diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000..44dd1d1
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,52 @@
+# EditorConfig - https://editorconfig.org
+# Helps maintain consistent coding styles across different editors
+
+root = true
+
+# Default settings for all files
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_style = space
+indent_size = 4
+
+# Rust files
+[*.rs]
+indent_size = 4
+max_line_length = 100
+
+# TOML files (Cargo.toml, etc.)
+[*.toml]
+indent_size = 4
+
+# YAML files
+[*.{yml,yaml}]
+indent_size = 2
+
+# JSON files
+[*.json]
+indent_size = 2
+
+# Markdown files
+[*.md]
+trim_trailing_whitespace = false
+max_line_length = off
+
+# Python files
+[*.py]
+indent_size = 4
+max_line_length = 100
+
+# Shell scripts
+[*.sh]
+indent_size = 2
+
+# Makefiles require tabs
+[Makefile]
+indent_style = tab
+
+# Git config files
+[.git*]
+indent_size = 4
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..4cb4704
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,247 @@
+name: CI
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:
+
+env:
+  CARGO_TERM_COLOR: always
+  RUST_BACKTRACE: 1
+  # Minimum supported Rust version
+  MSRV: "1.75"
+
+jobs:
+  # ==========================================================================
+  # Format check
+  # ==========================================================================
+  fmt:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: rustfmt
+
+      - name: Check formatting
+        run: cargo fmt --all -- --check
+
+  # ==========================================================================
+  # Clippy lints
+  # ==========================================================================
+  clippy:
+    name: Clippy
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: clippy
+
+      - name: Cache cargo
+        uses: Swatinem/rust-cache@v2
+
+      - name: Run Clippy
+        run: cargo clippy --all-targets --all-features -- -D warnings
+
+  # ==========================================================================
+  # Tests
+  # ==========================================================================
+  test:
+    name: Test (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache cargo
+        uses: Swatinem/rust-cache@v2
+
+      - name: Run tests
+        run: cargo test --all-features
+
+      - name: Run doc tests
+        run: cargo test --doc
+
+  # ==========================================================================
+  # MSRV check
+  # ==========================================================================
+  msrv:
+    name: MSRV (${{ env.MSRV }})
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust ${{ env.MSRV }}
+        uses: dtolnay/rust-toolchain@master
+        with:
+          toolchain: ${{ env.MSRV }}
+
+      - name: Cache cargo
+        uses: Swatinem/rust-cache@v2
+
+      - name: Check MSRV
+        run: cargo check --all-features
+
+  # ==========================================================================
+  # Documentation
+  # ==========================================================================
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache cargo
+        uses: Swatinem/rust-cache@v2
+
+      - name: Build docs
+        run: cargo doc --no-deps --all-features
+        env:
+          RUSTDOCFLAGS: -D warnings
+
+  # ==========================================================================
+  # Build
+  # ==========================================================================
+  build:
+    name: Build (${{ matrix.target }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - target: x86_64-unknown-linux-gnu
+            os: ubuntu-latest
+          - target: x86_64-unknown-linux-musl
+            os: ubuntu-latest
+          - target: aarch64-unknown-linux-gnu
+            os: ubuntu-latest
+          - target: x86_64-apple-darwin
+            os: macos-latest
+          - target: aarch64-apple-darwin
+            os: macos-latest
+          - target: x86_64-pc-windows-msvc
+            os: windows-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          targets: ${{ matrix.target }}
+
+      - name: Install cross-compilation tools
+        if: matrix.target == 'aarch64-unknown-linux-gnu'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gcc-aarch64-linux-gnu
+
+      - name: Install musl tools
+        if: matrix.target == 'x86_64-unknown-linux-musl'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y musl-tools
+
+      - name: Cache cargo
+        uses: Swatinem/rust-cache@v2
+        with:
+          key: ${{ matrix.target }}
+
+      - name: Build
+        run: cargo build --release --target ${{ matrix.target }}
+        env:
+          CARGO_TARGET_AARCH64_UNKNOWN_LINUX_GNU_LINKER: aarch64-linux-gnu-gcc
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: apc-${{ matrix.target }}
+          path: |
+            target/${{ matrix.target }}/release/apc
+            target/${{ matrix.target }}/release/apc.exe
+          if-no-files-found: ignore
+
+  # ==========================================================================
+  # Security audit
+  # ==========================================================================
+  security:
+    name: Security Audit
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install cargo-audit
+        run: cargo install cargo-audit
+
+      - name: Run audit
+        run: cargo audit
+
+  # ==========================================================================
+  # Coverage
+  # ==========================================================================
+  coverage:
+    name: Coverage
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: llvm-tools-preview
+
+      - name: Install cargo-llvm-cov
+        uses: taiki-e/install-action@cargo-llvm-cov
+
+      - name: Cache cargo
+        uses: Swatinem/rust-cache@v2
+
+      - name: Generate coverage
+        run: cargo llvm-cov --all-features --lcov --output-path lcov.info
+
+      - name: Upload to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: lcov.info
+          fail_ci_if_error: false
+
+  # ==========================================================================
+  # All checks passed
+  # ==========================================================================
+  ci-success:
+    name: CI Success
+    needs: [fmt, clippy, test, msrv, docs, build, security]
+    runs-on: ubuntu-latest
+    if: always()
+    steps:
+      - name: Check all jobs passed
+        run: |
+          if [[ "${{ needs.fmt.result }}" != "success" ]] || \
+             [[ "${{ needs.clippy.result }}" != "success" ]] || \
+             [[ "${{ needs.test.result }}" != "success" ]] || \
+             [[ "${{ needs.msrv.result }}" != "success" ]] || \
+             [[ "${{ needs.docs.result }}" != "success" ]] || \
+             [[ "${{ needs.build.result }}" != "success" ]] || \
+             [[ "${{ needs.security.result }}" != "success" ]]; then
+            echo "One or more jobs failed"
+            exit 1
+          fi
+          echo "All CI checks passed!"
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..8851d48
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,368 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: "Release tag (e.g., v0.1.0)"
+        required: true
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  # ==========================================================================
+  # Create release
+  # ==========================================================================
+  create-release:
+    name: Create Release
+    runs-on: ubuntu-latest
+    outputs:
+      upload_url: ${{ steps.create_release.outputs.upload_url }}
+      version: ${{ steps.get_version.outputs.version }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get version
+        id: get_version
+        run: |
+          if [ -n "${{ github.event.inputs.tag }}" ]; then
+            VERSION="${{ github.event.inputs.tag }}"
+          else
+            VERSION="${GITHUB_REF#refs/tags/}"
+          fi
+          echo "version=${VERSION}" >> $GITHUB_OUTPUT
+          echo "Version: ${VERSION}"
+
+      - name: Create Release
+        id: create_release
+        uses: softprops/action-gh-release@v1
+        with:
+          tag_name: ${{ steps.get_version.outputs.version }}
+          name: Release ${{ steps.get_version.outputs.version }}
+          draft: true
+          prerelease: ${{ contains(steps.get_version.outputs.version, '-') }}
+          generate_release_notes: true
+
+  # ==========================================================================
+  # Build binaries
+  # ==========================================================================
+  build-binaries:
+    name: Build (${{ matrix.target }})
+    needs: create-release
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # Linux x86_64 (glibc)
+          - target: x86_64-unknown-linux-gnu
+            os: ubuntu-latest
+            archive: tar.gz
+          # Linux x86_64 (musl - static)
+          - target: x86_64-unknown-linux-musl
+            os: ubuntu-latest
+            archive: tar.gz
+          # Linux ARM64
+          - target: aarch64-unknown-linux-gnu
+            os: ubuntu-latest
+            archive: tar.gz
+          # macOS x86_64
+          - target: x86_64-apple-darwin
+            os: macos-latest
+            archive: tar.gz
+          # macOS ARM64 (Apple Silicon)
+          - target: aarch64-apple-darwin
+            os: macos-latest
+            archive: tar.gz
+          # Windows x86_64
+          - target: x86_64-pc-windows-msvc
+            os: windows-latest
+            archive: zip
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          targets: ${{ matrix.target }}
+
+      - name: Install cross-compilation tools (Linux ARM64)
+        if: matrix.target == 'aarch64-unknown-linux-gnu'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gcc-aarch64-linux-gnu
+
+      - name: Install musl tools
+        if: matrix.target == 'x86_64-unknown-linux-musl'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y musl-tools
+
+      - name: Cache cargo
+        uses: Swatinem/rust-cache@v2
+        with:
+          key: release-${{ matrix.target }}
+
+      - name: Build release binary
+        run: cargo build --release --target ${{ matrix.target }}
+        env:
+          CARGO_TARGET_AARCH64_UNKNOWN_LINUX_GNU_LINKER: aarch64-linux-gnu-gcc
+
+      - name: Prepare archive (Unix)
+        if: matrix.os != 'windows-latest'
+        run: |
+          ARCHIVE_NAME="apc-${{ needs.create-release.outputs.version }}-${{ matrix.target }}"
+          mkdir -p "${ARCHIVE_NAME}"
+          cp "target/${{ matrix.target }}/release/apc" "${ARCHIVE_NAME}/"
+          cp Readme.md LICENSE* "${ARCHIVE_NAME}/" 2>/dev/null || true
+          tar -czvf "${ARCHIVE_NAME}.tar.gz" "${ARCHIVE_NAME}"
+          echo "ARCHIVE_NAME=${ARCHIVE_NAME}.tar.gz" >> $GITHUB_ENV
+
+      - name: Prepare archive (Windows)
+        if: matrix.os == 'windows-latest'
+        shell: pwsh
+        run: |
+          $ARCHIVE_NAME = "apc-${{ needs.create-release.outputs.version }}-${{ matrix.target }}"
+          New-Item -ItemType Directory -Force -Path $ARCHIVE_NAME
+          Copy-Item "target/${{ matrix.target }}/release/apc.exe" -Destination "$ARCHIVE_NAME/"
+          Copy-Item "Readme.md" -Destination "$ARCHIVE_NAME/" -ErrorAction SilentlyContinue
+          Compress-Archive -Path $ARCHIVE_NAME -DestinationPath "$ARCHIVE_NAME.zip"
+          echo "ARCHIVE_NAME=$ARCHIVE_NAME.zip" >> $env:GITHUB_ENV
+
+      - name: Upload release asset
+        uses: softprops/action-gh-release@v1
+        with:
+          tag_name: ${{ needs.create-release.outputs.version }}
+          files: ${{ env.ARCHIVE_NAME }}
+
+  # ==========================================================================
+  # Build Python wheels
+  # ==========================================================================
+  build-wheels:
+    name: Build Wheels (${{ matrix.os }})
+    needs: create-release
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Install maturin
+        run: pip install maturin
+
+      - name: Build wheels
+        run: |
+          maturin build --release --strip
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: target/wheels/*.whl
+
+  # ==========================================================================
+  # Publish to PyPI
+  # ==========================================================================
+  publish-pypi:
+    name: Publish to PyPI
+    needs: [create-release, build-wheels]
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - name: Download wheels
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          merge-multiple: true
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          skip-existing: true
+
+  # ==========================================================================
+  # Publish to crates.io
+  # ==========================================================================
+  publish-crates:
+    name: Publish to crates.io
+    needs: create-release
+    runs-on: ubuntu-latest
+    environment: crates-io
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Publish to crates.io
+        run: cargo publish
+        env:
+          CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
+
+  # ==========================================================================
+  # Update Homebrew
+  # ==========================================================================
+  update-homebrew:
+    name: Update Homebrew Formula
+    needs: [create-release, build-binaries]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Calculate checksums
+        run: |
+          VERSION="${{ needs.create-release.outputs.version }}"
+          BASE_URL="https://github.com/${{ github.repository }}/releases/download/${VERSION}"
+
+          # Download release assets and calculate checksums
+          for TARGET in x86_64-apple-darwin aarch64-apple-darwin x86_64-unknown-linux-gnu; do
+            ARCHIVE="apc-${VERSION}-${TARGET}.tar.gz"
+            curl -sL "${BASE_URL}/${ARCHIVE}" -o "${ARCHIVE}"
+            SHA=$(shasum -a 256 "${ARCHIVE}" | cut -d' ' -f1)
+            echo "${TARGET}_SHA256=${SHA}" >> $GITHUB_ENV
+          done
+
+      - name: Generate Homebrew formula
+        run: |
+          VERSION="${{ needs.create-release.outputs.version }}"
+          VERSION_NUM="${VERSION#v}"
+
+          cat > agent-precommit.rb << EOF
+          class AgentPrecommit < Formula
+            desc "Smart pre-commit hooks for humans and AI coding agents"
+            homepage "https://github.com/${{ github.repository }}"
+            version "${VERSION_NUM}"
+            license "MIT"
+
+            on_macos do
+              if Hardware::CPU.arm?
+                url "https://github.com/${{ github.repository }}/releases/download/${VERSION}/apc-${VERSION}-aarch64-apple-darwin.tar.gz"
+                sha256 "${{ env.aarch64-apple-darwin_SHA256 }}"
+              else
+                url "https://github.com/${{ github.repository }}/releases/download/${VERSION}/apc-${VERSION}-x86_64-apple-darwin.tar.gz"
+                sha256 "${{ env.x86_64-apple-darwin_SHA256 }}"
+              end
+            end
+
+            on_linux do
+              url "https://github.com/${{ github.repository }}/releases/download/${VERSION}/apc-${VERSION}-x86_64-unknown-linux-gnu.tar.gz"
+              sha256 "${{ env.x86_64-unknown-linux-gnu_SHA256 }}"
+            end
+
+            def install
+              bin.install "apc"
+            end
+
+            test do
+              system "#{bin}/apc", "--version"
+            end
+          end
+          EOF
+
+          cat agent-precommit.rb
+
+      - name: Upload formula
+        uses: actions/upload-artifact@v4
+        with:
+          name: homebrew-formula
+          path: agent-precommit.rb
+
+  # ==========================================================================
+  # Generate install script
+  # ==========================================================================
+  generate-install-script:
+    name: Generate Install Script
+    needs: create-release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Generate install.sh
+        run: |
+          VERSION="${{ needs.create-release.outputs.version }}"
+          cat > install.sh << 'SCRIPT'
+          #!/bin/sh
+          set -e
+
+          # agent-precommit installer
+          # Usage: curl -fsSL https://agent-precommit.dev/install.sh | sh
+
+          VERSION="${1:-latest}"
+          REPO="agent-precommit/agent-precommit"
+          INSTALL_DIR="${HOME}/.local/bin"
+
+          # Detect OS and architecture
+          OS=$(uname -s | tr '[:upper:]' '[:lower:]')
+          ARCH=$(uname -m)
+
+          case "${OS}" in
+            linux)
+              case "${ARCH}" in
+                x86_64) TARGET="x86_64-unknown-linux-gnu" ;;
+                aarch64) TARGET="aarch64-unknown-linux-gnu" ;;
+                *) echo "Unsupported architecture: ${ARCH}"; exit 1 ;;
+              esac
+              ;;
+            darwin)
+              case "${ARCH}" in
+                x86_64) TARGET="x86_64-apple-darwin" ;;
+                arm64) TARGET="aarch64-apple-darwin" ;;
+                *) echo "Unsupported architecture: ${ARCH}"; exit 1 ;;
+              esac
+              ;;
+            *)
+              echo "Unsupported OS: ${OS}"
+              exit 1
+              ;;
+          esac
+
+          # Get latest version if not specified
+          if [ "${VERSION}" = "latest" ]; then
+            VERSION=$(curl -sL "https://api.github.com/repos/${REPO}/releases/latest" | grep '"tag_name":' | sed -E 's/.*"([^"]+)".*/\1/')
+          fi
+
+          echo "Installing agent-precommit ${VERSION} for ${TARGET}..."
+
+          # Download and extract
+          ARCHIVE="apc-${VERSION}-${TARGET}.tar.gz"
+          URL="https://github.com/${REPO}/releases/download/${VERSION}/${ARCHIVE}"
+
+          mkdir -p "${INSTALL_DIR}"
+          curl -fsSL "${URL}" | tar -xz -C "${INSTALL_DIR}" --strip-components=1 apc-${VERSION}-${TARGET}/apc
+
+          chmod +x "${INSTALL_DIR}/apc"
+
+          echo ""
+          echo "✓ Installed apc to ${INSTALL_DIR}/apc"
+          echo ""
+          echo "Make sure ${INSTALL_DIR} is in your PATH:"
+          echo '  export PATH="${HOME}/.local/bin:${PATH}"'
+          echo ""
+          echo "Get started:"
+          echo "  apc init"
+          echo "  apc install"
+          SCRIPT
+
+          chmod +x install.sh
+
+      - name: Upload install script
+        uses: actions/upload-artifact@v4
+        with:
+          name: install-script
+          path: install.sh
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ae9a5ef
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,187 @@
+# =============================================================================
+# Rust
+# =============================================================================
+
+# Compiled files
+/target/
+**/*.rs.bk
+*.pdb
+
+# Cargo.lock for binaries (we track it for reproducible builds)
+# Uncomment if you want to ignore it:
+# Cargo.lock
+
+# =============================================================================
+# Python
+# =============================================================================
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Virtual environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Maturin
+target/wheels/
+
+# =============================================================================
+# IDE / Editors
+# =============================================================================
+
+# VS Code
+.vscode/
+*.code-workspace
+
+# IntelliJ IDEA
+.idea/
+*.iml
+*.ipr
+*.iws
+
+# Vim
+*.swp
+*.swo
+*~
+
+# Emacs
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Sublime Text
+*.sublime-workspace
+*.sublime-project
+
+# =============================================================================
+# OS-specific
+# =============================================================================
+
+# macOS
+.DS_Store
+.AppleDouble
+.LSOverride
+._*
+.Spotlight-V100
+.Trashes
+
+# Windows
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+*.stackdump
+[Dd]esktop.ini
+$RECYCLE.BIN/
+
+# Linux
+*~
+.fuse_hidden*
+.directory
+.Trash-*
+.nfs*
+
+# =============================================================================
+# Testing and benchmarking
+# =============================================================================
+
+# Test artifacts
+/tests/output/
+*.profraw
+*.profdata
+
+# Benchmarking
+/criterion/
+/flamegraph.svg
+/perf.data*
+
+# =============================================================================
+# Documentation
+# =============================================================================
+
+# Generated documentation
+/docs/_build/
+/site/
+
+# =============================================================================
+# Misc
+# =============================================================================
+
+# Secrets and credentials (NEVER commit these)
+.env.local
+.env.*.local
+*.pem
+*.key
+secrets.json
+credentials.json
+
+# Logs
+*.log
+logs/
+
+# Temporary files
+*.tmp
+*.temp
+.tmp/
+.temp/
+
+# Local configuration
+.local/
+*.local.toml
+*.local.yaml
+*.local.json
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..d05cf02
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,115 @@
+# Pre-commit configuration for agent-precommit
+# https://pre-commit.com
+
+repos:
+  # ==========================================================================
+  # General hooks
+  # ==========================================================================
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: check-added-large-files
+        args: ["--maxkb=1000"]
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: detect-private-key
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+
+  # ==========================================================================
+  # Rust hooks
+  # ==========================================================================
+  - repo: local
+    hooks:
+      # Format check
+      - id: cargo-fmt
+        name: cargo fmt
+        entry: cargo fmt --all -- --check
+        language: system
+        types: [rust]
+        pass_filenames: false
+
+      # Clippy lints
+      - id: cargo-clippy
+        name: cargo clippy
+        entry: cargo clippy --all-targets --all-features -- -D warnings
+        language: system
+        types: [rust]
+        pass_filenames: false
+
+      # Run tests
+      - id: cargo-test
+        name: cargo test
+        entry: cargo test --all-features
+        language: system
+        types: [rust]
+        pass_filenames: false
+        stages: [pre-push]
+
+      # Check for build errors
+      - id: cargo-check
+        name: cargo check
+        entry: cargo check --all-features
+        language: system
+        types: [rust]
+        pass_filenames: false
+
+  # ==========================================================================
+  # Python hooks (for Python wrapper)
+  # ==========================================================================
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.9
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+      - id: ruff-format
+
+  # ==========================================================================
+  # Markdown and documentation
+  # ==========================================================================
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.38.0
+    hooks:
+      - id: markdownlint
+        args: ["--fix", "--disable", "MD013", "MD033", "MD041", "--"]
+
+  # ==========================================================================
+  # YAML validation
+  # ==========================================================================
+  - repo: https://github.com/adrienverge/yamllint
+    rev: v1.33.0
+    hooks:
+      - id: yamllint
+        args: ["-d", "{extends: relaxed, rules: {line-length: disable}}"]
+
+  # ==========================================================================
+  # Security scanning
+  # ==========================================================================
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.18.1
+    hooks:
+      - id: gitleaks
+
+  # ==========================================================================
+  # Commit message format
+  # ==========================================================================
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v3.13.0
+    hooks:
+      - id: commitizen
+        stages: [commit-msg]
+
+# Default stages
+default_stages: [pre-commit]
+
+# CI configuration
+ci:
+  autofix_commit_msg: "style: auto-fix pre-commit hooks"
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autoupdate_schedule: monthly
+  skip: [cargo-test]
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..d51b9be
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,177 @@
+# Contributing to agent-precommit
+
+Thank you for your interest in contributing to agent-precommit! This document provides guidelines for contributing.
+
+## Development Setup
+
+### Prerequisites
+
+- Rust 1.75 or later
+- Python 3.8+ (for Python wrapper development)
+- Git
+
+### Getting Started
+
+1. Clone the repository:
+
+   ```bash
+   git clone https://github.com/agent-precommit/agent-precommit.git
+   cd agent-precommit
+   ```
+
+2. Install pre-commit hooks:
+
+   ```bash
+   pip install pre-commit
+   pre-commit install
+   ```
+
+3. Build the project:
+
+   ```bash
+   cargo build
+   ```
+
+4. Run tests:
+
+   ```bash
+   cargo test
+   ```
+
+## Code Quality Standards
+
+This project maintains extremely high code quality standards:
+
+### Rust
+
+- **Formatting**: All code must pass `cargo fmt --check`
+- **Linting**: All code must pass `cargo clippy` with no warnings
+- **Tests**: All tests must pass
+- **Documentation**: Public APIs must be documented
+
+### Linting Configuration
+
+The project uses strict Clippy linting. See `Cargo.toml` for the full configuration:
+
+- `unsafe_code = "deny"` - No unsafe code allowed
+- `unwrap_used = "deny"` - No `.unwrap()` calls
+- `expect_used = "deny"` - No `.expect()` calls
+- `panic = "deny"` - No explicit panics
+- `todo = "deny"` - No TODO macros in production code
+
+### Pre-commit Hooks
+
+The following checks run automatically on each commit:
+
+- `cargo fmt` - Code formatting
+- `cargo clippy` - Lints
+- `cargo check` - Compilation check
+- Various file quality checks
+
+## Making Changes
+
+### Branching
+
+- Create feature branches from `main`
+- Use descriptive branch names: `feature/add-go-preset`, `fix/timeout-handling`
+
+### Commits
+
+- Write clear, concise commit messages
+- Use conventional commit format:
+  - `feat:` for new features
+  - `fix:` for bug fixes
+  - `docs:` for documentation
+  - `refactor:` for code refactoring
+  - `test:` for tests
+  - `chore:` for maintenance
+
+### Pull Requests
+
+1. Ensure all CI checks pass
+2. Update documentation if needed
+3. Add tests for new functionality
+4. Request review from maintainers
+
+## Testing
+
+### Running Tests
+
+```bash
+# Run all tests
+cargo test
+
+# Run tests with output
+cargo test -- --nocapture
+
+# Run specific test
+cargo test test_name
+
+# Run integration tests
+cargo test --test '*'
+```
+
+### Writing Tests
+
+- Place unit tests in the same file as the code
+- Use the `#[cfg(test)]` attribute
+- Place integration tests in `tests/`
+- Aim for high coverage on critical paths
+
+## Documentation
+
+### Code Documentation
+
+- Document all public functions, structs, and modules
+- Use `///` for doc comments
+- Include examples where helpful
+
+### Building Docs
+
+```bash
+cargo doc --open
+```
+
+## Architecture Overview
+
+```text
+src/
+├── lib.rs           # Library root
+├── main.rs          # CLI entry point
+├── cli/             # CLI commands
+│   ├── mod.rs       # CLI structure
+│   └── commands.rs  # Command implementations
+├── config/          # Configuration handling
+│   └── mod.rs       # Config structs and loading
+├── core/            # Core functionality
+│   ├── mod.rs       # Module root
+│   ├── detector.rs  # Mode detection
+│   ├── error.rs     # Error types
+│   ├── executor.rs  # Command execution
+│   ├── git.rs       # Git operations
+│   └── runner.rs    # Check orchestration
+├── checks/          # Check implementations
+│   ├── mod.rs       # Module root
+│   ├── builtin.rs   # Built-in checks
+│   └── precommit.rs # Pre-commit integration
+└── presets/         # Configuration presets
+    └── mod.rs       # Preset definitions
+```
+
+## Release Process
+
+1. Update version in `Cargo.toml` and `pyproject.toml`
+2. Update CHANGELOG.md
+3. Create a git tag: `git tag v0.x.0`
+4. Push the tag: `git push origin v0.x.0`
+5. GitHub Actions handles the rest
+
+## Getting Help
+
+- Open an issue for bugs or feature requests
+- Check existing issues before creating new ones
+- Join discussions in pull requests
+
+## Code of Conduct
+
+Be respectful and inclusive. We welcome contributions from everyone.
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diff --git a/Cargo.toml b/Cargo.toml
new file mode 100644
index 0000000..118b34a
--- /dev/null
+++ b/Cargo.toml
@@ -0,0 +1,202 @@
+[package]
+name = "agent-precommit"
+version = "0.1.0"
+edition = "2021"
+rust-version = "1.75"
+authors = ["agent-precommit contributors"]
+description = "Smart pre-commit hooks for humans and AI coding agents"
+documentation = "https://docs.rs/agent-precommit"
+homepage = "https://github.com/agent-precommit/agent-precommit"
+repository = "https://github.com/agent-precommit/agent-precommit"
+readme = "Readme.md"
+license = "MIT"
+keywords = ["git", "precommit", "hooks", "ai", "agents"]
+categories = ["command-line-utilities", "development-tools"]
+
+[[bin]]
+name = "apc"
+path = "src/main.rs"
+
+[lib]
+name = "agent_precommit"
+path = "src/lib.rs"
+
+[dependencies]
+# CLI framework
+clap = { version = "4.5", features = ["derive", "env", "wrap_help", "string"] }
+clap_complete = "4.5"
+
+# Async runtime
+tokio = { version = "1.40", features = ["full"] }
+
+# Serialization
+serde = { version = "1.0", features = ["derive"] }
+serde_json = "1.0"
+toml = "0.8"
+
+# Error handling
+thiserror = "2.0"
+anyhow = "1.0"
+
+# Logging and output
+tracing = "0.1"
+tracing-subscriber = { version = "0.3", features = ["env-filter", "fmt", "ansi"] }
+
+# Terminal UI
+console = "0.15"
+indicatif = { version = "0.17", features = ["tokio"] }
+dialoguer = "0.11"
+
+# Process execution
+which = "7.0"
+
+# File system operations
+walkdir = "2.5"
+glob = "0.3"
+dirs = "6.0"
+
+# Git operations
+gix = { version = "0.68", default-features = false, features = ["blocking-http-transport-reqwest-rust-tls"] }
+
+# Time
+humantime = "2.1"
+chrono = { version = "0.4", default-features = false, features = ["clock", "std"] }
+
+# Regex for pattern matching
+regex = "1.11"
+
+[dev-dependencies]
+# Testing
+assert_cmd = "2.0"
+predicates = "3.1"
+tempfile = "3.14"
+rstest = "0.23"
+pretty_assertions = "1.4"
+insta = { version = "1.41", features = ["yaml", "redactions"] }
+mockall = "0.13"
+
+# Fuzzing support
+arbitrary = { version = "1.4", features = ["derive"] }
+
+# Benchmarking
+criterion = { version = "0.5", features = ["async_tokio"] }
+
+[[bench]]
+name = "benchmarks"
+harness = false
+
+[features]
+default = []
+# Enable additional checks during development
+dev = []
+
+[profile.release]
+lto = true
+codegen-units = 1
+panic = "abort"
+strip = true
+opt-level = 3
+
+[profile.dev]
+debug = true
+opt-level = 0
+
+[profile.dev.package."*"]
+opt-level = 2
+
+[profile.bench]
+debug = true
+
+# =============================================================================
+# Linting Configuration - Extremely Strict
+# =============================================================================
+
+[lints.rust]
+# Deny unsafe code by default
+unsafe_code = "deny"
+
+# Treat all warnings as errors
+warnings = "deny"
+
+# Future compatibility
+future_incompatible = { level = "deny", priority = -1 }
+rust_2018_idioms = { level = "deny", priority = -1 }
+rust_2021_compatibility = { level = "deny", priority = -1 }
+rust_2024_compatibility = { level = "warn", priority = -1 }
+
+# Documentation
+missing_docs = "warn"
+missing_debug_implementations = "warn"
+
+# Unsafe patterns
+let_underscore_drop = "deny"
+non_ascii_idents = "deny"
+
+[lints.clippy]
+# =============================================================================
+# Clippy Lint Groups - All set to deny/warn for maximum strictness
+# =============================================================================
+
+# Correctness - These are almost certainly bugs
+correctness = { level = "deny", priority = -1 }
+
+# Suspicious - Code that is most likely wrong or useless
+suspicious = { level = "deny", priority = -1 }
+
+# Style - Code that should be written in a more idiomatic way
+style = { level = "warn", priority = -1 }
+
+# Complexity - Code that does something simple but in a complex way
+complexity = { level = "warn", priority = -1 }
+
+# Performance - Code that can be written to run faster
+perf = { level = "warn", priority = -1 }
+
+# Pedantic - Lints which are rather strict or might have false positives
+pedantic = { level = "warn", priority = -1 }
+
+# Nursery - New lints that are still under development
+nursery = { level = "warn", priority = -1 }
+
+# =============================================================================
+# Individual Clippy Lints - Fine-grained control
+# =============================================================================
+
+# Absolutely deny these
+unwrap_used = "deny"
+expect_used = "deny"
+panic = "deny"
+todo = "deny"
+unimplemented = "deny"
+unreachable = "deny"
+dbg_macro = "deny"
+print_stdout = "deny"
+print_stderr = "deny"
+
+# Security-related
+hardcoded_credentials = "deny"
+
+# Error handling
+result_large_err = "warn"
+error_impl_error = "deny"
+
+# Code quality
+cognitive_complexity = "warn"
+too_many_lines = "warn"
+too_many_arguments = "warn"
+fn_params_excessive_bools = "warn"
+struct_excessive_bools = "warn"
+
+# Documentation
+missing_errors_doc = "warn"
+missing_panics_doc = "warn"
+missing_safety_doc = "deny"
+
+# Allow some pedantic lints that are too noisy
+module_name_repetitions = "allow"
+must_use_candidate = "allow"
+doc_markdown = "allow"
+
+[package.metadata.docs.rs]
+all-features = true
+rustdoc-args = ["--cfg", "docsrs"]
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..09173e6
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,109 @@
+# Makefile for agent-precommit development
+# Usage: make <target>
+
+.PHONY: all build release test lint fmt check clean install docs bench help
+
+# Default target
+all: fmt lint test build
+
+# Build debug version
+build:
+	cargo build
+
+# Build release version
+release:
+	cargo build --release
+
+# Run all tests
+test:
+	cargo test --all-features
+
+# Run tests with output
+test-verbose:
+	cargo test --all-features -- --nocapture
+
+# Run integration tests only
+test-integration:
+	cargo test --test '*'
+
+# Run lints (clippy)
+lint:
+	cargo clippy --all-targets --all-features -- -D warnings
+
+# Format code
+fmt:
+	cargo fmt --all
+
+# Check formatting
+fmt-check:
+	cargo fmt --all -- --check
+
+# Run all checks (format + lint + test)
+check: fmt-check lint test
+
+# Clean build artifacts
+clean:
+	cargo clean
+	rm -rf target/
+	rm -rf dist/
+	rm -rf *.egg-info/
+	find . -type d -name __pycache__ -exec rm -rf {} + 2>/dev/null || true
+
+# Install locally
+install:
+	cargo install --path .
+
+# Build documentation
+docs:
+	cargo doc --no-deps --open
+
+# Run benchmarks
+bench:
+	cargo bench
+
+# Security audit
+audit:
+	cargo audit
+
+# Update dependencies
+update:
+	cargo update
+
+# Generate coverage report
+coverage:
+	cargo llvm-cov --all-features --lcov --output-path lcov.info
+	cargo llvm-cov report --html
+
+# Build Python wheel
+wheel:
+	maturin build --release
+
+# Run pre-commit hooks
+pre-commit:
+	pre-commit run --all-files
+
+# Install development dependencies
+dev-setup:
+	rustup component add rustfmt clippy llvm-tools-preview
+	cargo install cargo-audit cargo-llvm-cov
+	pip install pre-commit maturin
+	pre-commit install
+
+# Show help
+help:
+	@echo "agent-precommit development targets:"
+	@echo ""
+	@echo "  make build        Build debug version"
+	@echo "  make release      Build release version"
+	@echo "  make test         Run all tests"
+	@echo "  make lint         Run Clippy lints"
+	@echo "  make fmt          Format code"
+	@echo "  make check        Run all checks (fmt + lint + test)"
+	@echo "  make clean        Clean build artifacts"
+	@echo "  make install      Install locally"
+	@echo "  make docs         Build and open documentation"
+	@echo "  make bench        Run benchmarks"
+	@echo "  make coverage     Generate coverage report"
+	@echo "  make wheel        Build Python wheel"
+	@echo "  make dev-setup    Install development dependencies"
+	@echo "  make help         Show this help"
diff --git a/agent-precommit.toml b/agent-precommit.toml
new file mode 100644
index 0000000..9201def
--- /dev/null
+++ b/agent-precommit.toml
@@ -0,0 +1,81 @@
+# agent-precommit configuration for the agent-precommit project itself
+# This serves as both a working example and dogfooding our own tool
+
+[detection]
+# Additional environment variables that indicate an agent
+agent_env_vars = []
+
+[integration]
+# We use pre-commit framework for base checks
+pre_commit = true
+pre_commit_path = ".pre-commit-config.yaml"
+
+[human]
+# Human mode: fast checks for quick iteration
+checks = ["pre-commit"]
+timeout = "30s"
+fail_fast = true
+
+[agent]
+# Agent mode: thorough checks for merge-ready commits
+checks = [
+    "pre-commit-all",
+    "no-merge-conflicts",
+    "fmt-check",
+    "clippy",
+    "test-unit",
+    "build-verify",
+]
+timeout = "15m"
+fail_fast = false
+
+# Run in parallel where possible
+parallel_groups = [
+    ["pre-commit-all", "no-merge-conflicts"],
+    ["fmt-check", "clippy"],
+    ["test-unit"],
+    ["build-verify"],
+]
+
+# =============================================================================
+# Check Definitions
+# =============================================================================
+
+[checks.pre-commit]
+run = "pre-commit run"
+description = "Run pre-commit on staged files"
+
+[checks.pre-commit-all]
+run = "pre-commit run --all-files"
+description = "Run pre-commit on all files"
+
+[checks.no-merge-conflicts]
+run = """
+git fetch origin main --quiet 2>/dev/null || git fetch origin master --quiet 2>/dev/null || true
+MAIN_BRANCH=$(git rev-parse --verify origin/main 2>/dev/null && echo "main" || echo "master")
+BASE=$(git merge-base HEAD origin/$MAIN_BRANCH 2>/dev/null || echo "")
+if [ -n "$BASE" ]; then
+    if git merge-tree $BASE HEAD origin/$MAIN_BRANCH 2>/dev/null | grep -q "^<<<<<<<"; then
+        echo "❌ Would conflict with $MAIN_BRANCH"
+        exit 1
+    fi
+fi
+echo "✓ No conflicts with main branch"
+"""
+description = "Check for merge conflicts with main/master"
+
+[checks.fmt-check]
+run = "cargo fmt --all -- --check"
+description = "Check Rust code formatting"
+
+[checks.clippy]
+run = "cargo clippy --all-targets --all-features -- -D warnings"
+description = "Run Clippy lints with strict warnings"
+
+[checks.test-unit]
+run = "cargo test --all-features"
+description = "Run all unit tests"
+
+[checks.build-verify]
+run = "cargo build --release"
+description = "Verify release build succeeds"
diff --git a/benches/benchmarks.rs b/benches/benchmarks.rs
new file mode 100644
index 0000000..2d5358e
--- /dev/null
+++ b/benches/benchmarks.rs
@@ -0,0 +1,34 @@
+//! Benchmarks for agent-precommit.
+
+use criterion::{black_box, criterion_group, criterion_main, Criterion};
+
+fn benchmark_mode_detection(c: &mut Criterion) {
+    c.bench_function("mode_detection", |b| {
+        b.iter(|| {
+            // Simple benchmark placeholder
+            // In a real benchmark, we'd test the detector
+            black_box(1 + 1)
+        });
+    });
+}
+
+fn benchmark_config_parsing(c: &mut Criterion) {
+    let toml_content = r#"
+[human]
+checks = ["pre-commit"]
+timeout = "30s"
+
+[agent]
+checks = ["pre-commit-all", "test-unit"]
+timeout = "15m"
+"#;
+
+    c.bench_function("config_parsing", |b| {
+        b.iter(|| {
+            let _: toml::Value = toml::from_str(black_box(toml_content)).unwrap();
+        });
+    });
+}
+
+criterion_group!(benches, benchmark_mode_detection, benchmark_config_parsing);
+criterion_main!(benches);
diff --git a/clippy.toml b/clippy.toml
new file mode 100644
index 0000000..9260f77
--- /dev/null
+++ b/clippy.toml
@@ -0,0 +1,79 @@
+# =============================================================================
+# Clippy Configuration - Strict Linting Thresholds
+# =============================================================================
+# This file provides additional configuration for Clippy lints
+# Main lint levels are configured in Cargo.toml under [lints.clippy]
+
+# Cognitive complexity threshold - functions more complex than this trigger a warning
+cognitive-complexity-threshold = 25
+
+# Maximum number of lines in a function before triggering too_many_lines
+too-many-lines-threshold = 100
+
+# Maximum number of function arguments before triggering too_many_arguments
+too-many-arguments-threshold = 7
+
+# Maximum number of bool parameters before triggering fn_params_excessive_bools
+max-fn-params-bools = 3
+
+# Maximum number of bool fields in a struct
+max-struct-bools = 3
+
+# MSRV - Minimum Supported Rust Version
+# This ensures suggested fixes are compatible with our rust-version in Cargo.toml
+msrv = "1.75"
+
+# Standard macros that should not trigger certain lints
+standard-macro-braces = []
+
+# Allowed duplicate modules for module_name_repetitions
+allowed-duplicate-crates = []
+
+# Type complexity threshold
+type-complexity-threshold = 250
+
+# Single char binding names allowed in specific contexts
+single-char-binding-names-threshold = 4
+
+# Trivial copy size limit (bytes)
+trivial-copy-size-limit = 16
+
+# Pass by value size limit (bytes)
+pass-by-value-size-limit = 256
+
+# Allowed wildcard imports (for tests)
+# allowed-wildcard-imports = ["crate::tests::*"]
+
+# Disallowed names (avoid generic names)
+disallowed-names = ["foo", "bar", "baz", "quux", "temp", "tmp"]
+
+# Enforce explicit return in closures
+accept-comment-above-statement = true
+accept-comment-above-attributes = true
+
+# Avoid assert in production code paths
+avoid-breaking-exported-api = true
+
+# Large error variant threshold for result_large_err
+large-error-threshold = 128
+
+# Future size threshold for large_futures lint
+future-size-threshold = 16384
+
+# Verbose bit mask threshold
+verbose-bit-mask-threshold = 1
+
+# Literal representation
+literal-representation-threshold = 16777215
+
+# Array size threshold for explicit iteration
+array-size-threshold = 512
+
+# Stack size threshold
+stack-size-threshold = 512000
+
+# Vec box size threshold
+vec-box-size-threshold = 4096
+
+# Allowed scripts for Unicode identifiers
+# We only allow ASCII identifiers (configured in Cargo.toml)
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..3ee25e4
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,80 @@
+[build-system]
+requires = ["maturin>=1.4,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "agent-precommit"
+version = "0.1.0"
+description = "Smart pre-commit hooks for humans and AI coding agents"
+readme = "Readme.md"
+license = { text = "MIT" }
+authors = [
+    { name = "agent-precommit contributors" }
+]
+keywords = ["git", "precommit", "hooks", "ai", "agents", "cli"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Rust",
+    "Topic :: Software Development :: Quality Assurance",
+    "Topic :: Software Development :: Version Control :: Git",
+]
+requires-python = ">=3.8"
+
+[project.urls]
+Homepage = "https://github.com/agent-precommit/agent-precommit"
+Documentation = "https://docs.rs/agent-precommit"
+Repository = "https://github.com/agent-precommit/agent-precommit"
+Changelog = "https://github.com/agent-precommit/agent-precommit/blob/main/CHANGELOG.md"
+
+[project.scripts]
+apc = "agent_precommit:main"
+agent-precommit = "agent_precommit:main"
+
+[tool.maturin]
+# Build only the binary, not a Python extension
+bindings = "bin"
+# Strip the binary for smaller size
+strip = true
+# Features to enable
+features = []
+# Module name
+module-name = "agent_precommit"
+
+# Compatibility settings
+compatibility = "manylinux2014"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+
+[tool.ruff]
+target-version = "py38"
+line-length = 100
+
+[tool.ruff.lint]
+select = [
+    "E",   # pycodestyle errors
+    "W",   # pycodestyle warnings
+    "F",   # pyflakes
+    "I",   # isort
+    "B",   # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "UP",  # pyupgrade
+]
+ignore = [
+    "E501",  # line too long, handled by formatter
+]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
diff --git a/python/agent_precommit/__init__.py b/python/agent_precommit/__init__.py
new file mode 100644
index 0000000..0674f22
--- /dev/null
+++ b/python/agent_precommit/__init__.py
@@ -0,0 +1,84 @@
+"""
+agent-precommit: Smart pre-commit hooks for humans and AI coding agents.
+
+This package provides a Python wrapper for the agent-precommit (apc) CLI tool.
+The actual binary is bundled with this package and called via subprocess.
+
+Usage:
+    $ apc init          # Initialize configuration
+    $ apc install       # Install git hook
+    $ apc run           # Run checks
+    $ apc detect        # Show detected mode
+"""
+
+import os
+import subprocess
+import sys
+from pathlib import Path
+
+__version__ = "0.1.0"
+__all__ = ["main", "run_apc"]
+
+
+def _get_binary_path() -> Path:
+    """Get the path to the bundled apc binary."""
+    # The binary is bundled in the same directory as this module
+    module_dir = Path(__file__).parent
+
+    if sys.platform == "win32":
+        binary_name = "apc.exe"
+    else:
+        binary_name = "apc"
+
+    binary_path = module_dir / binary_name
+
+    if not binary_path.exists():
+        # Fall back to looking in PATH
+        import shutil
+        found = shutil.which("apc")
+        if found:
+            return Path(found)
+        raise FileNotFoundError(
+            f"Could not find apc binary. Expected at {binary_path} or in PATH."
+        )
+
+    return binary_path
+
+
+def run_apc(*args: str) -> subprocess.CompletedProcess:
+    """
+    Run the apc binary with the given arguments.
+
+    Args:
+        *args: Command-line arguments to pass to apc.
+
+    Returns:
+        CompletedProcess with the result.
+
+    Example:
+        >>> result = run_apc("detect")
+        >>> print(result.stdout)
+    """
+    binary = _get_binary_path()
+    return subprocess.run(
+        [str(binary), *args],
+        capture_output=True,
+        text=True,
+    )
+
+
+def main() -> int:
+    """
+    Main entry point for the apc command.
+
+    This function is called when running `apc` or `agent-precommit` from the command line.
+    """
+    binary = _get_binary_path()
+
+    # Pass through all arguments to the binary
+    result = subprocess.run([str(binary), *sys.argv[1:]])
+    return result.returncode
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/rustfmt.toml b/rustfmt.toml
new file mode 100644
index 0000000..b9da50b
--- /dev/null
+++ b/rustfmt.toml
@@ -0,0 +1,69 @@
+# =============================================================================
+# Rustfmt Configuration - Consistent, Readable Code Style
+# =============================================================================
+# Using stable options only for maximum compatibility
+# Run with: cargo fmt
+# Check with: cargo fmt --check
+
+# Edition
+edition = "2021"
+
+# Maximum line width
+max_width = 100
+
+# Use 4 spaces for indentation
+tab_spaces = 4
+hard_tabs = false
+
+# Imports
+imports_granularity = "Module"
+group_imports = "StdExternalCrate"
+reorder_imports = true
+reorder_modules = true
+
+# Comments
+wrap_comments = true
+format_code_in_doc_comments = true
+doc_comment_code_block_width = 80
+normalize_comments = true
+normalize_doc_attributes = true
+
+# Formatting choices
+use_small_heuristics = "Default"
+fn_single_line = false
+where_single_line = false
+force_multiline_blocks = false
+format_strings = false
+
+# Struct and enum formatting
+struct_lit_single_line = true
+enum_discrim_align_threshold = 20
+
+# Match arms
+match_arm_blocks = true
+match_arm_leading_pipes = "Never"
+match_block_trailing_comma = true
+
+# Control flow
+control_brace_style = "AlwaysSameLine"
+brace_style = "SameLineWhere"
+
+# Other
+newline_style = "Unix"
+remove_nested_parens = true
+combine_control_expr = true
+overflow_delimited_expr = false
+trailing_comma = "Vertical"
+trailing_semicolon = true
+use_field_init_shorthand = true
+use_try_shorthand = true
+force_explicit_abi = true
+condense_wildcard_suffixes = false
+format_generated_files = true
+generated_marker_line_search_limit = 5
+hex_literal_case = "Lower"
+space_after_colon = true
+space_before_colon = false
+spaces_around_ranges = false
+binop_separator = "Front"
+type_punctuation_density = "Wide"
diff --git a/src/checks/builtin.rs b/src/checks/builtin.rs
new file mode 100644
index 0000000..1cbf56d
--- /dev/null
+++ b/src/checks/builtin.rs
@@ -0,0 +1,48 @@
+//! Built-in check definitions.
+//!
+//! These checks are available by default in all configurations.
+
+/// Names of built-in checks.
+pub mod names {
+    /// Run pre-commit on staged files.
+    pub const PRE_COMMIT: &str = "pre-commit";
+    /// Run pre-commit on all files.
+    pub const PRE_COMMIT_ALL: &str = "pre-commit-all";
+    /// Check for merge conflicts with main/master.
+    pub const NO_MERGE_CONFLICTS: &str = "no-merge-conflicts";
+    /// Run unit tests.
+    pub const TEST_UNIT: &str = "test-unit";
+    /// Run integration tests.
+    pub const TEST_INTEGRATION: &str = "test-integration";
+    /// Scan for secrets.
+    pub const SECURITY_SCAN: &str = "security-scan";
+    /// Verify build works.
+    pub const BUILD_VERIFY: &str = "build-verify";
+}
+
+/// Returns true if a check name is a built-in check.
+#[must_use]
+pub fn is_builtin(name: &str) -> bool {
+    matches!(
+        name,
+        names::PRE_COMMIT
+            | names::PRE_COMMIT_ALL
+            | names::NO_MERGE_CONFLICTS
+            | names::TEST_UNIT
+            | names::TEST_INTEGRATION
+            | names::SECURITY_SCAN
+            | names::BUILD_VERIFY
+    )
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_is_builtin() {
+        assert!(is_builtin("pre-commit"));
+        assert!(is_builtin("no-merge-conflicts"));
+        assert!(!is_builtin("custom-check"));
+    }
+}
diff --git a/src/checks/mod.rs b/src/checks/mod.rs
new file mode 100644
index 0000000..59c2f5e
--- /dev/null
+++ b/src/checks/mod.rs
@@ -0,0 +1,6 @@
+//! Built-in check implementations.
+//!
+//! This module provides the built-in checks that come with agent-precommit.
+
+pub mod builtin;
+pub mod precommit;
diff --git a/src/checks/precommit.rs b/src/checks/precommit.rs
new file mode 100644
index 0000000..a453ea0
--- /dev/null
+++ b/src/checks/precommit.rs
@@ -0,0 +1,77 @@
+//! Pre-commit framework integration.
+//!
+//! This module provides integration with the pre-commit framework.
+
+use crate::core::error::{Error, Result};
+use crate::core::executor::{ExecuteOptions, Executor};
+use std::path::Path;
+
+/// Path to the pre-commit config file.
+pub const PRE_COMMIT_CONFIG: &str = ".pre-commit-config.yaml";
+
+/// Checks if pre-commit is installed.
+pub fn is_installed() -> bool {
+    Executor::command_exists("pre-commit")
+}
+
+/// Checks if a pre-commit config exists.
+pub fn config_exists(repo_root: &Path) -> bool {
+    repo_root.join(PRE_COMMIT_CONFIG).exists()
+}
+
+/// Runs pre-commit on staged files.
+pub async fn run_staged(repo_root: &Path) -> Result<bool> {
+    run_with_args(repo_root, &[]).await
+}
+
+/// Runs pre-commit on all files.
+pub async fn run_all(repo_root: &Path) -> Result<bool> {
+    run_with_args(repo_root, &["--all-files"]).await
+}
+
+/// Runs pre-commit with custom arguments.
+async fn run_with_args(repo_root: &Path, args: &[&str]) -> Result<bool> {
+    if !is_installed() {
+        return Err(Error::PreCommitNotFound);
+    }
+
+    if !config_exists(repo_root) {
+        return Err(Error::PreCommitConfigNotFound {
+            path: repo_root.join(PRE_COMMIT_CONFIG),
+        });
+    }
+
+    let cmd = if args.is_empty() {
+        "pre-commit run".to_string()
+    } else {
+        format!("pre-commit run {}", args.join(" "))
+    };
+
+    let executor = Executor::new();
+    let output = executor
+        .execute(
+            &cmd,
+            ExecuteOptions::default()
+                .cwd(repo_root)
+                .capture_output(false),
+        )
+        .await?;
+
+    Ok(output.success())
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use tempfile::TempDir;
+
+    #[test]
+    fn test_config_exists() {
+        let temp = TempDir::new().expect("create temp dir");
+        assert!(!config_exists(temp.path()));
+
+        std::fs::write(temp.path().join(PRE_COMMIT_CONFIG), "repos: []")
+            .expect("write config");
+        assert!(config_exists(temp.path()));
+    }
+}
diff --git a/src/cli/commands.rs b/src/cli/commands.rs
new file mode 100644
index 0000000..f9aa8fd
--- /dev/null
+++ b/src/cli/commands.rs
@@ -0,0 +1,423 @@
+//! CLI command implementations.
+
+use crate::config::{Config, CONFIG_FILE_NAME};
+use crate::core::detector::{Detector, Mode};
+use crate::core::error::{Error, Result};
+use crate::core::git::GitRepo;
+use crate::core::runner::Runner;
+use console::style;
+use std::io::Write;
+use std::path::PathBuf;
+use std::process::ExitCode;
+
+/// Hook script template.
+const HOOK_SCRIPT: &str = r#"#!/bin/sh
+# agent-precommit hook - installed by `apc install`
+# https://github.com/agent-precommit/agent-precommit
+
+# Skip if APC_SKIP is set
+if [ "$APC_SKIP" = "1" ]; then
+    exit 0
+fi
+
+# Run agent-precommit
+exec apc run
+"#;
+
+/// Hook marker comment.
+const HOOK_MARKER: &str = "# agent-precommit hook";
+
+/// Initialize configuration.
+pub fn init(preset: Option<&str>, force: bool) -> Result<ExitCode> {
+    let config_path = PathBuf::from(CONFIG_FILE_NAME);
+
+    // Check if config already exists
+    if config_path.exists() && !force {
+        eprintln!(
+            "{} Configuration already exists: {}",
+            style("!").yellow(),
+            config_path.display()
+        );
+        eprintln!("  Use --force to overwrite.");
+        return Ok(ExitCode::FAILURE);
+    }
+
+    // Generate config
+    let config = match preset {
+        Some(p) => Config::for_preset(p),
+        None => {
+            // Auto-detect existing pre-commit config
+            let mut config = Config::default();
+            if PathBuf::from(".pre-commit-config.yaml").exists() {
+                config.integration.pre_commit = true;
+                eprintln!(
+                    "{} Detected .pre-commit-config.yaml - enabling integration",
+                    style("•").cyan()
+                );
+            }
+            config
+        }
+    };
+
+    // Write config
+    let toml = toml::to_string_pretty(&config)
+        .map_err(|e| Error::Internal {
+            message: format!("Failed to serialize config: {e}"),
+        })?;
+
+    std::fs::write(&config_path, toml).map_err(|e| Error::io("write config", e))?;
+
+    eprintln!(
+        "{} Created {}",
+        style("✓").green(),
+        config_path.display()
+    );
+
+    if let Some(p) = preset {
+        eprintln!("  Using preset: {p}");
+    }
+
+    eprintln!("\nNext steps:");
+    eprintln!("  1. Review and customize {CONFIG_FILE_NAME}");
+    eprintln!("  2. Run: apc install");
+
+    Ok(ExitCode::SUCCESS)
+}
+
+/// Install git hook.
+pub fn install(force: bool) -> Result<ExitCode> {
+    let repo = GitRepo::discover()?;
+    let hooks_dir = repo.hooks_dir();
+    let hook_path = hooks_dir.join("pre-commit");
+
+    // Create hooks directory if needed
+    if !hooks_dir.exists() {
+        std::fs::create_dir_all(&hooks_dir).map_err(|e| Error::io("create hooks dir", e))?;
+    }
+
+    // Check for existing hook
+    if hook_path.exists() {
+        let content =
+            std::fs::read_to_string(&hook_path).map_err(|e| Error::io("read existing hook", e))?;
+
+        // Check if it's our hook
+        if content.contains(HOOK_MARKER) {
+            eprintln!(
+                "{} Hook already installed at {}",
+                style("✓").green(),
+                hook_path.display()
+            );
+            return Ok(ExitCode::SUCCESS);
+        }
+
+        if !force {
+            return Err(Error::HookExists { path: hook_path });
+        }
+
+        // Backup existing hook
+        let backup_path = hooks_dir.join("pre-commit.bak");
+        std::fs::rename(&hook_path, &backup_path).map_err(|e| Error::io("backup hook", e))?;
+        eprintln!(
+            "{} Backed up existing hook to {}",
+            style("•").cyan(),
+            backup_path.display()
+        );
+    }
+
+    // Write hook
+    std::fs::write(&hook_path, HOOK_SCRIPT).map_err(|e| Error::io("write hook", e))?;
+
+    // Make executable on Unix
+    #[cfg(unix)]
+    {
+        use std::os::unix::fs::PermissionsExt;
+        let mut perms = std::fs::metadata(&hook_path)
+            .map_err(|e| Error::io("get hook metadata", e))?
+            .permissions();
+        perms.set_mode(0o755);
+        std::fs::set_permissions(&hook_path, perms).map_err(|e| Error::io("set hook perms", e))?;
+    }
+
+    eprintln!(
+        "{} Installed pre-commit hook at {}",
+        style("✓").green(),
+        hook_path.display()
+    );
+
+    Ok(ExitCode::SUCCESS)
+}
+
+/// Uninstall git hook.
+pub fn uninstall() -> Result<ExitCode> {
+    let repo = GitRepo::discover()?;
+    let hook_path = repo.hook_path("pre-commit");
+
+    if !hook_path.exists() {
+        eprintln!(
+            "{} No hook installed at {}",
+            style("•").cyan(),
+            hook_path.display()
+        );
+        return Ok(ExitCode::SUCCESS);
+    }
+
+    // Check if it's our hook
+    let content =
+        std::fs::read_to_string(&hook_path).map_err(|e| Error::io("read hook", e))?;
+
+    if !content.contains(HOOK_MARKER) {
+        eprintln!(
+            "{} Hook at {} was not installed by agent-precommit",
+            style("!").yellow(),
+            hook_path.display()
+        );
+        eprintln!("  Remove manually if desired.");
+        return Ok(ExitCode::FAILURE);
+    }
+
+    std::fs::remove_file(&hook_path).map_err(|e| Error::io("remove hook", e))?;
+
+    eprintln!(
+        "{} Removed pre-commit hook from {}",
+        style("✓").green(),
+        hook_path.display()
+    );
+
+    // Check for backup
+    let backup_path = repo.hooks_dir().join("pre-commit.bak");
+    if backup_path.exists() {
+        eprintln!(
+            "  Backup exists at {} - restore if needed",
+            backup_path.display()
+        );
+    }
+
+    Ok(ExitCode::SUCCESS)
+}
+
+/// Run checks.
+pub fn run(mode_override: Option<&str>, check: Option<&str>, _all: bool) -> Result<ExitCode> {
+    // Check for skip
+    if std::env::var("APC_SKIP").ok().as_deref() == Some("1") {
+        eprintln!("{} Skipping checks (APC_SKIP=1)", style("•").cyan());
+        return Ok(ExitCode::SUCCESS);
+    }
+
+    // Load config
+    let config = Config::load_or_default()?;
+
+    // Detect or override mode
+    let mode = if let Some(m) = mode_override {
+        m.parse().map_err(|e: String| Error::ConfigInvalid {
+            field: "mode".to_string(),
+            message: e,
+        })?
+    } else {
+        let detector = Detector::new(&config);
+        let detection = detector.detect();
+        eprintln!(
+            "{} Mode: {} ({})",
+            style("•").cyan(),
+            style(detection.mode.name()).bold(),
+            detection.reason
+        );
+        detection.mode
+    };
+
+    // Create runner
+    let runner = Runner::new(config);
+
+    // Run checks
+    let result = tokio::runtime::Runtime::new()
+        .map_err(|e| Error::Internal {
+            message: format!("Failed to create runtime: {e}"),
+        })?
+        .block_on(async {
+            if let Some(name) = check {
+                let check_result = runner.run_single(name, mode).await?;
+                Ok(crate::core::runner::RunResult {
+                    mode,
+                    checks: vec![check_result],
+                    duration: std::time::Duration::ZERO,
+                })
+            } else {
+                runner.run(mode).await
+            }
+        })?;
+
+    // Print summary
+    eprintln!();
+    if result.success() {
+        eprintln!(
+            "{} All checks passed ({} passed, {} skipped) in {:?}",
+            style("✓").green().bold(),
+            result.passed_count(),
+            result.skipped_count(),
+            result.duration
+        );
+        Ok(ExitCode::SUCCESS)
+    } else {
+        eprintln!(
+            "{} {} check(s) failed",
+            style("✗").red().bold(),
+            result.failed_count()
+        );
+
+        // Show failed check details
+        for check in result.failed_checks() {
+            eprintln!();
+            eprintln!("  {} {}", style("Failed:").red(), check.name);
+            if !check.output.combined_output().is_empty() {
+                for line in check.output.combined_output().lines().take(20) {
+                    eprintln!("    {line}");
+                }
+            }
+        }
+
+        Ok(ExitCode::FAILURE)
+    }
+}
+
+/// Show detected mode.
+pub fn detect() -> Result<ExitCode> {
+    let config = Config::load_or_default()?;
+    let detector = Detector::new(&config);
+    let detection = detector.detect();
+
+    eprintln!("Detected mode: {}", style(detection.mode.name()).bold());
+    eprintln!("Reason: {}", detection.reason);
+
+    // Show environment info
+    eprintln!();
+    eprintln!("Environment:");
+
+    let env_vars = ["APC_MODE", "AGENT_MODE", "CI", "GITHUB_ACTIONS"];
+    for var in env_vars {
+        if let Ok(value) = std::env::var(var) {
+            eprintln!("  {var}={value}");
+        }
+    }
+
+    eprintln!();
+    eprintln!("TTY: stdin={}, stdout={}",
+        std::io::stdin().is_terminal(),
+        std::io::stdout().is_terminal()
+    );
+
+    Ok(ExitCode::SUCCESS)
+}
+
+/// List configured checks.
+pub fn list(mode: Option<&str>) -> Result<ExitCode> {
+    let config = Config::load_or_default()?;
+
+    let mode: Option<Mode> = mode
+        .map(|m| m.parse())
+        .transpose()
+        .map_err(|e: String| Error::ConfigInvalid {
+            field: "mode".to_string(),
+            message: e,
+        })?;
+
+    // Print checks by mode
+    if mode.is_none() || mode == Some(Mode::Human) {
+        eprintln!("{}", style("Human mode checks:").bold());
+        for name in &config.human.checks {
+            print_check(&config, name);
+        }
+        eprintln!();
+    }
+
+    if mode.is_none() || mode == Some(Mode::Agent) || mode == Some(Mode::Ci) {
+        eprintln!("{}", style("Agent mode checks:").bold());
+        for name in &config.agent.checks {
+            print_check(&config, name);
+        }
+    }
+
+    Ok(ExitCode::SUCCESS)
+}
+
+/// Prints a check's details.
+fn print_check(config: &Config, name: &str) {
+    let check = config.checks.get(name);
+    let description = check
+        .map(|c| c.description.as_str())
+        .filter(|d| !d.is_empty())
+        .unwrap_or("(no description)");
+
+    eprintln!("  {} - {}", style(name).cyan(), description);
+}
+
+/// Validate configuration.
+pub fn validate() -> Result<ExitCode> {
+    match Config::load() {
+        Ok(config) => {
+            match config.validate() {
+                Ok(()) => {
+                    eprintln!("{} Configuration is valid", style("✓").green());
+                    Ok(ExitCode::SUCCESS)
+                }
+                Err(e) => {
+                    eprintln!("{} Configuration validation failed: {e}", style("✗").red());
+                    Ok(ExitCode::FAILURE)
+                }
+            }
+        }
+        Err(Error::ConfigNotFound { path }) => {
+            eprintln!(
+                "{} Configuration not found: {}",
+                style("!").yellow(),
+                path.display()
+            );
+            eprintln!("  Run: apc init");
+            Ok(ExitCode::FAILURE)
+        }
+        Err(e) => {
+            eprintln!("{} Failed to load configuration: {e}", style("✗").red());
+            Ok(ExitCode::FAILURE)
+        }
+    }
+}
+
+/// Show configuration.
+pub fn config(raw: bool) -> Result<ExitCode> {
+    match Config::find_config_file() {
+        Ok(path) => {
+            eprintln!("Configuration file: {}", path.display());
+
+            if raw {
+                let content =
+                    std::fs::read_to_string(&path).map_err(|e| Error::io("read config", e))?;
+                eprintln!();
+                std::io::stdout()
+                    .write_all(content.as_bytes())
+                    .map_err(|e| Error::io("write output", e))?;
+            }
+
+            Ok(ExitCode::SUCCESS)
+        }
+        Err(Error::ConfigNotFound { .. }) => {
+            eprintln!(
+                "{} No configuration file found",
+                style("!").yellow()
+            );
+            eprintln!("  Run: apc init");
+            Ok(ExitCode::FAILURE)
+        }
+        Err(e) => Err(e),
+    }
+}
+
+/// Generate shell completions.
+pub fn completions(shell: clap_complete::Shell) {
+    use clap::CommandFactory;
+    clap_complete::generate(
+        shell,
+        &mut super::Cli::command(),
+        "apc",
+        &mut std::io::stdout(),
+    );
+}
+
+use std::io::IsTerminal;
diff --git a/src/cli/mod.rs b/src/cli/mod.rs
new file mode 100644
index 0000000..996f41c
--- /dev/null
+++ b/src/cli/mod.rs
@@ -0,0 +1,243 @@
+//! Command-line interface for agent-precommit.
+//!
+//! This module provides the `apc` CLI with subcommands for:
+//! - `init`: Initialize configuration
+//! - `install`: Install git hook
+//! - `uninstall`: Remove git hook
+//! - `run`: Run checks manually
+//! - `detect`: Show detected mode
+//! - `list`: List configured checks
+//! - `validate`: Validate configuration
+
+mod commands;
+
+use crate::core::error::Result;
+use clap::{Parser, Subcommand};
+use std::process::ExitCode;
+use tracing_subscriber::EnvFilter;
+
+/// Smart pre-commit hooks for humans and AI coding agents.
+#[derive(Debug, Parser)]
+#[command(
+    name = "apc",
+    author,
+    version,
+    about = "Smart pre-commit hooks for humans and AI coding agents",
+    long_about = r#"
+agent-precommit (apc) provides intelligent pre-commit hooks that detect
+whether a commit is being made by a human or an AI coding agent.
+
+Human commits get fast, staged-only checks.
+Agent commits get thorough, merge-ready validation.
+
+Quick start:
+  apc init      # Create configuration
+  apc install   # Install git hook
+  # Done! Commits now auto-detect mode.
+
+Environment variables:
+  APC_MODE=human|agent|ci   Force a specific mode
+  AGENT_MODE=1              Trigger agent mode
+  APC_SKIP=1                Skip all checks
+"#,
+    propagate_version = true
+)]
+pub struct Cli {
+    /// Subcommand to run.
+    #[command(subcommand)]
+    pub command: Option<Commands>,
+
+    /// Enable verbose output.
+    #[arg(short, long, global = true)]
+    pub verbose: bool,
+
+    /// Suppress non-error output.
+    #[arg(short, long, global = true)]
+    pub quiet: bool,
+
+    /// Use color output.
+    #[arg(long, global = true, default_value = "auto")]
+    pub color: ColorChoice,
+}
+
+/// Color output choice.
+#[derive(Debug, Clone, Copy, PartialEq, Eq, Default, clap::ValueEnum)]
+pub enum ColorChoice {
+    /// Always use color.
+    Always,
+    /// Auto-detect color support.
+    #[default]
+    Auto,
+    /// Never use color.
+    Never,
+}
+
+/// Available subcommands.
+#[derive(Debug, Subcommand)]
+pub enum Commands {
+    /// Initialize agent-precommit configuration.
+    #[command(visible_alias = "i")]
+    Init {
+        /// Use a preset configuration.
+        #[arg(short, long, value_parser = ["python", "node", "rust", "go"])]
+        preset: Option<String>,
+
+        /// Overwrite existing configuration.
+        #[arg(short, long)]
+        force: bool,
+    },
+
+    /// Install the git pre-commit hook.
+    Install {
+        /// Overwrite existing hook.
+        #[arg(short, long)]
+        force: bool,
+    },
+
+    /// Remove the git pre-commit hook.
+    Uninstall,
+
+    /// Run checks manually.
+    #[command(visible_alias = "r")]
+    Run {
+        /// Force a specific mode.
+        #[arg(short, long, value_parser = ["human", "agent", "ci"])]
+        mode: Option<String>,
+
+        /// Run only a specific check.
+        #[arg(short, long)]
+        check: Option<String>,
+
+        /// Run all checks regardless of conditions.
+        #[arg(long)]
+        all: bool,
+    },
+
+    /// Show the detected mode and reasoning.
+    #[command(visible_alias = "d")]
+    Detect,
+
+    /// List all configured checks.
+    #[command(visible_alias = "l")]
+    List {
+        /// Show checks for a specific mode.
+        #[arg(short, long, value_parser = ["human", "agent", "ci"])]
+        mode: Option<String>,
+    },
+
+    /// Validate the configuration file.
+    #[command(visible_alias = "v")]
+    Validate,
+
+    /// Show configuration file location and contents.
+    Config {
+        /// Output raw TOML.
+        #[arg(long)]
+        raw: bool,
+    },
+
+    /// Generate shell completions.
+    Completions {
+        /// Shell to generate completions for.
+        #[arg(value_enum)]
+        shell: clap_complete::Shell,
+    },
+}
+
+/// Runs the CLI.
+pub fn run() -> Result<ExitCode> {
+    let cli = Cli::parse();
+
+    // Set up logging
+    setup_logging(cli.verbose, cli.quiet);
+
+    // Set up color
+    setup_color(cli.color);
+
+    // If no subcommand, run the default action (same as `apc run`)
+    match cli.command {
+        Some(Commands::Init { preset, force }) => commands::init(preset.as_deref(), force),
+        Some(Commands::Install { force }) => commands::install(force),
+        Some(Commands::Uninstall) => commands::uninstall(),
+        Some(Commands::Run { mode, check, all }) => {
+            commands::run(mode.as_deref(), check.as_deref(), all)
+        }
+        Some(Commands::Detect) => commands::detect(),
+        Some(Commands::List { mode }) => commands::list(mode.as_deref()),
+        Some(Commands::Validate) => commands::validate(),
+        Some(Commands::Config { raw }) => commands::config(raw),
+        Some(Commands::Completions { shell }) => {
+            commands::completions(shell);
+            Ok(ExitCode::SUCCESS)
+        }
+        None => commands::run(None, None, false),
+    }
+}
+
+/// Sets up logging based on verbosity flags.
+fn setup_logging(verbose: bool, quiet: bool) {
+    let filter = if quiet {
+        "error"
+    } else if verbose {
+        "debug"
+    } else {
+        "info"
+    };
+
+    let env_filter = EnvFilter::try_from_default_env()
+        .unwrap_or_else(|_| EnvFilter::new(filter));
+
+    tracing_subscriber::fmt()
+        .with_env_filter(env_filter)
+        .with_target(false)
+        .with_writer(std::io::stderr)
+        .init();
+}
+
+/// Sets up color output.
+fn setup_color(choice: ColorChoice) {
+    match choice {
+        ColorChoice::Always => {
+            console::set_colors_enabled(true);
+            console::set_colors_enabled_stderr(true);
+        }
+        ColorChoice::Never => {
+            console::set_colors_enabled(false);
+            console::set_colors_enabled_stderr(false);
+        }
+        ColorChoice::Auto => {
+            // Let console crate auto-detect
+        }
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_cli_parsing() {
+        // Test that CLI parses without errors
+        let cli = Cli::try_parse_from(["apc", "--help"]);
+        // --help causes early exit, so this will be an error
+        assert!(cli.is_err());
+    }
+
+    #[test]
+    fn test_cli_version() {
+        let cli = Cli::try_parse_from(["apc", "--version"]);
+        assert!(cli.is_err()); // --version causes early exit
+    }
+
+    #[test]
+    fn test_cli_subcommands() {
+        let cli = Cli::try_parse_from(["apc", "init"]);
+        assert!(cli.is_ok());
+
+        let cli = Cli::try_parse_from(["apc", "run", "--mode", "human"]);
+        assert!(cli.is_ok());
+
+        let cli = Cli::try_parse_from(["apc", "detect"]);
+        assert!(cli.is_ok());
+    }
+}
diff --git a/src/config/mod.rs b/src/config/mod.rs
new file mode 100644
index 0000000..57b1c23
--- /dev/null
+++ b/src/config/mod.rs
@@ -0,0 +1,653 @@
+//! Configuration handling for agent-precommit.
+//!
+//! This module provides configuration loading and validation,
+//! supporting both `agent-precommit.toml` files and sensible defaults.
+
+use crate::core::error::{Error, Result};
+use serde::{Deserialize, Serialize};
+use std::collections::HashMap;
+use std::path::{Path, PathBuf};
+
+/// Default configuration file name.
+pub const CONFIG_FILE_NAME: &str = "agent-precommit.toml";
+
+/// Main configuration structure.
+#[derive(Debug, Clone, Serialize, Deserialize)]
+#[serde(default)]
+pub struct Config {
+    /// Detection settings.
+    pub detection: DetectionConfig,
+    /// Integration with other tools.
+    pub integration: IntegrationConfig,
+    /// Human mode settings.
+    pub human: ModeConfig,
+    /// Agent mode settings.
+    pub agent: AgentModeConfig,
+    /// Check definitions.
+    #[serde(default)]
+    pub checks: HashMap<String, CheckConfig>,
+}
+
+impl Default for Config {
+    fn default() -> Self {
+        Self {
+            detection: DetectionConfig::default(),
+            integration: IntegrationConfig::default(),
+            human: ModeConfig::default_human(),
+            agent: AgentModeConfig::default(),
+            checks: default_checks(),
+        }
+    }
+}
+
+impl Config {
+    /// Loads configuration from the default location.
+    pub fn load() -> Result<Self> {
+        let path = Self::find_config_file()?;
+        Self::load_from(&path)
+    }
+
+    /// Loads configuration or returns defaults if not found.
+    pub fn load_or_default() -> Result<Self> {
+        match Self::find_config_file() {
+            Ok(path) => Self::load_from(&path),
+            Err(Error::ConfigNotFound { .. }) => Ok(Self::default()),
+            Err(e) => Err(e),
+        }
+    }
+
+    /// Loads configuration from a specific path.
+    pub fn load_from(path: &Path) -> Result<Self> {
+        let content = std::fs::read_to_string(path).map_err(|e| Error::io("read config", e))?;
+
+        let config: Self = toml::from_str(&content)
+            .map_err(|e| Error::config_parse_with_source("Failed to parse TOML", e))?;
+
+        config.validate()?;
+
+        Ok(config)
+    }
+
+    /// Finds the configuration file by searching up the directory tree.
+    pub fn find_config_file() -> Result<PathBuf> {
+        let cwd = std::env::current_dir().map_err(|e| Error::io("get current dir", e))?;
+
+        let mut current = cwd.as_path();
+        loop {
+            let config_path = current.join(CONFIG_FILE_NAME);
+            if config_path.exists() {
+                return Ok(config_path);
+            }
+
+            match current.parent() {
+                Some(parent) => current = parent,
+                None => break,
+            }
+        }
+
+        Err(Error::ConfigNotFound {
+            path: cwd.join(CONFIG_FILE_NAME),
+        })
+    }
+
+    /// Validates the configuration.
+    pub fn validate(&self) -> Result<()> {
+        // Validate timeouts are parseable
+        if humantime::parse_duration(&self.human.timeout).is_err() {
+            return Err(Error::ConfigInvalid {
+                field: "human.timeout".to_string(),
+                message: format!("Invalid duration: {}", self.human.timeout),
+            });
+        }
+
+        if humantime::parse_duration(&self.agent.timeout).is_err() {
+            return Err(Error::ConfigInvalid {
+                field: "agent.timeout".to_string(),
+                message: format!("Invalid duration: {}", self.agent.timeout),
+            });
+        }
+
+        Ok(())
+    }
+
+    /// Generates default configuration as a string.
+    #[must_use]
+    pub fn default_toml() -> String {
+        let config = Self::default();
+        toml::to_string_pretty(&config).unwrap_or_default()
+    }
+
+    /// Generates configuration for a specific preset.
+    #[must_use]
+    pub fn for_preset(preset: &str) -> Self {
+        let mut config = Self::default();
+
+        match preset {
+            "python" => {
+                config.agent.checks = vec![
+                    "pre-commit-all".to_string(),
+                    "no-merge-conflicts".to_string(),
+                    "test-unit".to_string(),
+                    "test-integration".to_string(),
+                    "security-scan".to_string(),
+                    "build-verify".to_string(),
+                ];
+                config.checks.extend(python_checks());
+            }
+            "node" | "nodejs" | "typescript" => {
+                config.agent.checks = vec![
+                    "pre-commit-all".to_string(),
+                    "no-merge-conflicts".to_string(),
+                    "lint".to_string(),
+                    "typecheck".to_string(),
+                    "test-unit".to_string(),
+                    "build-verify".to_string(),
+                ];
+                config.checks.extend(node_checks());
+            }
+            "rust" => {
+                config.agent.checks = vec![
+                    "no-merge-conflicts".to_string(),
+                    "fmt-check".to_string(),
+                    "clippy".to_string(),
+                    "test-unit".to_string(),
+                    "build-verify".to_string(),
+                ];
+                config.checks.extend(rust_checks());
+            }
+            "go" => {
+                config.agent.checks = vec![
+                    "no-merge-conflicts".to_string(),
+                    "fmt-check".to_string(),
+                    "lint".to_string(),
+                    "test-unit".to_string(),
+                    "build-verify".to_string(),
+                ];
+                config.checks.extend(go_checks());
+            }
+            _ => {}
+        }
+
+        config
+    }
+}
+
+/// Detection configuration.
+#[derive(Debug, Clone, Serialize, Deserialize, Default)]
+#[serde(default)]
+pub struct DetectionConfig {
+    /// Force a specific mode (overrides auto-detection).
+    pub mode: Option<String>,
+    /// Additional environment variables that indicate an agent.
+    pub agent_env_vars: Vec<String>,
+}
+
+/// Integration configuration.
+#[derive(Debug, Clone, Serialize, Deserialize)]
+#[serde(default)]
+pub struct IntegrationConfig {
+    /// Enable pre-commit framework integration.
+    pub pre_commit: bool,
+    /// Path to pre-commit config file.
+    pub pre_commit_path: String,
+}
+
+impl Default for IntegrationConfig {
+    fn default() -> Self {
+        Self {
+            pre_commit: false,
+            pre_commit_path: ".pre-commit-config.yaml".to_string(),
+        }
+    }
+}
+
+/// Mode-specific configuration.
+#[derive(Debug, Clone, Serialize, Deserialize)]
+#[serde(default)]
+pub struct ModeConfig {
+    /// Checks to run in this mode.
+    pub checks: Vec<String>,
+    /// Timeout for all checks.
+    pub timeout: String,
+    /// Whether to stop on first failure.
+    pub fail_fast: bool,
+}
+
+impl ModeConfig {
+    fn default_human() -> Self {
+        Self {
+            checks: vec!["pre-commit".to_string()],
+            timeout: "30s".to_string(),
+            fail_fast: true,
+        }
+    }
+}
+
+impl Default for ModeConfig {
+    fn default() -> Self {
+        Self::default_human()
+    }
+}
+
+/// Agent mode configuration with parallel execution support.
+#[derive(Debug, Clone, Serialize, Deserialize)]
+#[serde(default)]
+pub struct AgentModeConfig {
+    /// Checks to run in agent mode.
+    pub checks: Vec<String>,
+    /// Timeout for all checks.
+    pub timeout: String,
+    /// Whether to stop on first failure.
+    pub fail_fast: bool,
+    /// Groups of checks that can run in parallel.
+    pub parallel_groups: Vec<Vec<String>>,
+}
+
+impl Default for AgentModeConfig {
+    fn default() -> Self {
+        Self {
+            checks: vec![
+                "pre-commit-all".to_string(),
+                "no-merge-conflicts".to_string(),
+                "test-unit".to_string(),
+            ],
+            timeout: "15m".to_string(),
+            fail_fast: false,
+            parallel_groups: Vec::new(),
+        }
+    }
+}
+
+/// Configuration for a single check.
+#[derive(Debug, Clone, Serialize, Deserialize)]
+#[serde(default)]
+pub struct CheckConfig {
+    /// Command to run.
+    pub run: String,
+    /// Human-readable description.
+    pub description: String,
+    /// Condition for enabling the check.
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub enabled_if: Option<EnabledCondition>,
+    /// Environment variables to set.
+    #[serde(default)]
+    pub env: HashMap<String, String>,
+}
+
+impl Default for CheckConfig {
+    fn default() -> Self {
+        Self {
+            run: String::new(),
+            description: String::new(),
+            enabled_if: None,
+            env: HashMap::new(),
+        }
+    }
+}
+
+impl CheckConfig {
+    /// Creates a check config from a simple command.
+    #[must_use]
+    pub fn from_command(cmd: String) -> Self {
+        Self {
+            run: cmd.clone(),
+            description: cmd,
+            enabled_if: None,
+            env: HashMap::new(),
+        }
+    }
+}
+
+/// Condition for enabling a check.
+#[derive(Debug, Clone, Serialize, Deserialize, Default)]
+#[serde(default)]
+pub struct EnabledCondition {
+    /// Check if a file exists.
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub file_exists: Option<String>,
+    /// Check if a directory exists.
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub dir_exists: Option<String>,
+    /// Check if a command exists in PATH.
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub command_exists: Option<String>,
+}
+
+/// Default checks for all configurations.
+fn default_checks() -> HashMap<String, CheckConfig> {
+    let mut checks = HashMap::new();
+
+    checks.insert(
+        "pre-commit".to_string(),
+        CheckConfig {
+            run: "pre-commit run".to_string(),
+            description: "Run pre-commit on staged files".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some(".pre-commit-config.yaml".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "pre-commit-all".to_string(),
+        CheckConfig {
+            run: "pre-commit run --all-files".to_string(),
+            description: "Run pre-commit on all files".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some(".pre-commit-config.yaml".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "no-merge-conflicts".to_string(),
+        CheckConfig {
+            run: r#"
+git fetch origin main --quiet 2>/dev/null || git fetch origin master --quiet 2>/dev/null || true
+MAIN_BRANCH=$(git rev-parse --verify origin/main 2>/dev/null && echo "main" || echo "master")
+BASE=$(git merge-base HEAD origin/$MAIN_BRANCH 2>/dev/null || echo "")
+if [ -n "$BASE" ]; then
+    if git merge-tree $BASE HEAD origin/$MAIN_BRANCH 2>/dev/null | grep -q "^<<<<<<<"; then
+        echo "❌ Would conflict with $MAIN_BRANCH"
+        exit 1
+    fi
+fi
+echo "✓ No conflicts with $MAIN_BRANCH"
+"#
+            .trim()
+            .to_string(),
+            description: "Ensure no merge conflicts with main/master".to_string(),
+            enabled_if: None,
+            env: HashMap::new(),
+        },
+    );
+
+    checks
+}
+
+/// Python-specific checks.
+fn python_checks() -> HashMap<String, CheckConfig> {
+    let mut checks = HashMap::new();
+
+    checks.insert(
+        "test-unit".to_string(),
+        CheckConfig {
+            run: "pytest -x -q".to_string(),
+            description: "Run unit tests".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("pyproject.toml".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "test-integration".to_string(),
+        CheckConfig {
+            run: "pytest tests/integration/ -v".to_string(),
+            description: "Run integration tests".to_string(),
+            enabled_if: Some(EnabledCondition {
+                dir_exists: Some("tests/integration".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "security-scan".to_string(),
+        CheckConfig {
+            run: "gitleaks detect --source . --no-git".to_string(),
+            description: "Scan for secrets".to_string(),
+            enabled_if: Some(EnabledCondition {
+                command_exists: Some("gitleaks".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "build-verify".to_string(),
+        CheckConfig {
+            run: "python -m build --no-isolation".to_string(),
+            description: "Verify package builds".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("pyproject.toml".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks
+}
+
+/// Node.js/TypeScript checks.
+fn node_checks() -> HashMap<String, CheckConfig> {
+    let mut checks = HashMap::new();
+
+    checks.insert(
+        "lint".to_string(),
+        CheckConfig {
+            run: "npm run lint".to_string(),
+            description: "Run ESLint".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("package.json".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "typecheck".to_string(),
+        CheckConfig {
+            run: "npm run typecheck || npx tsc --noEmit".to_string(),
+            description: "Run TypeScript type checking".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("tsconfig.json".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "test-unit".to_string(),
+        CheckConfig {
+            run: "npm test".to_string(),
+            description: "Run unit tests".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("package.json".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "build-verify".to_string(),
+        CheckConfig {
+            run: "npm run build".to_string(),
+            description: "Verify build works".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("package.json".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks
+}
+
+/// Rust checks.
+fn rust_checks() -> HashMap<String, CheckConfig> {
+    let mut checks = HashMap::new();
+
+    checks.insert(
+        "fmt-check".to_string(),
+        CheckConfig {
+            run: "cargo fmt --all -- --check".to_string(),
+            description: "Check code formatting".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("Cargo.toml".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "clippy".to_string(),
+        CheckConfig {
+            run: "cargo clippy --all-targets --all-features -- -D warnings".to_string(),
+            description: "Run Clippy lints".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("Cargo.toml".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "test-unit".to_string(),
+        CheckConfig {
+            run: "cargo test".to_string(),
+            description: "Run unit tests".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("Cargo.toml".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "build-verify".to_string(),
+        CheckConfig {
+            run: "cargo build --release".to_string(),
+            description: "Verify release build".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("Cargo.toml".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks
+}
+
+/// Go checks.
+fn go_checks() -> HashMap<String, CheckConfig> {
+    let mut checks = HashMap::new();
+
+    checks.insert(
+        "fmt-check".to_string(),
+        CheckConfig {
+            run: "test -z \"$(gofmt -l .)\"".to_string(),
+            description: "Check code formatting".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("go.mod".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "lint".to_string(),
+        CheckConfig {
+            run: "golangci-lint run".to_string(),
+            description: "Run golangci-lint".to_string(),
+            enabled_if: Some(EnabledCondition {
+                command_exists: Some("golangci-lint".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "test-unit".to_string(),
+        CheckConfig {
+            run: "go test ./...".to_string(),
+            description: "Run unit tests".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("go.mod".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks.insert(
+        "build-verify".to_string(),
+        CheckConfig {
+            run: "go build ./...".to_string(),
+            description: "Verify build works".to_string(),
+            enabled_if: Some(EnabledCondition {
+                file_exists: Some("go.mod".to_string()),
+                ..Default::default()
+            }),
+            env: HashMap::new(),
+        },
+    );
+
+    checks
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_default_config() {
+        let config = Config::default();
+        assert!(!config.human.checks.is_empty());
+        assert!(!config.agent.checks.is_empty());
+    }
+
+    #[test]
+    fn test_config_validation() {
+        let config = Config::default();
+        assert!(config.validate().is_ok());
+    }
+
+    #[test]
+    fn test_invalid_timeout() {
+        let mut config = Config::default();
+        config.human.timeout = "invalid".to_string();
+        assert!(config.validate().is_err());
+    }
+
+    #[test]
+    fn test_preset_python() {
+        let config = Config::for_preset("python");
+        assert!(config.checks.contains_key("test-unit"));
+        assert!(config.checks.contains_key("build-verify"));
+    }
+
+    #[test]
+    fn test_preset_rust() {
+        let config = Config::for_preset("rust");
+        assert!(config.checks.contains_key("clippy"));
+        assert!(config.checks.contains_key("fmt-check"));
+    }
+
+    #[test]
+    fn test_default_toml_generation() {
+        let toml = Config::default_toml();
+        assert!(!toml.is_empty());
+        assert!(toml.contains("[human]"));
+        assert!(toml.contains("[agent]"));
+    }
+}
diff --git a/src/core/detector.rs b/src/core/detector.rs
new file mode 100644
index 0000000..8dcbb91
--- /dev/null
+++ b/src/core/detector.rs
@@ -0,0 +1,333 @@
+//! Mode detection for distinguishing human vs agent commits.
+//!
+//! The detector analyzes the environment to determine whether a commit
+//! is being made by a human developer or an AI coding agent.
+
+use crate::config::Config;
+use std::env;
+use std::io::IsTerminal;
+
+/// The detected commit mode.
+#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Default)]
+pub enum Mode {
+    /// Human developer - fast checks, staged files only.
+    #[default]
+    Human,
+    /// AI coding agent - thorough checks, full codebase.
+    Agent,
+    /// CI environment - same as agent, possibly with extra reporting.
+    Ci,
+}
+
+impl Mode {
+    /// Returns a human-readable name for the mode.
+    #[must_use]
+    pub const fn name(&self) -> &'static str {
+        match self {
+            Self::Human => "human",
+            Self::Agent => "agent",
+            Self::Ci => "ci",
+        }
+    }
+
+    /// Returns whether this mode requires thorough checks.
+    #[must_use]
+    pub const fn is_thorough(&self) -> bool {
+        matches!(self, Self::Agent | Self::Ci)
+    }
+}
+
+impl std::fmt::Display for Mode {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        write!(f, "{}", self.name())
+    }
+}
+
+impl std::str::FromStr for Mode {
+    type Err = String;
+
+    fn from_str(s: &str) -> std::result::Result<Self, Self::Err> {
+        match s.to_lowercase().as_str() {
+            "human" => Ok(Self::Human),
+            "agent" => Ok(Self::Agent),
+            "ci" => Ok(Self::Ci),
+            _ => Err(format!("Invalid mode: {s}. Expected: human, agent, or ci")),
+        }
+    }
+}
+
+/// Reason for mode detection - useful for debugging.
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub enum DetectionReason {
+    /// Mode set via APC_MODE environment variable.
+    ExplicitApcMode(String),
+    /// Mode set via AGENT_MODE environment variable.
+    ExplicitAgentMode,
+    /// Known agent environment variable detected.
+    KnownAgentEnvVar(String),
+    /// Custom agent environment variable from config.
+    CustomAgentEnvVar(String),
+    /// CI environment detected.
+    CiEnvironment(String),
+    /// No TTY detected (non-interactive).
+    NoTty,
+    /// Default fallback to human mode.
+    Default,
+}
+
+impl std::fmt::Display for DetectionReason {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Self::ExplicitApcMode(value) => write!(f, "APC_MODE={value}"),
+            Self::ExplicitAgentMode => write!(f, "AGENT_MODE=1"),
+            Self::KnownAgentEnvVar(var) => write!(f, "Known agent env var: {var}"),
+            Self::CustomAgentEnvVar(var) => write!(f, "Custom agent env var: {var}"),
+            Self::CiEnvironment(var) => write!(f, "CI environment: {var}"),
+            Self::NoTty => write!(f, "No TTY detected (non-interactive)"),
+            Self::Default => write!(f, "Default (no agent indicators)"),
+        }
+    }
+}
+
+/// Result of mode detection.
+#[derive(Debug, Clone)]
+pub struct Detection {
+    /// The detected mode.
+    pub mode: Mode,
+    /// Reason for the detection.
+    pub reason: DetectionReason,
+}
+
+/// Detector for determining commit mode.
+#[derive(Debug)]
+pub struct Detector<'a> {
+    config: &'a Config,
+}
+
+/// Known environment variables that indicate an AI agent.
+const KNOWN_AGENT_ENV_VARS: &[&str] = &[
+    // Claude Code
+    "CLAUDE_CODE",
+    "ANTHROPIC_PROJECT_ID",
+    // Cursor
+    "CURSOR_SESSION",
+    "CURSOR_TRACE_ID",
+    // Aider
+    "AIDER_MODEL",
+    "AIDER_CHAT_HISTORY_FILE",
+    // OpenAI Codex / ChatGPT
+    "CODEX_SESSION",
+    "OPENAI_API_KEY_FOR_AGENT",
+    // Devin
+    "DEVIN_SESSION",
+    "DEVIN_API_KEY",
+    // Cline
+    "CLINE_SESSION",
+    "CLINE_API_KEY",
+    // Continue.dev
+    "CONTINUE_SESSION",
+    "CONTINUE_GLOBAL_DIR",
+    // GitHub Copilot Workspace
+    "GITHUB_COPILOT_WORKSPACE",
+    // Amazon CodeWhisperer / Q
+    "AWS_CODEWHISPERER_SESSION",
+    "AMAZON_Q_SESSION",
+    // Sourcegraph Cody
+    "CODY_SESSION",
+    "SRC_ACCESS_TOKEN",
+    // Tabnine
+    "TABNINE_SESSION",
+    // Replit Agent
+    "REPLIT_AGENT",
+    "REPL_ID",
+    // Generic
+    "AI_AGENT",
+    "CODING_AGENT",
+];
+
+/// Known environment variables that indicate a CI environment.
+const KNOWN_CI_ENV_VARS: &[&str] = &[
+    "CI",
+    "GITHUB_ACTIONS",
+    "GITLAB_CI",
+    "CIRCLECI",
+    "TRAVIS",
+    "JENKINS_URL",
+    "BUILDKITE",
+    "BITBUCKET_PIPELINE",
+    "AZURE_PIPELINES",
+    "TEAMCITY_VERSION",
+    "DRONE",
+    "WOODPECKER",
+    "SEMAPHORE",
+    "APPVEYOR",
+    "CODEBUILD_BUILD_ID",
+    "TF_BUILD",
+    "NETLIFY",
+    "VERCEL",
+    "RENDER",
+    "RAILWAY_ENVIRONMENT",
+    "FLY_APP_NAME",
+];
+
+impl<'a> Detector<'a> {
+    /// Creates a new detector with the given configuration.
+    #[must_use]
+    pub const fn new(config: &'a Config) -> Self {
+        Self { config }
+    }
+
+    /// Detects the commit mode based on environment.
+    #[must_use]
+    pub fn detect(&self) -> Detection {
+        // Priority 1: Explicit APC_MODE override
+        if let Some(detection) = self.check_apc_mode() {
+            return detection;
+        }
+
+        // Priority 2: AGENT_MODE=1 flag
+        if let Some(detection) = self.check_agent_mode_flag() {
+            return detection;
+        }
+
+        // Priority 3: Known agent environment variables
+        if let Some(detection) = self.check_known_agent_env_vars() {
+            return detection;
+        }
+
+        // Priority 4: Custom agent environment variables from config
+        if let Some(detection) = self.check_custom_agent_env_vars() {
+            return detection;
+        }
+
+        // Priority 5: CI environment detection
+        if let Some(detection) = self.check_ci_environment() {
+            return detection;
+        }
+
+        // Priority 6: TTY detection (fallback heuristic)
+        if let Some(detection) = self.check_tty() {
+            return detection;
+        }
+
+        // Default: Human mode
+        Detection {
+            mode: Mode::Human,
+            reason: DetectionReason::Default,
+        }
+    }
+
+    /// Checks for explicit APC_MODE environment variable.
+    fn check_apc_mode(&self) -> Option<Detection> {
+        env::var("APC_MODE").ok().map(|value| {
+            let mode = value.parse().unwrap_or(Mode::Human);
+            Detection {
+                mode,
+                reason: DetectionReason::ExplicitApcMode(value),
+            }
+        })
+    }
+
+    /// Checks for AGENT_MODE=1 flag.
+    fn check_agent_mode_flag(&self) -> Option<Detection> {
+        env::var("AGENT_MODE").ok().and_then(|value| {
+            if value == "1" || value.eq_ignore_ascii_case("true") {
+                Some(Detection {
+                    mode: Mode::Agent,
+                    reason: DetectionReason::ExplicitAgentMode,
+                })
+            } else {
+                None
+            }
+        })
+    }
+
+    /// Checks for known agent environment variables.
+    fn check_known_agent_env_vars(&self) -> Option<Detection> {
+        for var in KNOWN_AGENT_ENV_VARS {
+            if env::var(var).is_ok() {
+                return Some(Detection {
+                    mode: Mode::Agent,
+                    reason: DetectionReason::KnownAgentEnvVar((*var).to_string()),
+                });
+            }
+        }
+        None
+    }
+
+    /// Checks for custom agent environment variables from config.
+    fn check_custom_agent_env_vars(&self) -> Option<Detection> {
+        for var in &self.config.detection.agent_env_vars {
+            if env::var(var).is_ok() {
+                return Some(Detection {
+                    mode: Mode::Agent,
+                    reason: DetectionReason::CustomAgentEnvVar(var.clone()),
+                });
+            }
+        }
+        None
+    }
+
+    /// Checks for CI environment variables.
+    fn check_ci_environment(&self) -> Option<Detection> {
+        for var in KNOWN_CI_ENV_VARS {
+            if env::var(var).is_ok() {
+                return Some(Detection {
+                    mode: Mode::Ci,
+                    reason: DetectionReason::CiEnvironment((*var).to_string()),
+                });
+            }
+        }
+        None
+    }
+
+    /// Checks for TTY presence (non-interactive = likely agent).
+    fn check_tty(&self) -> Option<Detection> {
+        let stdin_is_tty = std::io::stdin().is_terminal();
+        let stdout_is_tty = std::io::stdout().is_terminal();
+
+        // Only trigger if BOTH stdin and stdout are not TTY
+        // This avoids false positives from piped commands
+        if !stdin_is_tty && !stdout_is_tty {
+            return Some(Detection {
+                mode: Mode::Agent,
+                reason: DetectionReason::NoTty,
+            });
+        }
+
+        None
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_mode_display() {
+        assert_eq!(Mode::Human.to_string(), "human");
+        assert_eq!(Mode::Agent.to_string(), "agent");
+        assert_eq!(Mode::Ci.to_string(), "ci");
+    }
+
+    #[test]
+    fn test_mode_parse() {
+        assert_eq!("human".parse::<Mode>().ok(), Some(Mode::Human));
+        assert_eq!("AGENT".parse::<Mode>().ok(), Some(Mode::Agent));
+        assert_eq!("CI".parse::<Mode>().ok(), Some(Mode::Ci));
+        assert!("invalid".parse::<Mode>().is_err());
+    }
+
+    #[test]
+    fn test_mode_is_thorough() {
+        assert!(!Mode::Human.is_thorough());
+        assert!(Mode::Agent.is_thorough());
+        assert!(Mode::Ci.is_thorough());
+    }
+
+    #[test]
+    fn test_detection_reason_display() {
+        let reason = DetectionReason::ExplicitAgentMode;
+        assert_eq!(reason.to_string(), "AGENT_MODE=1");
+    }
+}
diff --git a/src/core/error.rs b/src/core/error.rs
new file mode 100644
index 0000000..7982ecc
--- /dev/null
+++ b/src/core/error.rs
@@ -0,0 +1,272 @@
+//! Error types for agent-precommit.
+//!
+//! This module defines all errors that can occur during operation.
+
+use std::path::PathBuf;
+
+/// Result type alias using our Error type.
+pub type Result<T> = std::result::Result<T, Error>;
+
+/// All possible errors in agent-precommit.
+#[derive(Debug, thiserror::Error)]
+pub enum Error {
+    // =========================================================================
+    // Configuration errors
+    // =========================================================================
+    /// Configuration file not found.
+    #[error("Configuration file not found: {path}")]
+    ConfigNotFound {
+        /// Path where config was expected.
+        path: PathBuf,
+    },
+
+    /// Failed to parse configuration file.
+    #[error("Failed to parse configuration: {message}")]
+    ConfigParse {
+        /// Description of the parse error.
+        message: String,
+        /// Optional source error.
+        #[source]
+        source: Option<Box<dyn std::error::Error + Send + Sync>>,
+    },
+
+    /// Invalid configuration value.
+    #[error("Invalid configuration: {field} - {message}")]
+    ConfigInvalid {
+        /// Field name that is invalid.
+        field: String,
+        /// Description of why it's invalid.
+        message: String,
+    },
+
+    // =========================================================================
+    // Git errors
+    // =========================================================================
+    /// Not in a Git repository.
+    #[error("Not in a Git repository")]
+    NotGitRepo,
+
+    /// Git operation failed.
+    #[error("Git operation failed: {operation} - {message}")]
+    GitOperation {
+        /// Name of the operation that failed.
+        operation: String,
+        /// Error message.
+        message: String,
+    },
+
+    /// Failed to detect Git hooks directory.
+    #[error("Failed to detect Git hooks directory")]
+    GitHooksDir,
+
+    // =========================================================================
+    // Check execution errors
+    // =========================================================================
+    /// Check not found.
+    #[error("Check not found: {name}")]
+    CheckNotFound {
+        /// Name of the check that wasn't found.
+        name: String,
+    },
+
+    /// Check execution failed.
+    #[error("Check '{name}' failed: {message}")]
+    CheckFailed {
+        /// Name of the check that failed.
+        name: String,
+        /// Error message or output.
+        message: String,
+        /// Exit code if available.
+        exit_code: Option<i32>,
+    },
+
+    /// Check timed out.
+    #[error("Check '{name}' timed out after {timeout}")]
+    CheckTimeout {
+        /// Name of the check that timed out.
+        name: String,
+        /// Timeout duration as string.
+        timeout: String,
+    },
+
+    /// Command not found.
+    #[error("Command not found: {command}")]
+    CommandNotFound {
+        /// The command that wasn't found.
+        command: String,
+    },
+
+    // =========================================================================
+    // Hook errors
+    // =========================================================================
+    /// Failed to install hook.
+    #[error("Failed to install Git hook: {message}")]
+    HookInstall {
+        /// Error message.
+        message: String,
+    },
+
+    /// Hook already exists and wasn't created by us.
+    #[error("Git hook already exists at {path}. Use --force to overwrite.")]
+    HookExists {
+        /// Path to existing hook.
+        path: PathBuf,
+    },
+
+    // =========================================================================
+    // I/O errors
+    // =========================================================================
+    /// File I/O error.
+    #[error("I/O error: {message}")]
+    Io {
+        /// Description of what failed.
+        message: String,
+        /// Source error.
+        #[source]
+        source: std::io::Error,
+    },
+
+    // =========================================================================
+    // Pre-commit integration errors
+    // =========================================================================
+    /// Pre-commit framework not found.
+    #[error("Pre-commit framework not found. Install with: pip install pre-commit")]
+    PreCommitNotFound,
+
+    /// Pre-commit config not found.
+    #[error("Pre-commit config not found: {path}")]
+    PreCommitConfigNotFound {
+        /// Path where config was expected.
+        path: PathBuf,
+    },
+
+    // =========================================================================
+    // Internal errors
+    // =========================================================================
+    /// Internal error (should never happen).
+    #[error("Internal error: {message}")]
+    Internal {
+        /// Error message.
+        message: String,
+    },
+}
+
+impl Error {
+    /// Creates a new configuration parse error.
+    pub fn config_parse(message: impl Into<String>) -> Self {
+        Self::ConfigParse {
+            message: message.into(),
+            source: None,
+        }
+    }
+
+    /// Creates a new configuration parse error with source.
+    pub fn config_parse_with_source(
+        message: impl Into<String>,
+        source: impl std::error::Error + Send + Sync + 'static,
+    ) -> Self {
+        Self::ConfigParse {
+            message: message.into(),
+            source: Some(Box::new(source)),
+        }
+    }
+
+    /// Creates a new I/O error with context.
+    pub fn io(message: impl Into<String>, source: std::io::Error) -> Self {
+        Self::Io {
+            message: message.into(),
+            source,
+        }
+    }
+
+    /// Creates a new Git operation error.
+    pub fn git(operation: impl Into<String>, message: impl Into<String>) -> Self {
+        Self::GitOperation {
+            operation: operation.into(),
+            message: message.into(),
+        }
+    }
+
+    /// Creates a new check failed error.
+    pub fn check_failed(
+        name: impl Into<String>,
+        message: impl Into<String>,
+        exit_code: Option<i32>,
+    ) -> Self {
+        Self::CheckFailed {
+            name: name.into(),
+            message: message.into(),
+            exit_code,
+        }
+    }
+
+    /// Returns true if this is a user-correctable error.
+    pub const fn is_user_error(&self) -> bool {
+        matches!(
+            self,
+            Self::ConfigNotFound { .. }
+                | Self::ConfigInvalid { .. }
+                | Self::NotGitRepo
+                | Self::HookExists { .. }
+                | Self::PreCommitNotFound
+                | Self::PreCommitConfigNotFound { .. }
+        )
+    }
+
+    /// Returns an exit code appropriate for this error.
+    #[must_use]
+    pub fn exit_code(&self) -> i32 {
+        match self {
+            Self::CheckFailed { exit_code, .. } => exit_code.unwrap_or(1),
+            Self::CheckTimeout { .. } => 124, // Standard timeout exit code
+            Self::ConfigNotFound { .. }
+            | Self::ConfigParse { .. }
+            | Self::ConfigInvalid { .. } => 78, // EX_CONFIG
+            Self::NotGitRepo | Self::GitOperation { .. } | Self::GitHooksDir => 65, // EX_DATAERR
+            _ => 1,
+        }
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_error_display() {
+        let err = Error::CheckNotFound {
+            name: "test".to_string(),
+        };
+        assert_eq!(err.to_string(), "Check not found: test");
+    }
+
+    #[test]
+    fn test_exit_codes() {
+        assert_eq!(
+            Error::CheckTimeout {
+                name: "test".into(),
+                timeout: "30s".into()
+            }
+            .exit_code(),
+            124
+        );
+
+        assert_eq!(
+            Error::ConfigNotFound {
+                path: PathBuf::from("/test")
+            }
+            .exit_code(),
+            78
+        );
+    }
+
+    #[test]
+    fn test_is_user_error() {
+        assert!(Error::NotGitRepo.is_user_error());
+        assert!(Error::PreCommitNotFound.is_user_error());
+        assert!(!Error::Internal {
+            message: "test".into()
+        }
+        .is_user_error());
+    }
+}
diff --git a/src/core/executor.rs b/src/core/executor.rs
new file mode 100644
index 0000000..6d549eb
--- /dev/null
+++ b/src/core/executor.rs
@@ -0,0 +1,317 @@
+//! Command execution for running checks.
+//!
+//! This module provides utilities for executing shell commands
+//! with timeout support, output capture, and error handling.
+
+use crate::core::error::{Error, Result};
+use std::path::Path;
+use std::process::Stdio;
+use std::time::Duration;
+use tokio::io::{AsyncBufReadExt, BufReader};
+use tokio::process::Command;
+use tokio::time::timeout;
+
+/// Output from a command execution.
+#[derive(Debug, Clone)]
+pub struct CommandOutput {
+    /// Exit code of the command.
+    pub exit_code: i32,
+    /// Standard output.
+    pub stdout: String,
+    /// Standard error.
+    pub stderr: String,
+    /// Whether the command was killed due to timeout.
+    pub timed_out: bool,
+    /// Duration the command took to run.
+    pub duration: Duration,
+}
+
+impl CommandOutput {
+    /// Returns true if the command succeeded (exit code 0).
+    #[must_use]
+    pub const fn success(&self) -> bool {
+        self.exit_code == 0 && !self.timed_out
+    }
+
+    /// Returns combined stdout and stderr output.
+    #[must_use]
+    pub fn combined_output(&self) -> String {
+        if self.stderr.is_empty() {
+            self.stdout.clone()
+        } else if self.stdout.is_empty() {
+            self.stderr.clone()
+        } else {
+            format!("{}\n{}", self.stdout, self.stderr)
+        }
+    }
+}
+
+/// Options for command execution.
+#[derive(Debug, Clone)]
+pub struct ExecuteOptions {
+    /// Working directory for the command.
+    pub cwd: Option<std::path::PathBuf>,
+    /// Timeout for the command.
+    pub timeout: Option<Duration>,
+    /// Environment variables to set.
+    pub env: Vec<(String, String)>,
+    /// Whether to capture output (vs streaming to console).
+    pub capture_output: bool,
+    /// Shell to use (default: sh on Unix, cmd on Windows).
+    pub shell: Option<String>,
+}
+
+impl Default for ExecuteOptions {
+    fn default() -> Self {
+        Self {
+            cwd: None,
+            timeout: Some(Duration::from_secs(300)), // 5 minutes default
+            env: Vec::new(),
+            capture_output: true,
+            shell: None,
+        }
+    }
+}
+
+impl ExecuteOptions {
+    /// Sets the working directory.
+    #[must_use]
+    pub fn cwd(mut self, path: impl AsRef<Path>) -> Self {
+        self.cwd = Some(path.as_ref().to_path_buf());
+        self
+    }
+
+    /// Sets the timeout.
+    #[must_use]
+    pub const fn timeout(mut self, duration: Duration) -> Self {
+        self.timeout = Some(duration);
+        self
+    }
+
+    /// Sets an environment variable.
+    #[must_use]
+    pub fn env(mut self, key: impl Into<String>, value: impl Into<String>) -> Self {
+        self.env.push((key.into(), value.into()));
+        self
+    }
+
+    /// Sets whether to capture output.
+    #[must_use]
+    pub const fn capture_output(mut self, capture: bool) -> Self {
+        self.capture_output = capture;
+        self
+    }
+}
+
+/// Executor for running shell commands.
+#[derive(Debug, Default)]
+pub struct Executor;
+
+impl Executor {
+    /// Creates a new executor.
+    #[must_use]
+    pub const fn new() -> Self {
+        Self
+    }
+
+    /// Executes a shell command.
+    pub async fn execute(&self, command: &str, options: ExecuteOptions) -> Result<CommandOutput> {
+        let start = std::time::Instant::now();
+
+        // Determine shell
+        let (shell, shell_arg) = if cfg!(windows) {
+            (
+                options.shell.as_deref().unwrap_or("cmd"),
+                "/C",
+            )
+        } else {
+            (
+                options.shell.as_deref().unwrap_or("sh"),
+                "-c",
+            )
+        };
+
+        // Build command
+        let mut cmd = Command::new(shell);
+        cmd.arg(shell_arg).arg(command);
+
+        // Set working directory
+        if let Some(ref cwd) = options.cwd {
+            cmd.current_dir(cwd);
+        }
+
+        // Set environment variables
+        for (key, value) in &options.env {
+            cmd.env(key, value);
+        }
+
+        // Configure output handling
+        cmd.stdin(Stdio::null());
+
+        if options.capture_output {
+            cmd.stdout(Stdio::piped());
+            cmd.stderr(Stdio::piped());
+        } else {
+            cmd.stdout(Stdio::inherit());
+            cmd.stderr(Stdio::inherit());
+        }
+
+        // Spawn the process
+        let mut child = cmd.spawn().map_err(|e| Error::io("spawn command", e))?;
+
+        // Handle timeout
+        let result = if let Some(timeout_duration) = options.timeout {
+            match timeout(timeout_duration, async {
+                self.wait_for_output(&mut child, options.capture_output).await
+            })
+            .await
+            {
+                Ok(result) => result,
+                Err(_) => {
+                    // Kill the process on timeout - ignore result since we're returning anyway
+                    drop(child.kill().await);
+                    return Ok(CommandOutput {
+                        exit_code: 124,
+                        stdout: String::new(),
+                        stderr: "Command timed out".to_string(),
+                        timed_out: true,
+                        duration: start.elapsed(),
+                    });
+                }
+            }
+        } else {
+            self.wait_for_output(&mut child, options.capture_output)
+                .await
+        };
+
+        let (exit_code, stdout, stderr) = result?;
+
+        Ok(CommandOutput {
+            exit_code,
+            stdout,
+            stderr,
+            timed_out: false,
+            duration: start.elapsed(),
+        })
+    }
+
+    /// Waits for the command to complete and captures output.
+    async fn wait_for_output(
+        &self,
+        child: &mut tokio::process::Child,
+        capture: bool,
+    ) -> Result<(i32, String, String)> {
+        if capture {
+            let stdout = child.stdout.take();
+            let stderr = child.stderr.take();
+
+            let stdout_handle = tokio::spawn(async move {
+                let mut output = String::new();
+                if let Some(stdout) = stdout {
+                    let mut reader = BufReader::new(stdout).lines();
+                    while let Ok(Some(line)) = reader.next_line().await {
+                        output.push_str(&line);
+                        output.push('\n');
+                    }
+                }
+                output
+            });
+
+            let stderr_handle = tokio::spawn(async move {
+                let mut output = String::new();
+                if let Some(stderr) = stderr {
+                    let mut reader = BufReader::new(stderr).lines();
+                    while let Ok(Some(line)) = reader.next_line().await {
+                        output.push_str(&line);
+                        output.push('\n');
+                    }
+                }
+                output
+            });
+
+            let status = child.wait().await.map_err(|e| Error::io("wait for command", e))?;
+
+            let stdout = stdout_handle
+                .await
+                .map_err(|e| Error::Internal {
+                    message: format!("stdout task failed: {e}"),
+                })?;
+            let stderr = stderr_handle
+                .await
+                .map_err(|e| Error::Internal {
+                    message: format!("stderr task failed: {e}"),
+                })?;
+
+            Ok((status.code().unwrap_or(1), stdout, stderr))
+        } else {
+            let status = child.wait().await.map_err(|e| Error::io("wait for command", e))?;
+            Ok((status.code().unwrap_or(1), String::new(), String::new()))
+        }
+    }
+
+    /// Checks if a command exists in PATH.
+    #[must_use]
+    pub fn command_exists(command: &str) -> bool {
+        which::which(command).is_ok()
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[tokio::test]
+    async fn test_execute_simple_command() {
+        let executor = Executor::new();
+        let result = executor
+            .execute("echo hello", ExecuteOptions::default())
+            .await;
+
+        assert!(result.is_ok());
+        let output = result.expect("should succeed");
+        assert!(output.success());
+        assert!(output.stdout.contains("hello"));
+    }
+
+    #[tokio::test]
+    async fn test_execute_failing_command() {
+        let executor = Executor::new();
+        let result = executor
+            .execute("exit 1", ExecuteOptions::default())
+            .await;
+
+        assert!(result.is_ok());
+        let output = result.expect("should complete");
+        assert!(!output.success());
+        assert_eq!(output.exit_code, 1);
+    }
+
+    #[tokio::test]
+    async fn test_execute_timeout() {
+        let executor = Executor::new();
+        let result = executor
+            .execute(
+                "sleep 10",
+                ExecuteOptions::default().timeout(Duration::from_millis(100)),
+            )
+            .await;
+
+        assert!(result.is_ok());
+        let output = result.expect("should complete");
+        assert!(output.timed_out);
+        assert_eq!(output.exit_code, 124);
+    }
+
+    #[test]
+    fn test_command_exists() {
+        // 'sh' should exist on Unix, 'cmd' on Windows
+        if cfg!(unix) {
+            assert!(Executor::command_exists("sh"));
+        } else {
+            assert!(Executor::command_exists("cmd"));
+        }
+
+        // This should not exist
+        assert!(!Executor::command_exists("definitely_not_a_real_command_12345"));
+    }
+}
diff --git a/src/core/git.rs b/src/core/git.rs
new file mode 100644
index 0000000..bf6cdd8
--- /dev/null
+++ b/src/core/git.rs
@@ -0,0 +1,262 @@
+//! Git repository operations.
+//!
+//! This module provides utilities for interacting with Git repositories,
+//! including finding the repository root, hooks directory, and staged files.
+
+use crate::core::error::{Error, Result};
+use std::path::{Path, PathBuf};
+use std::process::Command;
+
+/// Represents a Git repository.
+#[derive(Debug, Clone)]
+pub struct GitRepo {
+    /// Root directory of the repository (where .git is).
+    root: PathBuf,
+    /// Path to the .git directory (or file for worktrees).
+    git_dir: PathBuf,
+}
+
+impl GitRepo {
+    /// Discovers the Git repository from the current directory.
+    pub fn discover() -> Result<Self> {
+        Self::discover_from(&std::env::current_dir().map_err(|e| Error::io("get current dir", e))?)
+    }
+
+    /// Discovers the Git repository from a specific path.
+    pub fn discover_from(path: &Path) -> Result<Self> {
+        let output = Command::new("git")
+            .args(["rev-parse", "--show-toplevel", "--git-dir"])
+            .current_dir(path)
+            .output()
+            .map_err(|e| Error::io("run git rev-parse", e))?;
+
+        if !output.status.success() {
+            return Err(Error::NotGitRepo);
+        }
+
+        let stdout = String::from_utf8_lossy(&output.stdout);
+        let mut lines = stdout.lines();
+
+        let root = lines
+            .next()
+            .map(PathBuf::from)
+            .ok_or(Error::NotGitRepo)?;
+
+        let git_dir = lines
+            .next()
+            .map(|s| {
+                let p = PathBuf::from(s);
+                if p.is_absolute() {
+                    p
+                } else {
+                    root.join(p)
+                }
+            })
+            .ok_or(Error::NotGitRepo)?;
+
+        Ok(Self { root, git_dir })
+    }
+
+    /// Returns the root directory of the repository.
+    #[must_use]
+    pub fn root(&self) -> &Path {
+        &self.root
+    }
+
+    /// Returns the .git directory path.
+    #[must_use]
+    pub fn git_dir(&self) -> &Path {
+        &self.git_dir
+    }
+
+    /// Returns the hooks directory path.
+    #[must_use]
+    pub fn hooks_dir(&self) -> PathBuf {
+        // Check for custom hooks path first
+        if let Ok(output) = Command::new("git")
+            .args(["config", "--get", "core.hooksPath"])
+            .current_dir(&self.root)
+            .output()
+        {
+            if output.status.success() {
+                let path = String::from_utf8_lossy(&output.stdout).trim().to_string();
+                if !path.is_empty() {
+                    let hooks_path = PathBuf::from(&path);
+                    if hooks_path.is_absolute() {
+                        return hooks_path;
+                    }
+                    return self.root.join(hooks_path);
+                }
+            }
+        }
+
+        // Default to .git/hooks
+        self.git_dir.join("hooks")
+    }
+
+    /// Returns the path to a specific hook.
+    #[must_use]
+    pub fn hook_path(&self, hook_name: &str) -> PathBuf {
+        self.hooks_dir().join(hook_name)
+    }
+
+    /// Returns the list of staged files.
+    pub fn staged_files(&self) -> Result<Vec<PathBuf>> {
+        let output = Command::new("git")
+            .args(["diff", "--cached", "--name-only", "--diff-filter=ACMR"])
+            .current_dir(&self.root)
+            .output()
+            .map_err(|e| Error::io("get staged files", e))?;
+
+        if !output.status.success() {
+            return Err(Error::git("diff --cached", "Failed to get staged files"));
+        }
+
+        let files = String::from_utf8_lossy(&output.stdout)
+            .lines()
+            .filter(|s| !s.is_empty())
+            .map(|s| self.root.join(s))
+            .collect();
+
+        Ok(files)
+    }
+
+    /// Returns the current branch name.
+    pub fn current_branch(&self) -> Result<String> {
+        let output = Command::new("git")
+            .args(["rev-parse", "--abbrev-ref", "HEAD"])
+            .current_dir(&self.root)
+            .output()
+            .map_err(|e| Error::io("get current branch", e))?;
+
+        if !output.status.success() {
+            return Err(Error::git("rev-parse", "Failed to get current branch"));
+        }
+
+        Ok(String::from_utf8_lossy(&output.stdout).trim().to_string())
+    }
+
+    /// Returns the main branch name (main or master).
+    pub fn main_branch(&self) -> Result<String> {
+        // Try 'main' first
+        let output = Command::new("git")
+            .args(["rev-parse", "--verify", "origin/main"])
+            .current_dir(&self.root)
+            .output()
+            .map_err(|e| Error::io("verify main branch", e))?;
+
+        if output.status.success() {
+            return Ok("main".to_string());
+        }
+
+        // Fall back to 'master'
+        let output = Command::new("git")
+            .args(["rev-parse", "--verify", "origin/master"])
+            .current_dir(&self.root)
+            .output()
+            .map_err(|e| Error::io("verify master branch", e))?;
+
+        if output.status.success() {
+            return Ok("master".to_string());
+        }
+
+        // Default to 'main' if neither exists
+        Ok("main".to_string())
+    }
+
+    /// Fetches updates from the remote for a specific branch.
+    pub fn fetch_branch(&self, branch: &str) -> Result<()> {
+        let output = Command::new("git")
+            .args(["fetch", "origin", branch, "--quiet"])
+            .current_dir(&self.root)
+            .output()
+            .map_err(|e| Error::io("fetch branch", e))?;
+
+        if !output.status.success() {
+            let stderr = String::from_utf8_lossy(&output.stderr);
+            return Err(Error::git("fetch", stderr.trim().to_string()));
+        }
+
+        Ok(())
+    }
+
+    /// Checks if the repository has uncommitted changes.
+    pub fn has_uncommitted_changes(&self) -> Result<bool> {
+        let output = Command::new("git")
+            .args(["status", "--porcelain"])
+            .current_dir(&self.root)
+            .output()
+            .map_err(|e| Error::io("check uncommitted changes", e))?;
+
+        if !output.status.success() {
+            return Err(Error::git("status", "Failed to check status"));
+        }
+
+        Ok(!output.stdout.is_empty())
+    }
+
+    /// Checks if a file exists in the repository.
+    #[must_use]
+    pub fn file_exists(&self, relative_path: &str) -> bool {
+        self.root.join(relative_path).exists()
+    }
+
+    /// Checks if a directory exists in the repository.
+    #[must_use]
+    pub fn dir_exists(&self, relative_path: &str) -> bool {
+        self.root.join(relative_path).is_dir()
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use tempfile::TempDir;
+
+    fn create_test_repo() -> (TempDir, GitRepo) {
+        let temp = TempDir::new().expect("create temp dir");
+        let path = temp.path();
+
+        Command::new("git")
+            .args(["init"])
+            .current_dir(path)
+            .output()
+            .expect("init repo");
+
+        Command::new("git")
+            .args(["config", "user.email", "test@test.com"])
+            .current_dir(path)
+            .output()
+            .expect("set email");
+
+        Command::new("git")
+            .args(["config", "user.name", "Test"])
+            .current_dir(path)
+            .output()
+            .expect("set name");
+
+        let repo = GitRepo::discover_from(path).expect("discover repo");
+        (temp, repo)
+    }
+
+    #[test]
+    fn test_discover_repo() {
+        let (_temp, repo) = create_test_repo();
+        assert!(repo.root().exists());
+        assert!(repo.git_dir().exists());
+    }
+
+    #[test]
+    fn test_hooks_dir() {
+        let (_temp, repo) = create_test_repo();
+        let hooks_dir = repo.hooks_dir();
+        assert!(hooks_dir.ends_with("hooks"));
+    }
+
+    #[test]
+    fn test_not_git_repo() {
+        let temp = TempDir::new().expect("create temp dir");
+        let result = GitRepo::discover_from(temp.path());
+        assert!(matches!(result, Err(Error::NotGitRepo)));
+    }
+}
diff --git a/src/core/mod.rs b/src/core/mod.rs
new file mode 100644
index 0000000..8cee063
--- /dev/null
+++ b/src/core/mod.rs
@@ -0,0 +1,13 @@
+//! Core functionality for agent-precommit.
+//!
+//! This module contains the main components:
+//! - [`detector`]: Mode detection (human, agent, CI)
+//! - [`runner`]: Check execution engine
+//! - [`error`]: Error types and result handling
+//! - [`git`]: Git repository operations
+
+pub mod detector;
+pub mod error;
+pub mod executor;
+pub mod git;
+pub mod runner;
diff --git a/src/core/runner.rs b/src/core/runner.rs
new file mode 100644
index 0000000..c95c64e
--- /dev/null
+++ b/src/core/runner.rs
@@ -0,0 +1,494 @@
+//! Check runner for executing pre-commit checks.
+//!
+//! This module orchestrates the execution of checks based on the detected mode.
+
+// Allow this for Rust 2024 compatibility - the drop order change is harmless here
+#![allow(tail_expr_drop_order)]
+
+use crate::config::{CheckConfig, Config};
+use crate::core::detector::Mode;
+use crate::core::error::{Error, Result};
+use crate::core::executor::{CommandOutput, ExecuteOptions, Executor};
+use crate::core::git::GitRepo;
+use console::style;
+use indicatif::{ProgressBar, ProgressStyle};
+use std::collections::HashMap;
+use std::sync::Arc;
+use std::time::Duration;
+use tokio::sync::Semaphore;
+
+/// Result of running a single check.
+#[derive(Debug, Clone)]
+pub struct CheckResult {
+    /// Name of the check.
+    pub name: String,
+    /// Whether the check passed.
+    pub passed: bool,
+    /// Output from the check.
+    pub output: CommandOutput,
+    /// Whether the check was skipped.
+    pub skipped: bool,
+    /// Reason for skipping (if skipped).
+    pub skip_reason: Option<String>,
+}
+
+impl CheckResult {
+    /// Creates a skipped check result.
+    fn skipped(name: String, reason: String) -> Self {
+        Self {
+            name,
+            passed: true, // Skipped checks don't fail
+            output: CommandOutput {
+                exit_code: 0,
+                stdout: String::new(),
+                stderr: String::new(),
+                timed_out: false,
+                duration: Duration::ZERO,
+            },
+            skipped: true,
+            skip_reason: Some(reason),
+        }
+    }
+}
+
+/// Result of running all checks.
+#[derive(Debug)]
+pub struct RunResult {
+    /// Mode that was used.
+    pub mode: Mode,
+    /// Individual check results.
+    pub checks: Vec<CheckResult>,
+    /// Total duration.
+    pub duration: Duration,
+}
+
+impl RunResult {
+    /// Returns true if all checks passed.
+    #[must_use]
+    pub fn success(&self) -> bool {
+        self.checks.iter().all(|c| c.passed)
+    }
+
+    /// Returns the number of passed checks.
+    #[must_use]
+    pub fn passed_count(&self) -> usize {
+        self.checks.iter().filter(|c| c.passed && !c.skipped).count()
+    }
+
+    /// Returns the number of failed checks.
+    #[must_use]
+    pub fn failed_count(&self) -> usize {
+        self.checks.iter().filter(|c| !c.passed).count()
+    }
+
+    /// Returns the number of skipped checks.
+    #[must_use]
+    pub fn skipped_count(&self) -> usize {
+        self.checks.iter().filter(|c| c.skipped).count()
+    }
+
+    /// Returns failed check results.
+    pub fn failed_checks(&self) -> impl Iterator<Item = &CheckResult> {
+        self.checks.iter().filter(|c| !c.passed)
+    }
+}
+
+/// Runner for executing checks.
+#[derive(Debug)]
+pub struct Runner {
+    config: Config,
+    repo: Option<GitRepo>,
+}
+
+impl Runner {
+    /// Creates a new runner with the given configuration.
+    #[must_use]
+    pub fn new(config: Config) -> Self {
+        Self {
+            config,
+            repo: GitRepo::discover().ok(),
+        }
+    }
+
+    /// Creates a new runner with a specific repository.
+    #[must_use]
+    pub fn with_repo(config: Config, repo: GitRepo) -> Self {
+        Self {
+            config,
+            repo: Some(repo),
+        }
+    }
+
+    /// Runs checks for the given mode.
+    pub async fn run(&self, mode: Mode) -> Result<RunResult> {
+        let start = std::time::Instant::now();
+
+        // Get checks for this mode
+        let check_names = self.get_checks_for_mode(mode);
+
+        if check_names.is_empty() {
+            return Ok(RunResult {
+                mode,
+                checks: Vec::new(),
+                duration: start.elapsed(),
+            });
+        }
+
+        // Resolve check configurations
+        let checks = self.resolve_checks(&check_names)?;
+
+        // Run checks based on mode settings
+        let results = if mode.is_thorough() {
+            self.run_parallel_groups(mode, &checks).await?
+        } else {
+            self.run_sequential(mode, &checks).await?
+        };
+
+        Ok(RunResult {
+            mode,
+            checks: results,
+            duration: start.elapsed(),
+        })
+    }
+
+    /// Runs a single check by name.
+    pub async fn run_single(&self, name: &str, mode: Mode) -> Result<CheckResult> {
+        let check = self.config.checks.get(name).ok_or_else(|| Error::CheckNotFound {
+            name: name.to_string(),
+        })?;
+
+        self.run_check(name, check, mode).await
+    }
+
+    /// Gets the list of checks for a mode.
+    fn get_checks_for_mode(&self, mode: Mode) -> Vec<String> {
+        match mode {
+            Mode::Human => self.config.human.checks.clone(),
+            Mode::Agent | Mode::Ci => self.config.agent.checks.clone(),
+        }
+    }
+
+    /// Resolves check names to configurations.
+    fn resolve_checks(&self, names: &[String]) -> Result<Vec<(String, CheckConfig)>> {
+        let mut checks = Vec::with_capacity(names.len());
+
+        for name in names {
+            let check = self
+                .config
+                .checks
+                .get(name)
+                .cloned()
+                .unwrap_or_else(|| CheckConfig::from_command(name.clone()));
+
+            checks.push((name.clone(), check));
+        }
+
+        Ok(checks)
+    }
+
+    /// Runs checks sequentially (for human mode).
+    async fn run_sequential(
+        &self,
+        mode: Mode,
+        checks: &[(String, CheckConfig)],
+    ) -> Result<Vec<CheckResult>> {
+        let mut results = Vec::with_capacity(checks.len());
+
+        for (name, check) in checks {
+            let result = self.run_check(name, check, mode).await?;
+
+            let failed = !result.passed;
+            results.push(result);
+
+            // Fail fast in human mode
+            if failed && self.config.human.fail_fast {
+                break;
+            }
+        }
+
+        Ok(results)
+    }
+
+    /// Runs checks in parallel groups (for agent mode).
+    async fn run_parallel_groups(
+        &self,
+        mode: Mode,
+        checks: &[(String, CheckConfig)],
+    ) -> Result<Vec<CheckResult>> {
+        let check_map: HashMap<_, _> = checks.iter().cloned().collect();
+
+        // Get parallel groups or create default groups
+        let groups = if self.config.agent.parallel_groups.is_empty() {
+            // Default: run all checks in parallel
+            vec![checks.iter().map(|(n, _)| n.clone()).collect()]
+        } else {
+            self.config.agent.parallel_groups.clone()
+        };
+
+        let mut all_results = Vec::new();
+        let semaphore = Arc::new(Semaphore::new(num_cpus::get()));
+
+        for group in groups {
+            let group_checks: Vec<_> = group
+                .iter()
+                .filter_map(|name| check_map.get(name).map(|c| (name.clone(), c.clone())))
+                .collect();
+
+            if group_checks.is_empty() {
+                continue;
+            }
+
+            let mut handles = Vec::new();
+
+            for (name, check) in group_checks {
+                let sem = Arc::clone(&semaphore);
+                let config = self.config.clone();
+                let repo = self.repo.clone();
+
+                handles.push(tokio::spawn(async move {
+                    let _permit = sem.acquire().await;
+                    run_check_async(&name, &check, mode, &config, repo.as_ref()).await
+                }));
+            }
+
+            for handle in handles {
+                match handle.await {
+                    Ok(result) => all_results.push(result?),
+                    Err(e) => {
+                        return Err(Error::Internal {
+                            message: format!("Task join error: {e}"),
+                        });
+                    }
+                }
+            }
+
+            // Check for failures if not running all checks
+            if !self.config.agent.fail_fast {
+                continue;
+            }
+
+            if all_results.iter().any(|r: &CheckResult| !r.passed) {
+                break;
+            }
+        }
+
+        Ok(all_results)
+    }
+
+    /// Runs a single check.
+    async fn run_check(&self, name: &str, check: &CheckConfig, mode: Mode) -> Result<CheckResult> {
+        run_check_async(name, check, mode, &self.config, self.repo.as_ref()).await
+    }
+}
+
+/// Runs a check asynchronously (for parallel execution).
+async fn run_check_async(
+    name: &str,
+    check: &CheckConfig,
+    mode: Mode,
+    config: &Config,
+    repo: Option<&GitRepo>,
+) -> Result<CheckResult> {
+    // Check if the check is enabled
+    if !check_enabled(check, repo) {
+        return Ok(CheckResult::skipped(
+            name.to_string(),
+            "Condition not met".to_string(),
+        ));
+    }
+
+    // Build execution options
+    let timeout_str = match mode {
+        Mode::Human => &config.human.timeout,
+        Mode::Agent | Mode::Ci => &config.agent.timeout,
+    };
+
+    let timeout = parse_duration(timeout_str).unwrap_or(Duration::from_secs(300));
+
+    let mut options = ExecuteOptions::default().timeout(timeout);
+
+    if let Some(ref repo) = repo {
+        options = options.cwd(repo.root());
+    }
+
+    // Add environment variables from check config
+    for (key, value) in &check.env {
+        options = options.env(key.clone(), value.clone());
+    }
+
+    // Execute the command
+    let executor = Executor::new();
+
+    // Show progress
+    let pb = ProgressBar::new_spinner();
+    pb.set_style(
+        ProgressStyle::default_spinner()
+            .template("{spinner:.cyan} {msg}")
+            .ok()
+            .unwrap_or_else(ProgressStyle::default_spinner),
+    );
+    pb.set_message(format!("Running {name}..."));
+    pb.enable_steady_tick(Duration::from_millis(100));
+
+    let output = executor.execute(&check.run, options).await?;
+
+    pb.finish_and_clear();
+
+    // Format result
+    if output.success() {
+        eprintln!("{} {name}", style("✓").green());
+    } else if output.timed_out {
+        eprintln!("{} {name} (timed out)", style("✗").red());
+    } else {
+        eprintln!("{} {name}", style("✗").red());
+    }
+
+    Ok(CheckResult {
+        name: name.to_string(),
+        passed: output.success(),
+        output,
+        skipped: false,
+        skip_reason: None,
+    })
+}
+
+/// Checks if a check is enabled based on its conditions.
+fn check_enabled(check: &CheckConfig, repo: Option<&GitRepo>) -> bool {
+    let Some(ref condition) = check.enabled_if else {
+        return true;
+    };
+
+    // Check file_exists condition
+    if let Some(ref path) = condition.file_exists {
+        if let Some(repo) = repo {
+            if !repo.file_exists(path) {
+                return false;
+            }
+        }
+    }
+
+    // Check dir_exists condition
+    if let Some(ref path) = condition.dir_exists {
+        if let Some(repo) = repo {
+            if !repo.dir_exists(path) {
+                return false;
+            }
+        }
+    }
+
+    // Check command_exists condition
+    if let Some(ref cmd) = condition.command_exists {
+        if !Executor::command_exists(cmd) {
+            return false;
+        }
+    }
+
+    true
+}
+
+/// Parses a duration string like "30s", "5m", "1h".
+fn parse_duration(s: &str) -> Option<Duration> {
+    humantime::parse_duration(s).ok()
+}
+
+/// Gets the number of CPUs for parallel execution.
+mod num_cpus {
+    pub fn get() -> usize {
+        std::thread::available_parallelism()
+            .map(|p| p.get())
+            .unwrap_or(4)
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_parse_duration() {
+        assert_eq!(parse_duration("30s"), Some(Duration::from_secs(30)));
+        assert_eq!(parse_duration("5m"), Some(Duration::from_secs(300)));
+        assert_eq!(parse_duration("1h"), Some(Duration::from_secs(3600)));
+        assert_eq!(parse_duration("invalid"), None);
+    }
+
+    #[test]
+    fn test_run_result_success() {
+        let result = RunResult {
+            mode: Mode::Human,
+            checks: vec![
+                CheckResult {
+                    name: "test1".to_string(),
+                    passed: true,
+                    output: CommandOutput {
+                        exit_code: 0,
+                        stdout: String::new(),
+                        stderr: String::new(),
+                        timed_out: false,
+                        duration: Duration::ZERO,
+                    },
+                    skipped: false,
+                    skip_reason: None,
+                },
+                CheckResult {
+                    name: "test2".to_string(),
+                    passed: true,
+                    output: CommandOutput {
+                        exit_code: 0,
+                        stdout: String::new(),
+                        stderr: String::new(),
+                        timed_out: false,
+                        duration: Duration::ZERO,
+                    },
+                    skipped: false,
+                    skip_reason: None,
+                },
+            ],
+            duration: Duration::ZERO,
+        };
+
+        assert!(result.success());
+        assert_eq!(result.passed_count(), 2);
+        assert_eq!(result.failed_count(), 0);
+    }
+
+    #[test]
+    fn test_run_result_failure() {
+        let result = RunResult {
+            mode: Mode::Agent,
+            checks: vec![
+                CheckResult {
+                    name: "test1".to_string(),
+                    passed: true,
+                    output: CommandOutput {
+                        exit_code: 0,
+                        stdout: String::new(),
+                        stderr: String::new(),
+                        timed_out: false,
+                        duration: Duration::ZERO,
+                    },
+                    skipped: false,
+                    skip_reason: None,
+                },
+                CheckResult {
+                    name: "test2".to_string(),
+                    passed: false,
+                    output: CommandOutput {
+                        exit_code: 1,
+                        stdout: String::new(),
+                        stderr: "Error".to_string(),
+                        timed_out: false,
+                        duration: Duration::ZERO,
+                    },
+                    skipped: false,
+                    skip_reason: None,
+                },
+            ],
+            duration: Duration::ZERO,
+        };
+
+        assert!(!result.success());
+        assert_eq!(result.passed_count(), 1);
+        assert_eq!(result.failed_count(), 1);
+    }
+}
diff --git a/src/lib.rs b/src/lib.rs
new file mode 100644
index 0000000..33d3596
--- /dev/null
+++ b/src/lib.rs
@@ -0,0 +1,55 @@
+//! # agent-precommit
+//!
+//! Smart pre-commit hooks for humans and AI coding agents.
+//!
+//! Humans commit often and need fast checks. Agents commit once and need thorough checks.
+//! `agent-precommit` auto-detects which is which and runs the right checks.
+//!
+//! ## Features
+//!
+//! - **Automatic mode detection**: Detects human vs agent commits via environment variables,
+//!   TTY detection, and heuristics
+//! - **Pre-commit integration**: Works with existing `.pre-commit-config.yaml` setups
+//! - **Configurable checks**: Define custom checks for each mode in `agent-precommit.toml`
+//! - **Parallel execution**: Run independent checks concurrently for faster agent-mode runs
+//!
+//! ## Example
+//!
+//! ```rust,no_run
+//! use agent_precommit::{Config, Detector, Mode, Runner};
+//!
+//! #[tokio::main]
+//! async fn main() -> anyhow::Result<()> {
+//!     // Load configuration
+//!     let config = Config::load_or_default()?;
+//!
+//!     // Detect mode (human, agent, or ci)
+//!     let detector = Detector::new(&config);
+//!     let mode = detector.detect();
+//!
+//!     // Run appropriate checks
+//!     let runner = Runner::new(config);
+//!     let result = runner.run(mode).await?;
+//!
+//!     if result.success() {
+//!         Ok(())
+//!     } else {
+//!         std::process::exit(1);
+//!     }
+//! }
+//! ```
+
+#![doc(html_root_url = "https://docs.rs/agent-precommit/0.1.0")]
+#![cfg_attr(docsrs, feature(doc_cfg))]
+
+pub mod checks;
+pub mod cli;
+pub mod config;
+pub mod core;
+pub mod presets;
+
+// Re-export main types for convenience
+pub use config::Config;
+pub use core::detector::{Detector, Mode};
+pub use core::error::{Error, Result};
+pub use core::runner::{CheckResult, Runner, RunResult};
diff --git a/src/main.rs b/src/main.rs
new file mode 100644
index 0000000..f77c0a4
--- /dev/null
+++ b/src/main.rs
@@ -0,0 +1,14 @@
+//! Main entry point for the `apc` CLI.
+
+use agent_precommit::cli;
+use std::process::ExitCode;
+
+fn main() -> ExitCode {
+    match cli::run() {
+        Ok(code) => code,
+        Err(e) => {
+            eprintln!("Error: {e}");
+            ExitCode::FAILURE
+        }
+    }
+}
diff --git a/src/presets/mod.rs b/src/presets/mod.rs
new file mode 100644
index 0000000..21700fa
--- /dev/null
+++ b/src/presets/mod.rs
@@ -0,0 +1,64 @@
+//! Configuration presets for common project types.
+//!
+//! Presets provide sensible default configurations for different tech stacks.
+
+/// Available preset names.
+pub mod names {
+    /// Python projects (pytest, ruff, mypy).
+    pub const PYTHON: &str = "python";
+    /// Node.js/TypeScript projects (npm, eslint, jest).
+    pub const NODE: &str = "node";
+    /// Rust projects (cargo, clippy).
+    pub const RUST: &str = "rust";
+    /// Go projects (go test, golangci-lint).
+    pub const GO: &str = "go";
+}
+
+/// Returns a list of available preset names.
+#[must_use]
+pub const fn available() -> &'static [&'static str] {
+    &[names::PYTHON, names::NODE, names::RUST, names::GO]
+}
+
+/// Returns true if the preset name is valid.
+#[must_use]
+pub fn is_valid(name: &str) -> bool {
+    available().contains(&name)
+}
+
+/// Returns a description for a preset.
+#[must_use]
+pub fn description(name: &str) -> &'static str {
+    match name {
+        names::PYTHON => "Python projects (pytest, ruff, mypy, pre-commit integration)",
+        names::NODE => "Node.js/TypeScript projects (npm, eslint, jest, tsc)",
+        names::RUST => "Rust projects (cargo fmt, clippy, cargo test)",
+        names::GO => "Go projects (gofmt, golangci-lint, go test)",
+        _ => "Unknown preset",
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_available() {
+        assert!(!available().is_empty());
+        assert!(available().contains(&"python"));
+        assert!(available().contains(&"rust"));
+    }
+
+    #[test]
+    fn test_is_valid() {
+        assert!(is_valid("python"));
+        assert!(is_valid("node"));
+        assert!(!is_valid("invalid"));
+    }
+
+    #[test]
+    fn test_description() {
+        assert!(!description("python").is_empty());
+        assert!(!description("rust").is_empty());
+    }
+}
diff --git a/tests/integration_test.rs b/tests/integration_test.rs
new file mode 100644
index 0000000..0b435e1
--- /dev/null
+++ b/tests/integration_test.rs
@@ -0,0 +1,261 @@
+//! Integration tests for agent-precommit CLI.
+
+use assert_cmd::Command;
+use predicates::prelude::*;
+use tempfile::TempDir;
+
+/// Creates a test git repository.
+fn create_test_repo() -> TempDir {
+    let temp = TempDir::new().expect("create temp dir");
+
+    std::process::Command::new("git")
+        .args(["init"])
+        .current_dir(temp.path())
+        .output()
+        .expect("init repo");
+
+    std::process::Command::new("git")
+        .args(["config", "user.email", "test@test.com"])
+        .current_dir(temp.path())
+        .output()
+        .expect("set email");
+
+    std::process::Command::new("git")
+        .args(["config", "user.name", "Test"])
+        .current_dir(temp.path())
+        .output()
+        .expect("set name");
+
+    temp
+}
+
+#[test]
+fn test_help() {
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("--help")
+        .assert()
+        .success()
+        .stdout(predicate::str::contains("Smart pre-commit hooks"));
+}
+
+#[test]
+fn test_version() {
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("--version")
+        .assert()
+        .success()
+        .stdout(predicate::str::contains(env!("CARGO_PKG_VERSION")));
+}
+
+#[test]
+fn test_detect_default_human() {
+    let temp = create_test_repo();
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("detect")
+        .current_dir(temp.path())
+        .assert()
+        .success()
+        .stderr(predicate::str::contains("human"));
+}
+
+#[test]
+fn test_detect_agent_mode() {
+    let temp = create_test_repo();
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("detect")
+        .env("AGENT_MODE", "1")
+        .current_dir(temp.path())
+        .assert()
+        .success()
+        .stderr(predicate::str::contains("agent"));
+}
+
+#[test]
+fn test_init_creates_config() {
+    let temp = create_test_repo();
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("init")
+        .current_dir(temp.path())
+        .assert()
+        .success()
+        .stderr(predicate::str::contains("Created agent-precommit.toml"));
+
+    assert!(temp.path().join("agent-precommit.toml").exists());
+}
+
+#[test]
+fn test_init_with_preset() {
+    let temp = create_test_repo();
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .args(["init", "--preset", "rust"])
+        .current_dir(temp.path())
+        .assert()
+        .success();
+
+    let config = std::fs::read_to_string(temp.path().join("agent-precommit.toml"))
+        .expect("read config");
+
+    assert!(config.contains("clippy"));
+}
+
+#[test]
+fn test_init_already_exists() {
+    let temp = create_test_repo();
+    std::fs::write(temp.path().join("agent-precommit.toml"), "").expect("create config");
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("init")
+        .current_dir(temp.path())
+        .assert()
+        .failure()
+        .stderr(predicate::str::contains("already exists"));
+}
+
+#[test]
+fn test_init_force() {
+    let temp = create_test_repo();
+    std::fs::write(temp.path().join("agent-precommit.toml"), "").expect("create config");
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .args(["init", "--force"])
+        .current_dir(temp.path())
+        .assert()
+        .success();
+}
+
+#[test]
+fn test_validate_no_config() {
+    let temp = create_test_repo();
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("validate")
+        .current_dir(temp.path())
+        .assert()
+        .failure()
+        .stderr(predicate::str::contains("not found"));
+}
+
+#[test]
+fn test_validate_valid_config() {
+    let temp = create_test_repo();
+
+    // Initialize first
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("init")
+        .current_dir(temp.path())
+        .output()
+        .expect("init");
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("validate")
+        .current_dir(temp.path())
+        .assert()
+        .success()
+        .stderr(predicate::str::contains("valid"));
+}
+
+#[test]
+fn test_list_checks() {
+    let temp = create_test_repo();
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("init")
+        .current_dir(temp.path())
+        .output()
+        .expect("init");
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("list")
+        .current_dir(temp.path())
+        .assert()
+        .success()
+        .stderr(predicate::str::contains("Human mode checks"))
+        .stderr(predicate::str::contains("Agent mode checks"));
+}
+
+#[test]
+fn test_install_hook() {
+    let temp = create_test_repo();
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("install")
+        .current_dir(temp.path())
+        .assert()
+        .success()
+        .stderr(predicate::str::contains("Installed pre-commit hook"));
+
+    let hook_path = temp.path().join(".git/hooks/pre-commit");
+    assert!(hook_path.exists());
+
+    let hook_content = std::fs::read_to_string(&hook_path).expect("read hook");
+    assert!(hook_content.contains("agent-precommit"));
+}
+
+#[test]
+fn test_uninstall_hook() {
+    let temp = create_test_repo();
+
+    // Install first
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("install")
+        .current_dir(temp.path())
+        .output()
+        .expect("install");
+
+    // Then uninstall
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("uninstall")
+        .current_dir(temp.path())
+        .assert()
+        .success()
+        .stderr(predicate::str::contains("Removed"));
+
+    assert!(!temp.path().join(".git/hooks/pre-commit").exists());
+}
+
+#[test]
+fn test_skip_with_env_var() {
+    let temp = create_test_repo();
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("run")
+        .env("APC_SKIP", "1")
+        .current_dir(temp.path())
+        .assert()
+        .success()
+        .stderr(predicate::str::contains("Skipping"));
+}
+
+#[test]
+fn test_not_git_repo() {
+    let temp = TempDir::new().expect("create temp dir");
+
+    Command::cargo_bin("apc")
+        .unwrap()
+        .arg("detect")
+        .current_dir(temp.path())
+        .assert()
+        .failure()
+        .stderr(predicate::str::contains("Not in a Git repository"));
+}