 	@echo "✅ Dev environment ready"
 
 test:
diff --git a/README.md b/README.md
index 19948549..174113c0 100644
--- a/README.md
+++ b/README.md
@@ -94,8 +94,12 @@ python3 -m venv venv
 source venv/bin/activate
 
 # 3. Install Cortex
+# Using pyproject.toml (recommended)
 pip install -e .
 
+# Or install with dev dependencies
+pip install -e ".[dev]"
+
 # 4. Configure AI Provider (choose one):
 
 ## Option A: Ollama (FREE - Local LLM, no API key needed)
diff --git a/docs/guides/Developer-Guide.md b/docs/guides/Developer-Guide.md
index 99e5ab7a..4a06cead 100644
--- a/docs/guides/Developer-Guide.md
+++ b/docs/guides/Developer-Guide.md
@@ -11,8 +11,7 @@ python3 -m venv venv
 source venv/bin/activate
 
 # Install dev dependencies
-pip install -r requirements.txt
-pip install -r requirements-dev.txt
+pip install -e ".[dev]"
 
 # Run tests
 pytest tests/
diff --git a/docs/guides/Getting-Started.md b/docs/guides/Getting-Started.md
index 89b84ce9..5984a413 100644
--- a/docs/guides/Getting-Started.md
+++ b/docs/guides/Getting-Started.md
@@ -12,8 +12,8 @@
 git clone https://github.com/cortexlinux/cortex.git
 cd cortex
 
-# Install dependencies
-pip install -r requirements.txt
+# Install Cortex
+pip install -e .
 
 # Configure API key
 export ANTHROPIC_API_KEY="your-key-here"
diff --git a/pyproject.toml b/pyproject.toml
index e59f5b83..2879e774 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,23 +42,36 @@ classifiers = [
 ]
 requires-python = ">=3.10"
 dependencies = [
+    # LLM Provider APIs
     "anthropic>=0.18.0",
     "openai>=1.0.0",
-    "rich>=13.0.0",
+    # HTTP requests (for GitHub API, network operations)
+    "requests>=2.32.4",
+    # Configuration file parsing
     "pyyaml>=6.0.0",
+    # Environment variable loading from .env files
     "python-dotenv>=1.0.0",
+    # Encryption for environment variable secrets
+    "cryptography>=42.0.0",
+    # Terminal UI and formatting
+    "rich>=13.0.0",
+    # Type hints for older Python versions
+    "typing-extensions>=4.0.0",
 ]
 
 [project.optional-dependencies]
 dev = [
     "pytest>=7.0.0",
     "pytest-cov>=4.0.0",
-    "pytest-timeout>=2.0.0",
-    "black>=23.0.0",
-    "ruff>=0.1.0",
+    "pytest-asyncio>=0.23.0",
+    "pytest-mock>=3.12.0",
+    "pytest-timeout>=2.3.0",
+    "black>=24.0.0",
+    "ruff>=0.8.0",
     "mypy>=1.0.0",
     "pre-commit>=3.0.0",
     "isort>=5.0.0",
+    "build>=0.10.0",
 ]
 security = [
     "bandit>=1.7.0",
diff --git a/requirements-dev.txt b/requirements-dev.txt
deleted file mode 100644
index 2ccb0205..00000000
--- a/requirements-dev.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-# Development Dependencies
-pytest>=7.0.0
-pytest-cov>=4.0.0
-pytest-asyncio>=0.23.0
-pytest-mock>=3.12.0
-pytest-timeout>=2.3.1
-black>=24.0.0
-ruff>=0.8.0
-isort>=5.13.0
-pre-commit>=3.0.0
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 166a777e..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-# Cortex Linux - Core Dependencies
-
-# LLM Provider APIs
-anthropic>=0.18.0
-openai>=1.0.0
-requests>=2.32.4
-
-# Configuration
-PyYAML>=6.0.0
-
-# Environment variable loading from .env files
-python-dotenv>=1.0.0
-
-# Encryption for environment variable secrets
-cryptography>=42.0.0
-
-# Terminal UI
-rich>=13.0.0
-
-# Configuration
-pyyaml>=6.0.0
-
-# Type hints for older Python versions
-typing-extensions>=4.0.0
-PyYAML==6.0.3
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 3a218042..00000000
--- a/setup.py
+++ /dev/null
@@ -1,54 +0,0 @@
-import os
-
-from setuptools import find_packages, setup
-
-with open("README.md", encoding="utf-8") as fh:
-    long_description = fh.read()
-
-# Try to read requirements from root, fallback to LLM directory
-requirements_path = "requirements.txt"
-if not os.path.exists(requirements_path):
-    requirements_path = os.path.join("LLM", "requirements.txt")
-
-if os.path.exists(requirements_path):
-    with open(requirements_path, encoding="utf-8") as fh:
-        requirements = [
-            line.strip()
-            for line in fh
-            if line.strip() and not line.startswith("#") and not line.startswith("-r")
-        ]
-else:
-    requirements = ["anthropic>=0.18.0", "openai>=1.0.0"]
-
-setup(
-    name="cortex-linux",
-    version="0.1.0",
-    author="Cortex Linux",
-    author_email="mike@cortexlinux.com",
-    description="AI-powered Linux command interpreter",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/cortexlinux/cortex",
-    packages=find_packages(),
-    classifiers=[
-        "Development Status :: 3 - Alpha",
-        "Intended Audience :: Developers",
-        "Intended Audience :: System Administrators",
-        "Topic :: System :: Installation/Setup",
-        "Topic :: System :: Systems Administration",
-        "License :: OSI Approved :: Apache Software License",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Programming Language :: Python :: 3.12",
-        "Operating System :: POSIX :: Linux",
-    ],
-    python_requires=">=3.10",
-    install_requires=requirements,
-    entry_points={
-        "console_scripts": [
-            "cortex=cortex.cli:main",
-        ],
-    },
-    include_package_data=True,
-)
diff --git a/tests/integration/test_end_to_end.py b/tests/integration/test_end_to_end.py
index 00776095..ebf36bb8 100644
--- a/tests/integration/test_end_to_end.py
+++ b/tests/integration/test_end_to_end.py
@@ -17,8 +17,8 @@
     "PYTHONPATH": "/workspace",
     "PYTHONDONTWRITEBYTECODE": "1",
 }
-PIP_BOOTSTRAP = "python -m pip install --quiet --upgrade pip setuptools && python -m pip install --quiet --no-cache-dir -r /workspace/requirements.txt"
-PIP_BOOTSTRAP_DEV = "python -m pip install --quiet --upgrade pip setuptools && python -m pip install --quiet --no-cache-dir -r /workspace/requirements.txt -r /workspace/requirements-dev.txt"
+PIP_BOOTSTRAP = "python -m pip install --quiet --upgrade pip setuptools build && python -m pip install --quiet --no-cache-dir -e /workspace"
+PIP_BOOTSTRAP_DEV = "python -m pip install --quiet --upgrade pip setuptools build && python -m pip install --quiet --no-cache-dir -e /workspace[dev]"
 
 
 @unittest.skipUnless(docker_available(), "Docker is required for integration tests")