PHANTOM/paper/concat_code.sh

#!/bin/bash
# Script to concatenate all code from source directories for LaTeX inclusion

# Detect project root (parent of paper directory)
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
PROJECT_ROOT="$(cd "$SCRIPT_DIR/.." && pwd)"
OUTPUT_FILE="$PROJECT_ROOT/paper/build/concatenated_code.tex"

# Create output directory if it doesn't exist
mkdir -p "$(dirname "$OUTPUT_FILE")"

# Clear the output file
> "$OUTPUT_FILE"

# Function to add a file to the concatenated output
add_file() {
    local filepath="$1"
    local relpath="${filepath#$PROJECT_ROOT/}"
    local escaped_path="${relpath//_/\\_}"

    # Add section header and code listing (no language-specific highlighting)
    echo "\\subsection{${escaped_path}}" >> "$OUTPUT_FILE"
    echo "\\begin{lstlisting}[caption={${escaped_path}}]" >> "$OUTPUT_FILE"
    cat "$filepath" >> "$OUTPUT_FILE"
    echo "" >> "$OUTPUT_FILE"
    echo "\\end{lstlisting}" >> "$OUTPUT_FILE"
    echo "" >> "$OUTPUT_FILE"
}

# Add header
cat >> "$OUTPUT_FILE" << 'EOF'
% Auto-generated code concatenation
% DO NOT EDIT MANUALLY - Generated by concat_code.sh

\section{Source Code}

EOF

# Process each directory
echo "Concatenating code from source directories..."

# Backend
find "$PROJECT_ROOT/backend" -type f \( -name "*.py" -o -name "*.js" -o -name "*.sh" -o -name "*.yml" -o -name "*.yaml" \) | sort | while read -r file; do
    add_file "$file"
done

# Experiments
find "$PROJECT_ROOT/experiments" -type f \( -name "*.py" -o -name "*.js" -o -name "*.sh" -o -name "*.yml" -o -name "*.yaml" \) | sort | while read -r file; do
    add_file "$file"
done

# Docker
find "$PROJECT_ROOT/docker" -type f \( -name "*.py" -o -name "*.sh" -o -name "*.yml" -o -name "*.yaml" -o -name "Dockerfile*" \) | sort | while read -r file; do
    add_file "$file"
done

# Web/src
find "$PROJECT_ROOT/web/src" -type f \( -name "*.js" -o -name "*.jsx" -o -name "*.ts" -o -name "*.tsx" \) | sort | while read -r file; do
    add_file "$file"
done

echo "Code concatenation complete: $OUTPUT_FILE"