maestro-flow 0.5.36 → 0.5.38

package/.claude/skills/scholar-latex-organizer/phases/02-cleanup-organize.md

@@ -1,500 +1,500 @@
-# Phase 2: Cleanup & Organize
-
-## Objective
-
-Create a clean, Overleaf-ready directory structure from the analyzed template. Clean the main .tex file, create modular section files, copy assets to proper locations, and apply conference-specific configuration.
-
-> **COMPACT SENTINEL**: This is Phase 2 (Cleanup & Organize) of scholar-latex-organizer.
-> If only this sentinel remains after context compression, immediately `Read("phases/02-cleanup-organize.md")` to recover full phase content.
-> Status: Check TodoWrite for current step progress.
-
-## Input
-
-- `analysisResult`: From Phase 1 (fileInventory, mainFile, conferenceType, issues, tempDir)
-- `sectionStructure`: Standard (default) or custom section list
-- `outputDir`: Target output directory path
-
-## Execution
-
-### Step 2.1: Create Output Structure
-
-Create the clean directory structure for the organized template.
-
-```bash
-# Create output directory structure
-mkdir -p "$OUTPUT_DIR"
-mkdir -p "$OUTPUT_DIR/text"
-mkdir -p "$OUTPUT_DIR/figures"
-mkdir -p "$OUTPUT_DIR/tables"
-mkdir -p "$OUTPUT_DIR/styles"
-
-echo "Created directory structure:"
-find "$OUTPUT_DIR" -type d | sort
-```
-
-Target structure:
-```
-outputDir/
-├── main.tex              # Cleaned main file with \input references
-├── text/                 # Section content files
-│   ├── 01-introduction.tex
-│   ├── 02-related-work.tex
-│   ├── 03-method.tex
-│   ├── 04-experiments.tex
-│   └── 05-conclusion.tex
-├── figures/              # All image files
-├── tables/               # Table definitions
-│   └── example-table.tex # Placeholder to prevent Overleaf auto-deletion
-├── styles/               # .sty and .cls files (untouched)
-├── references.bib        # Consolidated bibliography
-└── README.md             # Generated in Phase 3
-```
-
-### Step 2.2: Clean Main File (main.tex)
-
-Read the original main file and create a cleaned version. The cleaned main.tex should:
-
-**Keep**:
-- `\documentclass` declaration with correct options
-- Required `\usepackage` declarations
-- Core configuration (page setup, theorem definitions, custom commands)
-- `\begin{document}` ... `\end{document}` wrapper
-- `\maketitle`, `\bibliography`, `\appendix` commands
-
-**Remove**:
-- Example/sample section content (everything between `\begin{document}` and `\end{document}` that is example text)
-- Verbose instructional comments (multi-line tutorial blocks)
-- Example `\author`, `\title`, `\affiliation` content (replace with TODO placeholders)
-- Lines containing `DELETE`, `REMOVE`, `Replace this`, `Your ... here`
-- Commented-out code blocks longer than 3 lines
-
-**Add**:
-- `\input{text/01-introduction}` imports for each section file
-- TODO comment placeholders for title, author, abstract
-
-**Example cleaned main.tex for ACM template**:
-
-```latex
-\documentclass[sigconf,anonymous,nonacm]{acmart}
-
-% --- Required Packages ---
-\usepackage{booktabs}
-\usepackage{graphicx}
-\usepackage{subcaption}
-\usepackage{amsmath}
-
-% --- Path Configuration ---
-\graphicspath{{figures/}}
-
-% --- Custom Commands ---
-% Add your custom commands here
-
-% === Document Metadata ===
-% TODO: Replace with your paper information
-\title{Your Paper Title}
-
-\author{Anonymous Author(s)}
-% \author{First Author}
-% \affiliation{%
-%   \institution{University Name}
-%   \city{City}
-%   \country{Country}
-% }
-% \email{author@example.com}
-
-\begin{document}
-
-% --- Abstract ---
-\begin{abstract}
-% TODO: Write your abstract here
-\end{abstract}
-
-\maketitle
-
-% --- Main Content ---
-\input{text/01-introduction}
-\input{text/02-related-work}
-\input{text/03-method}
-\input{text/04-experiments}
-\input{text/05-conclusion}
-
-% --- Acknowledgments ---
-% \begin{acks}
-% TODO: Add acknowledgments (hidden during anonymous review)
-% \end{acks}
-
-% --- References ---
-\bibliographystyle{ACM-Reference-Format}
-\bibliography{references}
-
-% --- Appendix ---
-% \appendix
-% \input{text/appendix}
-
-\end{document}
-```
-
----
-
-**CHECKPOINT**: Before proceeding to Step 2.3, verify:
-- [ ] Output directory structure created successfully
-- [ ] Main file cleaned and written to `outputDir/main.tex`
-- [ ] All `\input` references point to correct `text/` paths
-- [ ] `\graphicspath` set to `{figures/}`
-- [ ] `\bibliography` points to `references` (without .bib extension)
-
-If any check fails, fix before continuing.
-
----
-
-### Step 2.3: Conference-Specific Configuration
-
-Apply the correct configuration based on the detected conference type from `analysisResult.conferenceType`.
-
-#### KDD 2026 (ACM acmart with nonacm)
-
-**Submission version** (anonymous):
-```latex
-\documentclass[sigconf,anonymous,nonacm]{acmart}
-
-% KDD-specific settings
-\settopmatter{printacmref=false,printccs=false,printfolios=false}
-\setcopyright{none}
-\renewcommand\footnotetextcopyrightpermission[1]{}
-\pagestyle{plain}
-
-% Remove ACM reference format
-\AtBeginDocument{%
-  \providecommand\BibTeX{{%
-    Bib\TeX}}}
-```
-
-**Camera-ready version** (de-anonymized):
-```latex
-\documentclass[sigconf]{acmart}
-
-% KDD camera-ready settings
-\setcopyright{acmlicensed}
-\acmConference[KDD '26]{Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining}{August 3--7, 2026}{Toronto, ON, Canada}
-\acmBooktitle{Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD '26), August 3--7, 2026, Toronto, ON, Canada}
-\acmDOI{10.1145/xxxxxxx.xxxxxxx}
-\acmISBN{978-x-xxxx-xxxx-x}
-
-% Include author information
-\author{First Author}
-\affiliation{%
-  \institution{University Name}
-  \city{City}
-  \country{Country}
-}
-\email{author@example.com}
-```
-
-#### General ACM (acmart)
-
-```latex
-\documentclass[sigconf,anonymous,review]{acmart}
-
-% Standard ACM anonymous submission
-\settopmatter{printacmref=false}
-\setcopyright{none}
-\renewcommand\footnotetextcopyrightpermission[1]{}
-```
-
-#### NeurIPS
-
-```latex
-\documentclass{neurips_2025}
-% Options: [preprint] for preprint, [final] for camera-ready
-% Default (no option) = anonymous submission
-
-\usepackage[utf8]{inputenc}
-\usepackage[T1]{fontenc}
-\usepackage{hyperref}
-\usepackage{url}
-\usepackage{booktabs}
-\usepackage{amsfonts}
-\usepackage{nicefrac}
-\usepackage{microtype}
-```
-
-#### ICLR
-
-```latex
-\documentclass{iclr2025_conference}
-% Anonymous submission by default
-
-\usepackage{amsmath}
-\usepackage{amssymb}
-\usepackage{natbib}
-\usepackage{graphicx}
-\usepackage{hyperref}
-\usepackage{url}
-```
-
-#### CVPR/ICCV
-
-```latex
-\documentclass[10pt,twocolumn,letterpaper]{article}
-\usepackage{cvpr}
-
-% Submission mode
-\usepackage[pagenumbers]{cvpr} % Use this for submission
-% \usepackage{cvpr}            % Use this for camera-ready
-
-\usepackage{graphicx}
-\usepackage{amsmath}
-\usepackage{amssymb}
-\usepackage{booktabs}
-
-\def\cvprPaperID{****} % Replace with your paper ID
-```
-
-#### AAAI
-
-```latex
-\documentclass[letterpaper]{article}
-\usepackage{aaai25}
-\usepackage{times}
-\usepackage{helvet}
-\usepackage{courier}
-\usepackage[hyphens]{url}
-\usepackage{graphicx}
-\urlstyle{rm}
-
-\pdfinfo{
-/Title (Your Paper Title)
-/Author (Anonymous)
-}
-```
-
-Apply the matching configuration to `main.tex`. If the conference type is uncertain, keep the original `\documentclass` line and add a comment noting the detected type.
-
-### Step 2.4: Create Section Files (text/)
-
-Create independent .tex files for each section. Each file contains ONLY the section content -- no preamble, no `\begin{document}`, no `\end{document}`.
-
-**Standard section structure** (default):
-
-```bash
-# Create section files
-cat > "$OUTPUT_DIR/text/01-introduction.tex" << 'SECTION_EOF'
-\section{Introduction}
-\label{sec:introduction}
-
-% TODO: Write your introduction here
-%
-% Suggested structure:
-% - Problem statement and motivation
-% - Key challenges
-% - Your approach and contributions
-% - Paper organization
-
-SECTION_EOF
-
-cat > "$OUTPUT_DIR/text/02-related-work.tex" << 'SECTION_EOF'
-\section{Related Work}
-\label{sec:related-work}
-
-% TODO: Write your related work review here
-%
-% Suggested structure:
-% - Group related work by topic/approach
-% - Compare and contrast with your work
-% - Identify gaps your work addresses
-
-SECTION_EOF
-
-cat > "$OUTPUT_DIR/text/03-method.tex" << 'SECTION_EOF'
-\section{Method}
-\label{sec:method}
-
-% TODO: Describe your method/approach here
-%
-% Suggested structure:
-% - Problem formulation
-% - Overview of your approach
-% - Technical details (subsections)
-% - Theoretical analysis (if applicable)
-
-SECTION_EOF
-
-cat > "$OUTPUT_DIR/text/04-experiments.tex" << 'SECTION_EOF'
-\section{Experiments}
-\label{sec:experiments}
-
-% TODO: Present your experimental evaluation here
-%
-% Suggested structure:
-% - Experimental setup (datasets, baselines, metrics)
-% - Main results
-% - Ablation studies
-% - Case studies / qualitative analysis
-
-SECTION_EOF
-
-cat > "$OUTPUT_DIR/text/05-conclusion.tex" << 'SECTION_EOF'
-\section{Conclusion}
-\label{sec:conclusion}
-
-% TODO: Write your conclusion here
-%
-% Suggested structure:
-% - Summary of contributions
-% - Key findings
-% - Limitations
-% - Future work
-
-SECTION_EOF
-
-echo "Created section files:"
-ls -la "$OUTPUT_DIR/text/"
-```
-
-**IMPORTANT**: Section files must contain ONLY section content. Never include:
-- `\documentclass`
-- `\usepackage`
-- `\begin{document}` / `\end{document}`
-- Preamble configuration
-
-If the user specified custom sections, create files matching their structure instead.
-
-### Step 2.5: Copy Assets
-
-Copy all supporting files to their correct locations.
-
-**Style files** (.sty, .cls, .bst):
-```bash
-# Copy style files to styles/ directory
-find "$TEMP_DIR" \( -name "*.sty" -o -name "*.cls" -o -name "*.bst" \) -type f -exec cp {} "$OUTPUT_DIR/styles/" \;
-
-echo "Copied style files:"
-ls -la "$OUTPUT_DIR/styles/"
-```
-
-**IMPORTANT**: Never modify .sty or .cls files. Copy them exactly as-is.
-
-If style files are in the styles/ subdirectory, ensure `main.tex` can find them. Add to main.tex preamble if needed:
-```latex
-% Style file path (if styles are in subdirectory)
-\makeatletter
-\def\input@path{{styles/}}
-\makeatother
-```
-
-**Images** (.png, .jpg, .jpeg, .pdf, .eps):
-```bash
-# Copy non-PDF image files to figures/ directory
-find "$TEMP_DIR" \( -name "*.png" -o -name "*.jpg" -o -name "*.jpeg" -o -name "*.eps" \) -type f -exec cp {} "$OUTPUT_DIR/figures/" \;
-
-# For PDF files, only copy those actually referenced by \includegraphics in .tex files
-# Step 1: Extract referenced PDF filenames from all .tex files
-REFERENCED_PDFS=$(grep -roh '\\includegraphics\[.*\]{[^}]*\.pdf}' "$TEMP_DIR"/*.tex "$TEMP_DIR"/**/*.tex 2>/dev/null \
-  | sed 's/.*{\([^}]*\)}/\1/' | xargs -I{} basename {} 2>/dev/null | sort -u)
-
-# Step 2: Copy only referenced PDFs
-if [ -n "$REFERENCED_PDFS" ]; then
-  echo "$REFERENCED_PDFS" | while read pdf_name; do
-    find "$TEMP_DIR" -name "$pdf_name" -type f -exec cp {} "$OUTPUT_DIR/figures/" \;
-  done
-fi
-
-# Step 3: List unreferenced PDFs for user review
-echo "--- Unreferenced PDF files (may need manual placement) ---"
-find "$TEMP_DIR" -name "*.pdf" -type f | while read pdf_file; do
-  pdf_basename=$(basename "$pdf_file")
-  if ! echo "$REFERENCED_PDFS" | grep -q "$pdf_basename"; then
-    echo "  $pdf_file"
-  fi
-done
-
-echo "Copied image files:"
-ls -la "$OUTPUT_DIR/figures/"
-```
-
-**Tables placeholder** (prevent Overleaf auto-deletion of empty dirs):
-```bash
-# Create example table file
-cat > "$OUTPUT_DIR/tables/example-table.tex" << 'TABLE_EOF'
-% Example table template
-% Usage in section files: \input{tables/example-table}
-%
-% \begin{table}[t]
-%   \caption{Your Table Caption}
-%   \label{tab:example}
-%   \begin{tabular}{lcc}
-%     \toprule
-%     Method & Metric 1 & Metric 2 \\
-%     \midrule
-%     Baseline & 0.00 & 0.00 \\
-%     Ours     & 0.00 & 0.00 \\
-%     \bottomrule
-%   \end{tabular}
-% \end{table}
-TABLE_EOF
-```
-
-**Bibliography** (.bib):
-```bash
-# Consolidate bibliography files
-# If multiple .bib files exist, merge them
-BIB_FILES=$(find "$TEMP_DIR" -name "*.bib" -type f)
-BIB_COUNT=$(echo "$BIB_FILES" | grep -c .)
-
-if [ "$BIB_COUNT" -eq 1 ]; then
-  cp "$BIB_FILES" "$OUTPUT_DIR/references.bib"
-elif [ "$BIB_COUNT" -gt 1 ]; then
-  # Merge multiple .bib files
-  cat $BIB_FILES > "$OUTPUT_DIR/references.bib"
-  echo "Merged $BIB_COUNT .bib files into references.bib"
-else
-  # Create empty .bib file
-  cat > "$OUTPUT_DIR/references.bib" << 'BIB_EOF'
-% Bibliography file
-% Add your references here or use a reference manager export
-
-% Example entry:
-% @inproceedings{author2025title,
-%   title={Paper Title},
-%   author={Author, First and Author, Second},
-%   booktitle={Conference Name},
-%   year={2025}
-% }
-BIB_EOF
-  echo "Created empty references.bib template"
-fi
-```
-
-### Final Verification
-
-After all steps, verify the output structure:
-
-```bash
-echo "=== Final Output Structure ==="
-find "$OUTPUT_DIR" -type f | sort
-
-echo ""
-echo "=== File Counts ==="
-echo "Section files: $(ls "$OUTPUT_DIR/text/"*.tex 2>/dev/null | wc -l)"
-echo "Style files: $(ls "$OUTPUT_DIR/styles/"* 2>/dev/null | wc -l)"
-echo "Figures: $(ls "$OUTPUT_DIR/figures/"* 2>/dev/null | wc -l)"
-echo "Tables: $(ls "$OUTPUT_DIR/tables/"* 2>/dev/null | wc -l)"
-echo "Main file: $(test -f "$OUTPUT_DIR/main.tex" && echo 'YES' || echo 'MISSING')"
-echo "Bibliography: $(test -f "$OUTPUT_DIR/references.bib" && echo 'YES' || echo 'MISSING')"
-```
-
-## Output
-
-Organized template directory at `outputDir/` containing:
-- `main.tex` -- cleaned and configured for the detected conference
-- `text/` -- modular section files (01 through 05)
-- `figures/` -- all image assets
-- `tables/` -- table templates with placeholder
-- `styles/` -- all .sty/.cls/.bst files (unmodified)
-- `references.bib` -- consolidated bibliography
-
-## Next Phase
-
-Phase 3: README & Finalize (`phases/03-readme-finalize.md`)
-- Receives: `analysisResult`, `conferenceInfo`, `outputDir`
-- Generates README.md with submission requirements and usage instructions
+# Phase 2: Cleanup & Organize
+
+## Objective
+
+Create a clean, Overleaf-ready directory structure from the analyzed template. Clean the main .tex file, create modular section files, copy assets to proper locations, and apply conference-specific configuration.
+
+> **COMPACT SENTINEL**: This is Phase 2 (Cleanup & Organize) of scholar-latex-organizer.
+> If only this sentinel remains after context compression, immediately `Read("phases/02-cleanup-organize.md")` to recover full phase content.
+> Status: Check TodoWrite for current step progress.
+
+## Input
+
+- `analysisResult`: From Phase 1 (fileInventory, mainFile, conferenceType, issues, tempDir)
+- `sectionStructure`: Standard (default) or custom section list
+- `outputDir`: Target output directory path
+
+## Execution
+
+### Step 2.1: Create Output Structure
+
+Create the clean directory structure for the organized template.
+
+```bash
+# Create output directory structure
+mkdir -p "$OUTPUT_DIR"
+mkdir -p "$OUTPUT_DIR/text"
+mkdir -p "$OUTPUT_DIR/figures"
+mkdir -p "$OUTPUT_DIR/tables"
+mkdir -p "$OUTPUT_DIR/styles"
+
+echo "Created directory structure:"
+find "$OUTPUT_DIR" -type d | sort
+```
+
+Target structure:
+```
+outputDir/
+├── main.tex              # Cleaned main file with \input references
+├── text/                 # Section content files
+│   ├── 01-introduction.tex
+│   ├── 02-related-work.tex
+│   ├── 03-method.tex
+│   ├── 04-experiments.tex
+│   └── 05-conclusion.tex
+├── figures/              # All image files
+├── tables/               # Table definitions
+│   └── example-table.tex # Placeholder to prevent Overleaf auto-deletion
+├── styles/               # .sty and .cls files (untouched)
+├── references.bib        # Consolidated bibliography
+└── README.md             # Generated in Phase 3
+```
+
+### Step 2.2: Clean Main File (main.tex)
+
+Read the original main file and create a cleaned version. The cleaned main.tex should:
+
+**Keep**:
+- `\documentclass` declaration with correct options
+- Required `\usepackage` declarations
+- Core configuration (page setup, theorem definitions, custom commands)
+- `\begin{document}` ... `\end{document}` wrapper
+- `\maketitle`, `\bibliography`, `\appendix` commands
+
+**Remove**:
+- Example/sample section content (everything between `\begin{document}` and `\end{document}` that is example text)
+- Verbose instructional comments (multi-line tutorial blocks)
+- Example `\author`, `\title`, `\affiliation` content (replace with TODO placeholders)
+- Lines containing `DELETE`, `REMOVE`, `Replace this`, `Your ... here`
+- Commented-out code blocks longer than 3 lines
+
+**Add**:
+- `\input{text/01-introduction}` imports for each section file
+- TODO comment placeholders for title, author, abstract
+
+**Example cleaned main.tex for ACM template**:
+
+```latex
+\documentclass[sigconf,anonymous,nonacm]{acmart}
+
+% --- Required Packages ---
+\usepackage{booktabs}
+\usepackage{graphicx}
+\usepackage{subcaption}
+\usepackage{amsmath}
+
+% --- Path Configuration ---
+\graphicspath{{figures/}}
+
+% --- Custom Commands ---
+% Add your custom commands here
+
+% === Document Metadata ===
+% TODO: Replace with your paper information
+\title{Your Paper Title}
+
+\author{Anonymous Author(s)}
+% \author{First Author}
+% \affiliation{%
+%   \institution{University Name}
+%   \city{City}
+%   \country{Country}
+% }
+% \email{author@example.com}
+
+\begin{document}
+
+% --- Abstract ---
+\begin{abstract}
+% TODO: Write your abstract here
+\end{abstract}
+
+\maketitle
+
+% --- Main Content ---
+\input{text/01-introduction}
+\input{text/02-related-work}
+\input{text/03-method}
+\input{text/04-experiments}
+\input{text/05-conclusion}
+
+% --- Acknowledgments ---
+% \begin{acks}
+% TODO: Add acknowledgments (hidden during anonymous review)
+% \end{acks}
+
+% --- References ---
+\bibliographystyle{ACM-Reference-Format}
+\bibliography{references}
+
+% --- Appendix ---
+% \appendix
+% \input{text/appendix}
+
+\end{document}
+```
+
+---
+
+**CHECKPOINT**: Before proceeding to Step 2.3, verify:
+- [ ] Output directory structure created successfully
+- [ ] Main file cleaned and written to `outputDir/main.tex`
+- [ ] All `\input` references point to correct `text/` paths
+- [ ] `\graphicspath` set to `{figures/}`
+- [ ] `\bibliography` points to `references` (without .bib extension)
+
+If any check fails, fix before continuing.
+
+---
+
+### Step 2.3: Conference-Specific Configuration
+
+Apply the correct configuration based on the detected conference type from `analysisResult.conferenceType`.
+
+#### KDD 2026 (ACM acmart with nonacm)
+
+**Submission version** (anonymous):
+```latex
+\documentclass[sigconf,anonymous,nonacm]{acmart}
+
+% KDD-specific settings
+\settopmatter{printacmref=false,printccs=false,printfolios=false}
+\setcopyright{none}
+\renewcommand\footnotetextcopyrightpermission[1]{}
+\pagestyle{plain}
+
+% Remove ACM reference format
+\AtBeginDocument{%
+  \providecommand\BibTeX{{%
+    Bib\TeX}}}
+```
+
+**Camera-ready version** (de-anonymized):
+```latex
+\documentclass[sigconf]{acmart}
+
+% KDD camera-ready settings
+\setcopyright{acmlicensed}
+\acmConference[KDD '26]{Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining}{August 3--7, 2026}{Toronto, ON, Canada}
+\acmBooktitle{Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD '26), August 3--7, 2026, Toronto, ON, Canada}
+\acmDOI{10.1145/xxxxxxx.xxxxxxx}
+\acmISBN{978-x-xxxx-xxxx-x}
+
+% Include author information
+\author{First Author}
+\affiliation{%
+  \institution{University Name}
+  \city{City}
+  \country{Country}
+}
+\email{author@example.com}
+```
+
+#### General ACM (acmart)
+
+```latex
+\documentclass[sigconf,anonymous,review]{acmart}
+
+% Standard ACM anonymous submission
+\settopmatter{printacmref=false}
+\setcopyright{none}
+\renewcommand\footnotetextcopyrightpermission[1]{}
+```
+
+#### NeurIPS
+
+```latex
+\documentclass{neurips_2025}
+% Options: [preprint] for preprint, [final] for camera-ready
+% Default (no option) = anonymous submission
+
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{hyperref}
+\usepackage{url}
+\usepackage{booktabs}
+\usepackage{amsfonts}
+\usepackage{nicefrac}
+\usepackage{microtype}
+```
+
+#### ICLR
+
+```latex
+\documentclass{iclr2025_conference}
+% Anonymous submission by default
+
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{natbib}
+\usepackage{graphicx}
+\usepackage{hyperref}
+\usepackage{url}
+```
+
+#### CVPR/ICCV
+
+```latex
+\documentclass[10pt,twocolumn,letterpaper]{article}
+\usepackage{cvpr}
+
+% Submission mode
+\usepackage[pagenumbers]{cvpr} % Use this for submission
+% \usepackage{cvpr}            % Use this for camera-ready
+
+\usepackage{graphicx}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{booktabs}
+
+\def\cvprPaperID{****} % Replace with your paper ID
+```
+
+#### AAAI
+
+```latex
+\documentclass[letterpaper]{article}
+\usepackage{aaai25}
+\usepackage{times}
+\usepackage{helvet}
+\usepackage{courier}
+\usepackage[hyphens]{url}
+\usepackage{graphicx}
+\urlstyle{rm}
+
+\pdfinfo{
+/Title (Your Paper Title)
+/Author (Anonymous)
+}
+```
+
+Apply the matching configuration to `main.tex`. If the conference type is uncertain, keep the original `\documentclass` line and add a comment noting the detected type.
+
+### Step 2.4: Create Section Files (text/)
+
+Create independent .tex files for each section. Each file contains ONLY the section content -- no preamble, no `\begin{document}`, no `\end{document}`.
+
+**Standard section structure** (default):
+
+```bash
+# Create section files
+cat > "$OUTPUT_DIR/text/01-introduction.tex" << 'SECTION_EOF'
+\section{Introduction}
+\label{sec:introduction}
+
+% TODO: Write your introduction here
+%
+% Suggested structure:
+% - Problem statement and motivation
+% - Key challenges
+% - Your approach and contributions
+% - Paper organization
+
+SECTION_EOF
+
+cat > "$OUTPUT_DIR/text/02-related-work.tex" << 'SECTION_EOF'
+\section{Related Work}
+\label{sec:related-work}
+
+% TODO: Write your related work review here
+%
+% Suggested structure:
+% - Group related work by topic/approach
+% - Compare and contrast with your work
+% - Identify gaps your work addresses
+
+SECTION_EOF
+
+cat > "$OUTPUT_DIR/text/03-method.tex" << 'SECTION_EOF'
+\section{Method}
+\label{sec:method}
+
+% TODO: Describe your method/approach here
+%
+% Suggested structure:
+% - Problem formulation
+% - Overview of your approach
+% - Technical details (subsections)
+% - Theoretical analysis (if applicable)
+
+SECTION_EOF
+
+cat > "$OUTPUT_DIR/text/04-experiments.tex" << 'SECTION_EOF'
+\section{Experiments}
+\label{sec:experiments}
+
+% TODO: Present your experimental evaluation here
+%
+% Suggested structure:
+% - Experimental setup (datasets, baselines, metrics)
+% - Main results
+% - Ablation studies
+% - Case studies / qualitative analysis
+
+SECTION_EOF
+
+cat > "$OUTPUT_DIR/text/05-conclusion.tex" << 'SECTION_EOF'
+\section{Conclusion}
+\label{sec:conclusion}
+
+% TODO: Write your conclusion here
+%
+% Suggested structure:
+% - Summary of contributions
+% - Key findings
+% - Limitations
+% - Future work
+
+SECTION_EOF
+
+echo "Created section files:"
+ls -la "$OUTPUT_DIR/text/"
+```
+
+**IMPORTANT**: Section files must contain ONLY section content. Never include:
+- `\documentclass`
+- `\usepackage`
+- `\begin{document}` / `\end{document}`
+- Preamble configuration
+
+If the user specified custom sections, create files matching their structure instead.
+
+### Step 2.5: Copy Assets
+
+Copy all supporting files to their correct locations.
+
+**Style files** (.sty, .cls, .bst):
+```bash
+# Copy style files to styles/ directory
+find "$TEMP_DIR" \( -name "*.sty" -o -name "*.cls" -o -name "*.bst" \) -type f -exec cp {} "$OUTPUT_DIR/styles/" \;
+
+echo "Copied style files:"
+ls -la "$OUTPUT_DIR/styles/"
+```
+
+**IMPORTANT**: Never modify .sty or .cls files. Copy them exactly as-is.
+
+If style files are in the styles/ subdirectory, ensure `main.tex` can find them. Add to main.tex preamble if needed:
+```latex
+% Style file path (if styles are in subdirectory)
+\makeatletter
+\def\input@path{{styles/}}
+\makeatother
+```
+
+**Images** (.png, .jpg, .jpeg, .pdf, .eps):
+```bash
+# Copy non-PDF image files to figures/ directory
+find "$TEMP_DIR" \( -name "*.png" -o -name "*.jpg" -o -name "*.jpeg" -o -name "*.eps" \) -type f -exec cp {} "$OUTPUT_DIR/figures/" \;
+
+# For PDF files, only copy those actually referenced by \includegraphics in .tex files
+# Step 1: Extract referenced PDF filenames from all .tex files
+REFERENCED_PDFS=$(grep -roh '\\includegraphics\[.*\]{[^}]*\.pdf}' "$TEMP_DIR"/*.tex "$TEMP_DIR"/**/*.tex 2>/dev/null \
+  | sed 's/.*{\([^}]*\)}/\1/' | xargs -I{} basename {} 2>/dev/null | sort -u)
+
+# Step 2: Copy only referenced PDFs
+if [ -n "$REFERENCED_PDFS" ]; then
+  echo "$REFERENCED_PDFS" | while read pdf_name; do
+    find "$TEMP_DIR" -name "$pdf_name" -type f -exec cp {} "$OUTPUT_DIR/figures/" \;
+  done
+fi
+
+# Step 3: List unreferenced PDFs for user review
+echo "--- Unreferenced PDF files (may need manual placement) ---"
+find "$TEMP_DIR" -name "*.pdf" -type f | while read pdf_file; do
+  pdf_basename=$(basename "$pdf_file")
+  if ! echo "$REFERENCED_PDFS" | grep -q "$pdf_basename"; then
+    echo "  $pdf_file"
+  fi
+done
+
+echo "Copied image files:"
+ls -la "$OUTPUT_DIR/figures/"
+```
+
+**Tables placeholder** (prevent Overleaf auto-deletion of empty dirs):
+```bash
+# Create example table file
+cat > "$OUTPUT_DIR/tables/example-table.tex" << 'TABLE_EOF'
+% Example table template
+% Usage in section files: \input{tables/example-table}
+%
+% \begin{table}[t]
+%   \caption{Your Table Caption}
+%   \label{tab:example}
+%   \begin{tabular}{lcc}
+%     \toprule
+%     Method & Metric 1 & Metric 2 \\
+%     \midrule
+%     Baseline & 0.00 & 0.00 \\
+%     Ours     & 0.00 & 0.00 \\
+%     \bottomrule
+%   \end{tabular}
+% \end{table}
+TABLE_EOF
+```
+
+**Bibliography** (.bib):
+```bash
+# Consolidate bibliography files
+# If multiple .bib files exist, merge them
+BIB_FILES=$(find "$TEMP_DIR" -name "*.bib" -type f)
+BIB_COUNT=$(echo "$BIB_FILES" | grep -c .)
+
+if [ "$BIB_COUNT" -eq 1 ]; then
+  cp "$BIB_FILES" "$OUTPUT_DIR/references.bib"
+elif [ "$BIB_COUNT" -gt 1 ]; then
+  # Merge multiple .bib files
+  cat $BIB_FILES > "$OUTPUT_DIR/references.bib"
+  echo "Merged $BIB_COUNT .bib files into references.bib"
+else
+  # Create empty .bib file
+  cat > "$OUTPUT_DIR/references.bib" << 'BIB_EOF'
+% Bibliography file
+% Add your references here or use a reference manager export
+
+% Example entry:
+% @inproceedings{author2025title,
+%   title={Paper Title},
+%   author={Author, First and Author, Second},
+%   booktitle={Conference Name},
+%   year={2025}
+% }
+BIB_EOF
+  echo "Created empty references.bib template"
+fi
+```
+
+### Final Verification
+
+After all steps, verify the output structure:
+
+```bash
+echo "=== Final Output Structure ==="
+find "$OUTPUT_DIR" -type f | sort
+
+echo ""
+echo "=== File Counts ==="
+echo "Section files: $(ls "$OUTPUT_DIR/text/"*.tex 2>/dev/null | wc -l)"
+echo "Style files: $(ls "$OUTPUT_DIR/styles/"* 2>/dev/null | wc -l)"
+echo "Figures: $(ls "$OUTPUT_DIR/figures/"* 2>/dev/null | wc -l)"
+echo "Tables: $(ls "$OUTPUT_DIR/tables/"* 2>/dev/null | wc -l)"
+echo "Main file: $(test -f "$OUTPUT_DIR/main.tex" && echo 'YES' || echo 'MISSING')"
+echo "Bibliography: $(test -f "$OUTPUT_DIR/references.bib" && echo 'YES' || echo 'MISSING')"
+```
+
+## Output
+
+Organized template directory at `outputDir/` containing:
+- `main.tex` -- cleaned and configured for the detected conference
+- `text/` -- modular section files (01 through 05)
+- `figures/` -- all image assets
+- `tables/` -- table templates with placeholder
+- `styles/` -- all .sty/.cls/.bst files (unmodified)
+- `references.bib` -- consolidated bibliography
+
+## Next Phase
+
+Phase 3: README & Finalize (`phases/03-readme-finalize.md`)
+- Receives: `analysisResult`, `conferenceInfo`, `outputDir`
+- Generates README.md with submission requirements and usage instructions