@kortix/sandbox 0.4.1

package/opencode/skills/KORTIX-paper-creator/SKILL.md

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+---
+name: kortix-paper-creator
+description: "Scientific paper writing in LaTeX -- full pipeline from structure to compiled PDF. TDD-driven: every section is compiled and verified before moving to the next. Covers project scaffolding, citation management (OpenAlex to BibTeX), per-section academic writing with self-reflection, figure/table inclusion, LaTeX compilation, and comprehensive verification. Triggers on: 'write a paper', 'create a paper', 'academic paper about', 'scientific paper', 'LaTeX paper', 'write up results as a paper', 'draft a paper on', 'research paper about', any request to produce a formal academic/scientific paper in LaTeX. Assumes research findings, data, and/or figures already exist or will be provided -- this skill handles the WRITING, not the experimentation."
+---
+
+# Scientific Paper Creator
+
+Write publication-quality scientific papers in LaTeX with a **test-driven workflow**: every section is compiled and verified before moving to the next. The paper is never in a broken state.
+
+## Bundled Resources
+
+This skill includes ready-to-use scripts and templates. Paths are relative to the skill directory (find it via `glob("**/KORTIX-paper-creator/")`):
+
+| Resource | Path | Purpose |
+|----------|------|---------|
+| **LaTeX template** | `assets/template.tex` | Minimal IMRaD template -- copy to `main.tex` |
+| **BibTeX generator** | `scripts/openalex_to_bibtex.py` | Convert OpenAlex API JSON to `.bib` entries |
+| **Compiler** | `scripts/compile.sh` | `pdflatex + bibtex` pipeline with error reporting |
+| **Verifier** | `scripts/verify.sh` | TDD verification suite (12 checks) |
+
+## The TDD Rule
+
+**After writing every section:**
+
+```
+1. WRITE section → sections/{name}.tex
+2. COMPILE: bash compile.sh paper/{slug}/main.tex
+3. VERIFY:  bash verify.sh paper/{slug}/
+4. If FAIL → FIX → go to 2
+5. If PASS → move to next section
+```
+
+The paper must compile and pass verification at every step. Never batch errors. Never skip verification. This is non-negotiable.
+
+## Pipeline Overview
+
+```
+Phase 1: SCAFFOLD  →  Create project, copy template, initialize empty sections
+                       Verify: compiles to valid (empty) PDF ✓
+
+Phase 2: CITE      →  Search literature (OpenAlex), build references.bib
+                       Verify: bibliography builds without errors ✓
+
+Phase 3: WRITE     →  Per-section composition in writing order
+                       Verify: compile + verify after EACH section ✓
+
+Phase 4: POLISH    →  Self-reflection pass, strict verification, final build
+                       Verify: verify.sh --strict passes with zero warnings ✓
+```
+
+## Filesystem Architecture
+
+```
+paper/{paper-slug}/
+├── main.tex                    # Master file (\input sections)
+├── references.bib              # BibTeX bibliography
+├── sections/
+│   ├── abstract.tex
+│   ├── introduction.tex
+│   ├── related-work.tex
+│   ├── methods.tex
+│   ├── results.tex
+│   ├── discussion.tex
+│   └── conclusion.tex
+├── figures/                    # .pdf/.png figures (+ generation scripts)
+├── data/                       # Supporting data, CSVs (optional)
+└── build/                      # Compilation output
+    └── main.pdf
+```
+
+## Phase 1: Scaffold
+
+### 1a. Create project structure
+
+```bash
+SLUG="paper-slug-here"
+mkdir -p "paper/$SLUG"/{sections,figures,data,build}
+```
+
+### 1b. Copy and adapt the template
+
+```bash
+SKILL_DIR=$(find . -path "*/KORTIX-paper-creator/assets/template.tex" -exec dirname {} \; | head -1 | sed 's|/assets||')
+cp "$SKILL_DIR/assets/template.tex" "paper/$SLUG/main.tex"
+```
+
+Edit `main.tex`: set `\title{}`, `\author{}`, and adapt `\documentclass` if targeting a specific venue:
+
+| Venue | Document class | Notes |
+|-------|---------------|-------|
+| General / arXiv | `\documentclass[11pt,a4paper]{article}` | Default in template |
+| IEEE conference | `\documentclass[conference]{IEEEtran}` | Remove geometry package |
+| ACM conference | `\documentclass[sigconf]{acmart}` | Remove geometry, use acmart bib style |
+| Springer LNCS | `\documentclass{llncs}` | Remove geometry, use splncs04 bib style |
+
+### 1c. Initialize section stubs
+
+Create each section file with a section header and TODO marker:
+
+```bash
+for sec in abstract introduction related-work methods results discussion conclusion; do
+    SECTION_TITLE=$(echo "$sec" | sed 's/-/ /g; s/\b\(.\)/\u\1/g')
+    if [ "$sec" = "abstract" ]; then
+        echo '\begin{abstract}' > "paper/$SLUG/sections/$sec.tex"
+        echo "% TODO: Write abstract" >> "paper/$SLUG/sections/$sec.tex"
+        echo '\end{abstract}' >> "paper/$SLUG/sections/$sec.tex"
+    else
+        echo "\\section{$SECTION_TITLE}" > "paper/$SLUG/sections/$sec.tex"
+        echo "\\label{sec:$sec}" >> "paper/$SLUG/sections/$sec.tex"
+        echo "% TODO: Write $sec" >> "paper/$SLUG/sections/$sec.tex"
+    fi
+done
+```
+
+### 1d. Initialize empty bibliography
+
+```bash
+echo "% References for $SLUG" > "paper/$SLUG/references.bib"
+echo "% Generated by openalex_to_bibtex.py and manual entries" >> "paper/$SLUG/references.bib"
+```
+
+### 1e. VERIFY: First green state
+
+```bash
+bash "$SKILL_DIR/scripts/compile.sh" "paper/$SLUG/main.tex"
+bash "$SKILL_DIR/scripts/verify.sh" "paper/$SLUG/"
+```
+
+The empty paper must compile cleanly. This is your baseline. Every subsequent change maintains this green state.
+
+## Phase 2: Literature & Citations
+
+### 2a. Search for papers
+
+Load the `kortix-paper-search` skill for OpenAlex API reference. Search strategy:
+
+```bash
+# Seminal/highly-cited papers
+curl -s "https://api.openalex.org/works?search=YOUR+TOPIC&filter=cited_by_count:>50,type:article,has_abstract:true&sort=cited_by_count:desc&per_page=15&select=id,display_name,publication_year,cited_by_count,doi,authorships,abstract_inverted_index&mailto=agent@kortix.ai"
+
+# Recent work (last 2-3 years)
+curl -s "https://api.openalex.org/works?search=YOUR+TOPIC&filter=publication_year:>2023,type:article&sort=publication_date:desc&per_page=15&mailto=agent@kortix.ai"
+
+# Review/survey papers
+curl -s "https://api.openalex.org/works?search=YOUR+TOPIC&filter=type:review&sort=cited_by_count:desc&per_page=10&mailto=agent@kortix.ai"
+```
+
+### 2b. Generate BibTeX entries
+
+Pipe OpenAlex results through the converter:
+
+```bash
+curl -s "https://api.openalex.org/works?search=YOUR+TOPIC&per_page=20&mailto=agent@kortix.ai" | \
+    python3 "$SKILL_DIR/scripts/openalex_to_bibtex.py" >> "paper/$SLUG/references.bib"
+```
+
+For non-OpenAlex sources (web pages, books, reports), add manual BibTeX entries:
+
+```bibtex
+@misc{authorYYYYtitle,
+  title = {Page Title},
+  author = {Author Name},
+  year = {2024},
+  url = {https://example.com/page},
+  note = {Accessed: 2024-01-15}
+}
+
+@book{authorYYYYbook,
+  title = {Book Title},
+  author = {First Author and Second Author},
+  year = {2024},
+  publisher = {Publisher Name},
+  edition = {2nd}
+}
+```
+
+### 2c. VERIFY: Bibliography builds
+
+```bash
+bash "$SKILL_DIR/scripts/compile.sh" "paper/$SLUG/main.tex"
+bash "$SKILL_DIR/scripts/verify.sh" "paper/$SLUG/"
+```
+
+Check: zero BibTeX errors, all `.bib` entries parse correctly.
+
+## Phase 3: Per-Section Writing
+
+### Writing Order
+
+Write sections in this order (each one builds on context from the previous):
+
+1. **Abstract** (draft) -- establishes scope, will be revised last
+2. **Introduction** -- context, problem, gap, contribution
+3. **Methods** -- what you did and how
+4. **Results** -- what you found
+5. **Discussion** -- what it means, limitations
+6. **Related Work** -- needs full paper context to position contribution
+7. **Conclusion** -- recap, future work
+8. **Abstract** (final) -- revise to match actual paper content
+
+### The Writing Loop (for each section)
+
+```
+1. READ all previously written sections to build context
+2. WRITE the section following the guidance below
+3. COMPILE + VERIFY
+4. SELF-REFLECT: re-read critically
+   - Every factual claim has a \cite{}?
+   - No filler words or empty hedging?
+   - Logical flow between paragraphs?
+   - Consistent with other sections?
+   - Quantitative where possible?
+5. REVISE if needed → COMPILE + VERIFY again
+6. Section DONE → next
+```
+
+### Section-Specific Guidance
+
+#### Abstract (150-300 words)
+
+Structure: **Context** (1-2 sentences) → **Problem** → **Approach** → **Key results** (quantitative!) → **Implications**.
+
+```latex
+\begin{abstract}
+[Context sentence setting the broad area.]
+[Problem: what gap or challenge exists.]
+[Approach: what this paper does -- "We propose/present/introduce..."]
+[Results: key quantitative findings -- "Our method achieves X\% on Y, outperforming Z by N\%."]
+[Implications: why it matters.]
+\end{abstract}
+```
+
+Rules: No citations in abstract. No undefined acronyms. Every number must appear in the actual results.
+
+#### Introduction
+
+**Funnel structure:** broad context → specific problem → gap in existing work → your contribution → paper outline.
+
+```latex
+\section{Introduction}
+\label{sec:introduction}
+
+% Paragraph 1: Broad context (2-3 sentences)
+% Paragraph 2: Narrow to specific problem
+% Paragraph 3: What's been tried, what's missing (the gap)
+% Paragraph 4: Your contribution -- be specific and concrete
+%   "Our contributions are as follows:
+%   \begin{itemize}
+%     \item We propose...
+%     \item We demonstrate...
+%     \item We release...
+%   \end{itemize}"
+% Paragraph 5: Paper outline
+%   "The remainder of this paper is organized as follows. \secref{sec:related-work} reviews..."
+```
+
+Rules: End with explicit contribution list. Every contribution claimed here must be backed by evidence in Results/Discussion.
+
+#### Methods
+
+**Reproducible detail.** Another researcher should be able to replicate your work from this section alone.
+
+```latex
+\section{Methods}
+\label{sec:methods}
+
+% Define notation before using it:
+% "Let $\mathcal{D} = \{(x_i, y_i)\}_{i=1}^{N}$ denote the training set..."
+
+% Algorithms as pseudocode:
+% \begin{algorithm}[t]
+%   \caption{Algorithm Name}
+%   \label{alg:name}
+%   \begin{algorithmic}[1]
+%     \REQUIRE Input description
+%     \ENSURE Output description
+%     \STATE Step 1
+%     \FOR{condition}
+%       \STATE Step in loop
+%     \ENDFOR
+%     \RETURN result
+%   \end{algorithmic}
+% \end{algorithm}
+```
+
+Rules: Define all notation. Be precise about dimensions, loss functions, optimization details. Use consistent math notation throughout (define `\newcommand` macros in `main.tex` preamble).
+
+#### Results
+
+**Lead with the main finding.** Then support with details.
+
+```latex
+\section{Results}
+\label{sec:results}
+
+% Paragraph 1: Main result (the headline number)
+% "Our method achieves X\% accuracy on Y benchmark, representing a Z\% improvement
+%  over the previous state of the art~\citep{baseline2024}."
+
+% Table with main results:
+% \begin{table}[t]
+%   \centering
+%   \caption{Main results on [benchmark]. Bold = best, underline = second best.}
+%   \label{tab:main-results}
+%   \begin{tabular}{lcc}
+%     \toprule
+%     Method & Metric 1 & Metric 2 \\
+%     \midrule
+%     Baseline A~\citep{ref} & 82.3 & 91.1 \\
+%     Baseline B~\citep{ref} & 84.7 & 92.4 \\
+%     \textbf{Ours} & \textbf{87.2} & \textbf{94.1} \\
+%     \bottomrule
+%   \end{tabular}
+% \end{table}
+
+% Subsequent paragraphs: ablation studies, analysis, per-dataset breakdown
+% Every figure and table MUST be referenced: "As shown in \figref{fig:x}..."
+```
+
+Rules: Every figure/table referenced in text at least once. Report statistical significance or confidence intervals where applicable. No cherry-picking -- report all metrics, including where you don't win.
+
+#### Discussion
+
+**Interpretation, not repetition.** Don't restate results -- explain what they mean.
+
+```latex
+\section{Discussion}
+\label{sec:discussion}
+
+% Paragraph 1: Interpret main findings -- what do the results tell us?
+% Paragraph 2: Compare with prior work -- how do results relate to existing literature?
+% Paragraph 3: Limitations -- be honest and specific
+%   "Our approach has several limitations. First, ... Second, ..."
+% Paragraph 4: Broader implications -- what does this enable?
+% Paragraph 5: Future work -- concrete directions, not vague hand-waving
+```
+
+Rules: Limitations must be genuine, not token gestures. Future work should be specific enough to be actionable.
+
+#### Related Work
+
+Written **after** Methods/Results/Discussion so you can precisely position your contribution against the literature.
+
+```latex
+\section{Related Work}
+\label{sec:related-work}
+
+% Organize THEMATICALLY, not chronologically:
+% \subsection{Theme A}
+% "Several works have addressed ... \citep{a,b,c}. Specifically, A does X, B does Y.
+%  In contrast, our approach differs by Z."
+%
+% \subsection{Theme B}
+% "Another line of work focuses on ... \citep{d,e,f}.
+%  While these methods ..., they do not address ..., which is the focus of our work."
+```
+
+Rules: For each group of related work, explicitly state how your work differs. Don't just list papers -- synthesize and contrast. Every paper cited here should be in `references.bib`.
+
+#### Conclusion
+
+**No new information.** Brief recap of contribution and results, then future directions.
+
+```latex
+\section{Conclusion}
+\label{sec:conclusion}
+
+% Paragraph 1: What we did and what we found (3-4 sentences max)
+% "In this paper, we presented [method] for [problem].
+%  Our approach [key insight]. Experiments on [benchmarks] demonstrate [main result]."
+%
+% Paragraph 2: Future directions (2-3 sentences)
+% "In future work, we plan to explore ... and extend our approach to ..."
+```
+
+Rules: Claims here must match what's in Results. Don't overclaim. 0.5-1 page max.
+
+### LaTeX Conventions
+
+Enforce these throughout all sections:
+
+**Cross-references** (defined as macros in template):
+```latex
+\figref{fig:architecture}    % → "Figure 1"  (via cleveref)
+\tabref{tab:main-results}    % → "Table 2"
+\eqnref{eq:loss}             % → "Equation 3"
+\secref{sec:methods}         % → "Section 4"
+```
+
+**Citations:**
+```latex
+\citet{smith2024}            % → "Smith et al. (2024)"     (textual -- subject of sentence)
+\citep{smith2024}            % → "(Smith et al., 2024)"    (parenthetical)
+\citep{smith2024,jones2023}  % → "(Smith et al., 2024; Jones et al., 2023)"
+```
+
+Use `\citet` when the author is the grammatical subject: "**\citet{smith2024} showed** that...". Use `\citep` for parenthetical: "Recent work has shown significant gains **\citep{smith2024}**."
+
+**Figures:**
+```latex
+\begin{figure}[t]
+  \centering
+  \includegraphics[width=\linewidth]{figure-name}
+  \caption{Descriptive caption. Best viewed in color.}
+  \label{fig:figure-name}
+\end{figure}
+```
+
+**Tables:**
+```latex
+\begin{table}[t]
+  \centering
+  \caption{Caption ABOVE the table (convention).}
+  \label{tab:table-name}
+  \begin{tabular}{lcc}
+    \toprule
+    Column 1 & Column 2 & Column 3 \\
+    \midrule
+    Row 1 & data & data \\
+    Row 2 & data & data \\
+    \bottomrule
+  \end{tabular}
+\end{table}
+```
+
+**Math notation:** Define reusable macros in the preamble of `main.tex`:
+```latex
+\newcommand{\loss}{\mathcal{L}}
+\newcommand{\model}{\mathcal{M}}
+\newcommand{\dataset}{\mathcal{D}}
+\newcommand{\R}{\mathbb{R}}
+\newcommand{\E}{\mathbb{E}}
+\newcommand{\argmin}{\operatorname{argmin}}
+```
+
+## Phase 4: Polish & Final Verification
+
+### 4a. Self-Reflection Pass
+
+After all sections are written, re-read the entire paper and check:
+
+1. **Consistency:** Same terminology throughout? Abstract claims match Results numbers?
+2. **Redundancy:** Any paragraph repeated across sections? Cut ruthlessly.
+3. **Flow:** Smooth transitions between sections? Each section starts by connecting to the previous?
+4. **Claims:** Every claim in Intro/Abstract backed by evidence in Results?
+5. **Notation:** Math notation consistent? All symbols defined before first use?
+
+### 4b. Strict Verification
+
+```bash
+bash "$SKILL_DIR/scripts/verify.sh" "paper/$SLUG/" --strict
+```
+
+The `--strict` flag treats warnings as failures. All 12 checks must pass:
+
+- [ ] PDF exists and is non-trivial size
+- [ ] Zero LaTeX errors
+- [ ] Zero undefined `\ref{}` references
+- [ ] Zero undefined `\cite{}` citations
+- [ ] Zero BibTeX errors
+- [ ] Zero overfull boxes > 10pt
+- [ ] All referenced figure files exist
+- [ ] All sections have content (no empty stubs)
+- [ ] All `.bib` entries cited at least once (no dead refs)
+- [ ] Zero TODO/FIXME comments remaining
+- [ ] Abstract word count 100-300
+- [ ] All figures/tables referenced in text
+
+### 4c. Final Build
+
+```bash
+bash "$SKILL_DIR/scripts/compile.sh" "paper/$SLUG/main.tex" --clean
+```
+
+The `--clean` flag removes auxiliary files, leaving only the PDF. Deliverable: `paper/{slug}/build/main.pdf`.
+
+## Figure Generation
+
+When the paper needs figures, generate them as PDF or high-res PNG and save to `figures/`. Keep the generation script alongside for reproducibility.
+
+### matplotlib (recommended for most plots)
+
+```python
+import matplotlib.pyplot as plt
+import matplotlib
+matplotlib.rcParams.update({
+    'font.size': 12,
+    'font.family': 'serif',
+    'figure.figsize': (6, 4),
+    'figure.dpi': 150,
+    'savefig.dpi': 300,
+    'savefig.bbox': 'tight',
+    'axes.grid': True,
+    'grid.alpha': 0.3,
+})
+
+fig, ax = plt.subplots()
+# ... plot data ...
+ax.set_xlabel('X Label')
+ax.set_ylabel('Y Label')
+ax.legend()
+fig.savefig('paper/{slug}/figures/plot-name.pdf')
+plt.close()
+```
+
+Rules:
+- **Always save as PDF** for vector quality (PNG only for raster images like photos/heatmaps)
+- Font size >= 10pt (readable when scaled to column width)
+- Save the plotting script to `figures/plot_name.py` for reproducibility
+- Use consistent color palettes across all figures
+- Include axis labels, legends, and titles
+
+### Diagrams and Architecture Figures
+
+For architecture/flow diagrams, either:
+- Generate with matplotlib/tikz and save as PDF
+- Use `image-gen` tool and save to `figures/`
+- Hand-draw in any tool and export as PDF/PNG
+
+## LaTeX Troubleshooting
+
+Common errors and fixes:
+
+| Error | Cause | Fix |
+|-------|-------|-----|
+| `Missing $ inserted` | Math symbol outside math mode | Wrap in `$...$` |
+| `Undefined control sequence` | Typo in command or missing package | Check spelling, add `\usepackage` |
+| `File not found` | Wrong path in `\includegraphics` | Check `\graphicspath` and filename |
+| `Citation undefined` | Key mismatch between `\cite` and `.bib` | Check exact key spelling |
+| `Missing \begin{document}` | Error in preamble | Check for typos above `\begin{document}` |
+| `Overfull \hbox` | Line too wide | Rephrase, add `\linebreak`, or use `\sloppy` locally |
+| `Package clash` | Two packages conflict | Check compatibility, load order matters |
+
+When compile fails: read the **first** error in the log (subsequent errors often cascade from the first). Fix it, recompile. Don't try to fix multiple errors at once.
+
+## Scientific Writing Standards
+
+Quick-reference checklist for quality prose:
+
+- **Active voice:** "We propose X" not "X is proposed"
+- **Strong verbs:** "achieves" not "is able to achieve", "reduces" not "leads to a reduction in"
+- **Quantitative:** "improves by 12%" not "significantly improves"
+- **Define before use:** Every acronym, symbol, and technical term defined on first use
+- **Parallel structure:** Lists and comparisons use the same grammatical form
+- **No orphan pronouns:** "This approach" not "This" alone at the start of a sentence
+- **Hedging (appropriate):** "suggests" / "indicates" for uncertain claims; "demonstrates" / "establishes" for proven ones
+- **Person:** "We" for authors' actions; passive voice sparingly for general facts; never "I" in multi-author papers
+- **Tense:** Present for established facts and paper structure ("Section 3 presents..."); past for what you did ("We trained the model on...")
+- **Citations as nouns:** "\citet{smith2024} showed..." (not "It was shown in \citep{smith2024}...")

package/opencode/skills/KORTIX-paper-creator/assets/template.tex

@@ -0,0 +1,101 @@
+% Minimal IMRaD Scientific Paper Template
+% Usage: Copy this to paper/{slug}/main.tex and adapt
+%
+% Document class options:
+%   \documentclass[11pt,a4paper]{article}          -- default, any venue
+%   \documentclass[conference]{IEEEtran}           -- IEEE conferences
+%   \documentclass[sigconf]{acmart}                -- ACM conferences
+%   \documentclass{llncs}                          -- Springer LNCS
+%
+% To switch venue: replace the documentclass line and adjust package imports.
+% Most of this template works unchanged across venues.
+
+\documentclass[11pt,a4paper]{article}
+
+% === Core Packages ===
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{lmodern}                    % Better fonts
+\usepackage[margin=1in]{geometry}       % Margins (remove for venue templates)
+\usepackage{microtype}                  % Better typography
+
+% === Math ===
+\usepackage{amsmath,amssymb,amsfonts}
+\usepackage{mathtools}                  % Extensions to amsmath
+
+% === Figures & Tables ===
+\usepackage{graphicx}
+\usepackage{booktabs}                   % Professional tables (\toprule, \midrule, \bottomrule)
+\usepackage{subcaption}                 % Subfigures
+\usepackage{float}                      % Better float control
+
+% === Algorithms ===
+\usepackage{algorithm}
+\usepackage{algorithmic}
+
+% === Code Listings (optional) ===
+\usepackage{listings}
+\lstset{basicstyle=\ttfamily\small, breaklines=true, frame=single}
+
+% === References & Hyperlinks ===
+\usepackage[numbers]{natbib}            % Citations: \citep{}, \citet{}
+\usepackage{hyperref}
+\hypersetup{
+    colorlinks=true,
+    linkcolor=blue,
+    citecolor=blue,
+    urlcolor=blue
+}
+\usepackage{cleveref}                   % Smart references: \cref{fig:x} -> "Figure 1"
+
+% === Convenience Macros ===
+\newcommand{\figref}[1]{\cref{#1}}
+\newcommand{\tabref}[1]{\cref{#1}}
+\newcommand{\eqnref}[1]{\cref{#1}}
+\newcommand{\secref}[1]{\cref{#1}}
+\newcommand{\algref}[1]{\cref{#1}}
+
+% === Paper-Specific Macros (define your own here) ===
+% \newcommand{\methodname}{MethodName}
+% \newcommand{\loss}{\mathcal{L}}
+% \newcommand{\R}{\mathbb{R}}
+
+% === Graphics Path ===
+\graphicspath{{figures/}}
+
+% === Title Block ===
+\title{Paper Title Here}
+\author{
+    First Author\thanks{Affiliation, email@example.com} \and
+    Second Author\thanks{Affiliation, email@example.com}
+}
+\date{}  % Leave empty for submission; set for preprints
+
+\begin{document}
+
+\maketitle
+
+% === Abstract ===
+\input{sections/abstract}
+
+% === Main Sections ===
+\input{sections/introduction}
+\input{sections/related-work}
+\input{sections/methods}
+\input{sections/results}
+\input{sections/discussion}
+\input{sections/conclusion}
+
+% === Acknowledgments (optional) ===
+% \section*{Acknowledgments}
+% We thank...
+
+% === Bibliography ===
+\bibliographystyle{plainnat}
+\bibliography{references}
+
+% === Appendix (optional) ===
+% \appendix
+% \input{sections/appendix}
+
+\end{document}