added dev containers, added AGENTS.md, added wdl_to_bash extractor and tester

Author: jyang-broad

.devcontainer/.gitignore

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+# Dev Container artifacts
+.devcontainer/womtool*.jar
+
+# Python cache
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+env/
+venv/
+ENV/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+.hypothesis/
+
+# IDE
+.vscode/settings.json
+.vscode/launch.json
+.idea/
+
+# OS
+.DS_Store
+Thumbs.db

.devcontainer/Dockerfile

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+# .devcontainer/Dockerfile - Custom development container for WARP
+FROM mcr.microsoft.com/devcontainers/base:ubuntu-22.04
+
+LABEL maintainer="WARP Development"
+LABEL description="Development container for WARP WDL pipelines"
+
+# Avoid interactive prompts during package installation
+ENV DEBIAN_FRONTEND=noninteractive
+ENV WARP_HOME=/workspace
+
+# Update and install system dependencies
+RUN apt-get update && apt-get upgrade -y && \
+    apt-get install -y --no-install-recommends \
+    curl \
+    wget \
+    git \
+    build-essential \
+    ca-certificates \
+    openjdk-17-jdk-headless \
+    python3 \
+    python3-pip \
+    python3-venv \
+    python3-dev && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Setup womtool for WDL validation
+RUN mkdir -p /opt/womtool && \
+    cd /opt/womtool && \
+    WOMTOOL_VERSION="90" && \
+    wget -q "https://github.com/broadinstitute/cromwell/releases/download/${WOMTOOL_VERSION}/womtool-${WOMTOOL_VERSION}.jar" 2>/dev/null || \
+    echo "Note: womtool will be downloaded on first use" && \
+    ln -sf "womtool-${WOMTOOL_VERSION}.jar" womtool.jar 2>/dev/null || true
+
+# Create wrapper script for womtool
+RUN cat > /usr/local/bin/womtool << 'EOF' && chmod +x /usr/local/bin/womtool
+#!/bin/bash
+java -jar /opt/womtool/womtool.jar "$@"
+EOF
+
+# Upgrade pip and install core Python packages
+RUN python3 -m pip install --no-cache-dir --upgrade pip setuptools wheel && \
+    python3 -m pip install --no-cache-dir \
+    miniwdl==1.9.1 \
+    pytest==7.4.3 \
+    pytest-xdist==3.5.0 \
+    pytest-timeout==2.2.0 \
+    pytest-cov==4.1.0 \
+    pyyaml==6.0.1 \
+    jinja2==3.1.6 \
+    jsonschema==4.20.0 \
+    black==23.12.0 \
+    pylint==3.0.3 \
+    mypy==1.8.0 \
+    ruff==0.1.11 \
+    ipython \
+    jupyter \
+    jupyterlab
+
+# Set working directory
+WORKDIR /workspace
+
+# Display versions on container startup
+RUN cat > /usr/local/bin/show-versions << 'EOF' && chmod +x /usr/local/bin/show-versions
+#!/bin/bash
+echo "WARP Development Environment Versions:"
+echo "======================================"
+echo "Java: $(java -version 2>&1 | head -n1)"
+echo "Python: $(python3 --version)"
+echo "Pip: $(python3 -m pip --version | cut -d' ' -f1-2)"
+echo "Git: $(git --version)"
+echo ""
+echo "Python Packages:"
+python3 -m pip list | grep -E "miniwdl|pytest|black|mypy|ruff"
+EOF
+
+# Default command
+CMD ["/bin/bash"]