@wentorai/research-plugins 1.0.0

package/skills/writing/latex/latex-ecosystem-guide/SKILL.md

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+---
+name: latex-ecosystem-guide
+description: "Comprehensive guide to LaTeX editors, packages, and typesetting workflows"
+metadata:
+  openclaw:
+    emoji: "📐"
+    category: "writing"
+    subcategory: "latex"
+    keywords: ["LaTeX typesetting", "LaTeX template", "LaTeX package management", "online LaTeX editor"]
+    source: "https://github.com/egeerardyn/awesome-LaTeX"
+---
+
+# LaTeX Ecosystem Guide
+
+## Overview
+
+LaTeX remains the gold standard for typesetting academic documents in mathematics, computer science, physics, and engineering. Its precise control over document layout, equation rendering, and bibliography management makes it indispensable for journal and conference submissions.
+
+This guide consolidates the best resources from the awesome-LaTeX repository (1,600+ stars) into an actionable reference covering editors, essential packages, document classes, bibliography management, and workflow optimization. Whether you are a LaTeX beginner setting up your first paper or an experienced user looking to streamline your pipeline, this skill provides the tools and techniques you need.
+
+The LaTeX ecosystem is vast -- over 6,000 packages on CTAN alone. Rather than cataloging everything, this guide focuses on the packages and tools that researchers use most frequently and the workflows that save the most time.
+
+## Editors and IDEs
+
+### Editor Comparison
+
+| Editor | Platform | Real-time Preview | Collaboration | Free |
+|--------|----------|-------------------|---------------|------|
+| Overleaf | Web | Yes | Real-time | Yes (limited) |
+| TeXstudio | Desktop | Compile-based | No | Yes |
+| VS Code + LaTeX Workshop | Desktop | Yes (SyncTeX) | Live Share | Yes |
+| Texifier | macOS/iOS | Live | No | Paid |
+| Vim + VimTeX | Terminal | Zathura/Skim | No | Yes |
+
+### Recommended Setup: VS Code + LaTeX Workshop
+
+```json
+// .vscode/settings.json
+{
+  "latex-workshop.latex.autoBuild.run": "onSave",
+  "latex-workshop.latex.recipe.default": "latexmk (xelatex)",
+  "latex-workshop.latex.recipes": [
+    {
+      "name": "latexmk (xelatex)",
+      "tools": ["latexmk-xelatex"]
+    }
+  ],
+  "latex-workshop.latex.tools": [
+    {
+      "name": "latexmk-xelatex",
+      "command": "latexmk",
+      "args": [
+        "-xelatex",
+        "-synctex=1",
+        "-interaction=nonstopmode",
+        "-file-line-error",
+        "%DOC%"
+      ]
+    }
+  ],
+  "latex-workshop.view.pdf.viewer": "tab"
+}
+```
+
+## Essential Packages
+
+### Document Structure
+
+```latex
+\usepackage[margin=1in]{geometry}    % Page margins
+\usepackage{setspace}                 % Line spacing
+\usepackage{fancyhdr}                 % Headers and footers
+\usepackage{titlesec}                 % Section heading styles
+\usepackage[hidelinks]{hyperref}      % Clickable cross-references
+\usepackage{cleveref}                 % Smart cross-references (\cref)
+```
+
+### Mathematics
+
+```latex
+\usepackage{amsmath}      % Core math environments
+\usepackage{amssymb}      % Extended symbols
+\usepackage{amsthm}       % Theorem environments
+\usepackage{mathtools}    % Extensions to amsmath
+\usepackage{bm}           % Bold math symbols
+```
+
+### Figures and Tables
+
+```latex
+\usepackage{graphicx}     % Include images
+\usepackage{subcaption}   % Subfigures
+\usepackage{booktabs}     % Professional tables (\toprule, \midrule, \bottomrule)
+\usepackage{multirow}     % Multi-row cells
+\usepackage{siunitx}      % SI units and number formatting
+```
+
+### Code Listings
+
+```latex
+\usepackage{listings}     % Basic code listings
+\usepackage{minted}       % Syntax-highlighted code (requires Pygments)
+\usepackage{algorithm2e}  % Algorithm pseudocode
+```
+
+## Document Classes for Research
+
+| Class | Use Case | Key Feature |
+|-------|----------|-------------|
+| `article` | Short papers, preprints | Standard LaTeX |
+| `revtex4-2` | APS journals (Phys Rev) | Built-in journal styles |
+| `IEEEtran` | IEEE conferences/journals | Two-column, IEEE format |
+| `acmart` | ACM conferences/journals | Multiple formats (sigconf, sigplan) |
+| `elsarticle` | Elsevier journals | Preprint and journal modes |
+| `svjour3` | Springer journals | Springer Nature format |
+| `aaai` | AAAI conference | AAAI formatting |
+
+### Example: ACM Conference Paper
+
+```latex
+\documentclass[sigconf,review]{acmart}
+
+\begin{document}
+\title{Your Paper Title}
+\author{First Author}
+\affiliation{%
+  \institution{University Name}
+  \city{City}
+  \country{Country}
+}
+\email{author@university.edu}
+
+\begin{abstract}
+Your abstract here.
+\end{abstract}
+
+\maketitle
+\section{Introduction}
+...
+\end{document}
+```
+
+## Bibliography Management
+
+### BibLaTeX + Biber (Recommended)
+
+```latex
+\usepackage[
+  backend=biber,
+  style=numeric-comp,
+  sorting=none,
+  maxbibnames=99
+]{biblatex}
+\addbibresource{refs.bib}
+
+% In document body:
+As shown in prior work~\cite{vaswani2017attention}...
+
+% At the end:
+\printbibliography
+```
+
+### Quick Reference: BibTeX Entry Types
+
+```bibtex
+@article{key,
+  author  = {Last, First and Last2, First2},
+  title   = {Paper Title},
+  journal = {Journal Name},
+  year    = {2024},
+  volume  = {42},
+  pages   = {1--15},
+  doi     = {10.xxxx/xxxxx}
+}
+
+@inproceedings{key2,
+  author    = {Last, First},
+  title     = {Conference Paper Title},
+  booktitle = {Proceedings of Conference},
+  year      = {2024},
+  pages     = {100--110}
+}
+```
+
+## Workflow Automation
+
+### Makefile for LaTeX Projects
+
+```makefile
+MAIN = paper
+TEX = $(MAIN).tex
+PDF = $(MAIN).pdf
+
+.PHONY: all clean watch
+
+all: $(PDF)
+
+$(PDF): $(TEX) refs.bib
+	latexmk -xelatex -interaction=nonstopmode $(TEX)
+
+clean:
+	latexmk -C
+
+watch:
+	latexmk -xelatex -pvc -interaction=nonstopmode $(TEX)
+```
+
+### Git Integration for LaTeX
+
+```bash
+# .gitignore for LaTeX projects
+*.aux
+*.bbl
+*.blg
+*.log
+*.out
+*.synctex.gz
+*.fdb_latexmk
+*.fls
+*.toc
+*.nav
+*.snm
+```
+
+## Best Practices
+
+- **Use `latexmk` instead of manual compilation chains.** It handles multi-pass compilation automatically.
+- **Prefer `booktabs` for tables.** Never use vertical lines (`|`) in academic tables.
+- **Use `\cref{}` from cleveref.** It automatically prepends "Figure," "Table," or "Equation."
+- **Keep one sentence per line in source files.** This makes Git diffs readable and merges cleaner.
+- **Pin your TeX distribution version.** Use Docker or Nix to ensure reproducible builds across machines.
+- **Store figures as PDF or SVG for vector graphics, PNG for raster.** Never upscale low-resolution images.
+
+## References
+
+- [awesome-LaTeX](https://github.com/egeerardyn/awesome-LaTeX) -- Curated list of LaTeX resources (1,600+ stars)
+- [CTAN](https://ctan.org/) -- Comprehensive TeX Archive Network
+- [LaTeX Wikibook](https://en.wikibooks.org/wiki/LaTeX) -- Community-maintained reference
+- [Overleaf Documentation](https://www.overleaf.com/learn) -- Tutorials and templates
+- [LaTeX Workshop for VS Code](https://github.com/James-Yu/LaTeX-Workshop) -- VS Code extension

package/skills/writing/latex/math-typesetting-guide/SKILL.md

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+---
+name: math-typesetting-guide
+description: "LaTeX math typesetting, equation formatting, and cross-referencing"
+metadata:
+  openclaw:
+    emoji: "sigma"
+    category: "writing"
+    subcategory: "latex"
+    keywords: ["LaTeX math typesetting", "equation formatting", "mathematical notation", "cross-reference"]
+    source: "wentor-research-plugins"
+---
+
+# Math Typesetting Guide
+
+Comprehensive reference for typesetting mathematical notation, equations, and theorems in LaTeX with correct formatting, numbering, and cross-referencing.
+
+## Essential Packages
+
+```latex
+\usepackage{amsmath}    % Core math environments (align, gather, etc.)
+\usepackage{amssymb}    % Additional math symbols
+\usepackage{amsthm}     % Theorem environments
+\usepackage{mathtools}  % Extensions to amsmath (dcases, coloneqq, etc.)
+\usepackage{bm}         % Bold math symbols (\bm{x})
+\usepackage{bbm}        % Blackboard bold for indicators (\mathbbm{1})
+\usepackage{nicefrac}   % Inline fractions (\nicefrac{1}{2})
+\usepackage{siunitx}    % SI units (\SI{9.8}{m/s^2})
+```
+
+## Inline vs. Display Math
+
+### Inline Math
+
+Use `$...$` or `\(...\)` for math within text:
+
+```latex
+The loss function $\mathcal{L}(\theta) = -\sum_{i=1}^{N} \log p(y_i | x_i; \theta)$
+minimizes the negative log-likelihood.
+```
+
+### Display Math (Unnumbered)
+
+Use `\[...\]` for centered, unnumbered equations:
+
+```latex
+\[
+  \nabla_\theta \mathcal{L}(\theta) = -\frac{1}{N} \sum_{i=1}^{N}
+  \nabla_\theta \log p(y_i | x_i; \theta)
+\]
+```
+
+### Display Math (Numbered)
+
+Use the `equation` environment for numbered equations:
+
+```latex
+\begin{equation}
+  E = mc^2
+  \label{eq:einstein}
+\end{equation}
+```
+
+Reference with `\eqref{eq:einstein}` to produce "(1)" with parentheses automatically.
+
+## Multi-Line Equations
+
+### align Environment
+
+Use `align` for multi-line equations with alignment points (`&`):
+
+```latex
+\begin{align}
+  \mathcal{L}(\theta) &= \mathbb{E}_{(x,y) \sim \mathcal{D}} \left[ \ell(f_\theta(x), y) \right] \label{eq:loss} \\
+  &= \frac{1}{N} \sum_{i=1}^{N} \ell(f_\theta(x_i), y_i) \label{eq:empirical-loss} \\
+  &\approx \frac{1}{B} \sum_{j=1}^{B} \ell(f_\theta(x_j), y_j) \label{eq:minibatch-loss}
+\end{align}
+```
+
+Use `align*` for unnumbered multi-line equations. Use `\nonumber` to suppress numbering on specific lines.
+
+### split Environment
+
+Use `split` inside `equation` for a single equation number spanning multiple lines:
+
+```latex
+\begin{equation}
+\begin{split}
+  \text{ELBO}(\theta, \phi; x) &= \mathbb{E}_{q_\phi(z|x)} \left[ \log p_\theta(x|z) \right] \\
+  &\quad - D_\text{KL}\left( q_\phi(z|x) \| p(z) \right)
+\end{split}
+\label{eq:elbo}
+\end{equation}
+```
+
+### cases Environment
+
+For piecewise functions:
+
+```latex
+\begin{equation}
+  \text{ReLU}(x) =
+  \begin{cases}
+    x & \text{if } x > 0 \\
+    0 & \text{otherwise}
+  \end{cases}
+  \label{eq:relu}
+\end{equation}
+```
+
+## Common Mathematical Notation
+
+### Symbols Reference Table
+
+| Notation | LaTeX | Category |
+|----------|-------|----------|
+| Real numbers | `\mathbb{R}` | Sets |
+| Integers | `\mathbb{Z}` | Sets |
+| Natural numbers | `\mathbb{N}` | Sets |
+| Expectation | `\mathbb{E}` | Probability |
+| Probability | `\mathbb{P}` or `\Pr` | Probability |
+| Normal distribution | `\mathcal{N}(\mu, \sigma^2)` | Distributions |
+| Partial derivative | `\frac{\partial f}{\partial x}` | Calculus |
+| Gradient | `\nabla f` | Calculus |
+| Matrix transpose | `\mathbf{A}^\top` | Linear algebra |
+| Matrix inverse | `\mathbf{A}^{-1}` | Linear algebra |
+| Frobenius norm | `\|\mathbf{A}\|_F` | Linear algebra |
+| L2 norm | `\|\mathbf{x}\|_2` | Linear algebra |
+| Inner product | `\langle \mathbf{x}, \mathbf{y} \rangle` | Linear algebra |
+| Indicator function | `\mathbbm{1}_{[condition]}` | Functions |
+| Summation | `\sum_{i=1}^{N}` | Operations |
+| Product | `\prod_{i=1}^{N}` | Operations |
+| Argmin/argmax | `\operatorname*{argmin}_\theta` | Optimization |
+| KL divergence | `D_\text{KL}(p \| q)` | Information theory |
+
+### Custom Operators
+
+Define custom operators for clean notation:
+
+```latex
+% In preamble
+\DeclareMathOperator*{\argmin}{arg\,min}
+\DeclareMathOperator*{\argmax}{arg\,max}
+\DeclareMathOperator{\Tr}{Tr}        % Matrix trace
+\DeclareMathOperator{\diag}{diag}    % Diagonal matrix
+\DeclareMathOperator{\softmax}{softmax}
+\DeclareMathOperator{\sigmoid}{\sigma}
+\newcommand{\R}{\mathbb{R}}         % Shorthand for real numbers
+\newcommand{\E}{\mathbb{E}}         % Shorthand for expectation
+\newcommand{\norm}[1]{\left\| #1 \right\|}  % Norm shorthand
+\newcommand{\abs}[1]{\left| #1 \right|}     % Absolute value
+\newcommand{\inner}[2]{\langle #1, #2 \rangle}  % Inner product
+```
+
+## Matrices and Arrays
+
+```latex
+% Matrix with parentheses
+\begin{equation}
+  \mathbf{W} = \begin{pmatrix}
+    w_{11} & w_{12} & \cdots & w_{1n} \\
+    w_{21} & w_{22} & \cdots & w_{2n} \\
+    \vdots & \vdots & \ddots & \vdots \\
+    w_{m1} & w_{m2} & \cdots & w_{mn}
+  \end{pmatrix}
+\end{equation}
+
+% Matrix with square brackets
+\begin{equation}
+  \mathbf{A} = \begin{bmatrix} 1 & 0 \\ 0 & 1 \end{bmatrix}
+\end{equation}
+```
+
+## Theorems and Proofs
+
+```latex
+% In preamble: define theorem environments
+\newtheorem{theorem}{Theorem}[section]
+\newtheorem{lemma}[theorem]{Lemma}
+\newtheorem{proposition}[theorem]{Proposition}
+\newtheorem{corollary}[theorem]{Corollary}
+\theoremstyle{definition}
+\newtheorem{definition}[theorem]{Definition}
+\theoremstyle{remark}
+\newtheorem{remark}[theorem]{Remark}
+
+% In document:
+\begin{theorem}[Universal Approximation]
+\label{thm:universal-approx}
+For any continuous function $f: [0,1]^n \to \mathbb{R}$ and any
+$\epsilon > 0$, there exists a feedforward neural network $g$ with
+one hidden layer such that $\sup_{x \in [0,1]^n} |f(x) - g(x)| < \epsilon$.
+\end{theorem}
+
+\begin{proof}
+The proof proceeds by construction. Consider a network with
+$\sigmoid$ activation functions...
+
+% End proof with QED symbol (automatic with amsthm)
+\end{proof}
+```
+
+## Cross-Referencing Best Practices
+
+```latex
+% Use cleveref for automatic reference formatting
+\usepackage[capitalise,noabbrev]{cleveref}
+
+% Then reference with:
+\cref{eq:loss}       % -> "Equation 1"
+\cref{thm:universal-approx}  % -> "Theorem 1"
+\Cref{eq:loss}       % -> "Equation 1" (capital, for start of sentence)
+\crefrange{eq:loss}{eq:minibatch-loss}  % -> "Equations 1 to 3"
+
+% Label naming conventions:
+% eq:name   for equations
+% thm:name  for theorems
+% lem:name  for lemmas
+% def:name  for definitions
+% fig:name  for figures
+% tab:name  for tables
+% sec:name  for sections
+```
+
+## Formatting Tips
+
+- Use `\left(` and `\right)` for auto-sizing delimiters, or explicit sizes: `\big(`, `\Big(`, `\bigg(`, `\Bigg(`
+- Use `\text{...}` for words within math mode: `$p(\text{data} | \theta)$`
+- Use `\quad` or `\qquad` for spacing in equations
+- Use `\phantom{x}` for invisible spacing to align elements
+- Avoid `$$...$$` (plain TeX); use `\[...\]` or environments instead
+- Number only equations that are referenced in the text

package/skills/writing/latex/overleaf-collaboration-guide/SKILL.md

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+---
+name: overleaf-collaboration-guide
+description: "Guide to collaborative LaTeX editing with Overleaf"
+metadata:
+  openclaw:
+    emoji: "team"
+    category: "writing"
+    subcategory: "latex"
+    keywords: ["online LaTeX editor", "collaborative LaTeX", "Overleaf", "LaTeX environment setup"]
+    source: "wentor-research-plugins"
+---
+
+# Overleaf Collaboration Guide
+
+Set up and manage collaborative LaTeX projects on Overleaf with best practices for multi-author workflows, version control, and project organization.
+
+## Getting Started with Overleaf
+
+### Creating a Project
+
+Overleaf (overleaf.com) is a browser-based LaTeX editor that provides real-time collaboration, automatic compilation, and integrated version history.
+
+Project creation options:
+
+| Method | When to Use |
+|--------|-------------|
+| Blank project | Starting from scratch |
+| Upload project | Migrating existing local LaTeX project |
+| Import from GitHub | Existing repo-based project |
+| Use a template | Conference/journal submissions (IEEE, ACM, Springer, Elsevier templates available) |
+| Copy from existing | Forking a previous project |
+
+### Recommended Project Structure
+
+```
+project-root/
+├── main.tex              # Main document (entry point)
+├── preamble.tex          # Packages, macros, custom commands
+├── sections/
+│   ├── 01-introduction.tex
+│   ├── 02-related-work.tex
+│   ├── 03-methods.tex
+│   ├── 04-results.tex
+│   ├── 05-discussion.tex
+│   └── 06-conclusion.tex
+├── figures/
+│   ├── fig1-overview.pdf
+│   ├── fig2-results.pdf
+│   └── fig3-comparison.pdf
+├── tables/
+│   └── results-table.tex
+├── references.bib        # Bibliography database
+└── README.md             # Project notes (not compiled)
+```
+
+### Main File Setup
+
+```latex
+% main.tex
+\documentclass[conference]{IEEEtran}  % or article, etc.
+\input{preamble}  % load packages and macros
+
+\begin{document}
+
+\title{Your Paper Title}
+\author{Author One \and Author Two \and Author Three}
+\maketitle
+
+\begin{abstract}
+Your abstract here.
+\end{abstract}
+
+\input{sections/01-introduction}
+\input{sections/02-related-work}
+\input{sections/03-methods}
+\input{sections/04-results}
+\input{sections/05-discussion}
+\input{sections/06-conclusion}
+
+\bibliographystyle{IEEEtran}
+\bibliography{references}
+
+\end{document}
+```
+
+## Multi-Author Collaboration
+
+### Sharing and Permissions
+
+| Role | Capabilities |
+|------|-------------|
+| Owner | Full control, can delete project, manage collaborators |
+| Editor | Can edit all files, cannot manage collaborators |
+| Viewer | Read-only access, can download but not modify |
+
+Share via:
+- **Link sharing**: Generate a read-only or edit link (anyone with the link can access)
+- **Email invitation**: Invite specific collaborators by email with role assignment
+
+### Author Coordination Best Practices
+
+1. **Assign sections**: Each author owns specific `.tex` files to minimize merge conflicts.
+2. **Use comments**: Overleaf supports inline comments (`% TODO: revise this paragraph`) and threaded review comments.
+3. **Use custom commands for notes**:
+
+```latex
+% In preamble.tex, define author-specific annotation commands
+\usepackage{xcolor}
+\newcommand{\alice}[1]{\textcolor{blue}{[Alice: #1]}}
+\newcommand{\bob}[1]{\textcolor{red}{[Bob: #1]}}
+\newcommand{\todo}[1]{\textcolor{orange}{[TODO: #1]}}
+
+% In text:
+This result is surprising \alice{Should we add more analysis here?}
+and warrants further investigation \todo{Add statistical test}.
+```
+
+4. **Track changes**: Overleaf Premium includes a track-changes mode. For free plans, use the `changes` package:
+
+```latex
+\usepackage{changes}
+\definechangesauthor[name={Alice}, color=blue]{AL}
+\definechangesauthor[name={Bob}, color=red]{BO}
+
+% Usage:
+\added[id=AL]{This is new text added by Alice.}
+\deleted[id=BO]{This text was removed by Bob.}
+\replaced[id=AL]{new text}{old text}
+```
+
+## Git Integration
+
+### Overleaf + GitHub Sync
+
+Overleaf Premium supports bidirectional GitHub sync:
+
+1. In Overleaf, go to Menu > Sync > GitHub
+2. Link your GitHub account and select or create a repository
+3. Pull/push changes between Overleaf and GitHub
+
+### Overleaf + Local Git
+
+```bash
+# Clone your Overleaf project via git
+git clone https://git.overleaf.com/YOUR_PROJECT_ID my-paper
+cd my-paper
+
+# Edit locally, then push back to Overleaf
+git add -A
+git commit -m "Updated results table"
+git push origin master
+
+# Pull changes made on Overleaf
+git pull origin master
+```
+
+**Credentials**: Use your Overleaf email as username and an Overleaf-generated token as password.
+
+## Compilation and Debugging
+
+### Common Compilation Errors
+
+| Error | Cause | Fix |
+|-------|-------|-----|
+| `Undefined control sequence` | Missing package or typo in command | Check `\usepackage` or spelling |
+| `Missing $ inserted` | Math symbol outside math mode | Wrap in `$...$` or `\text{...}` |
+| `File not found` | Incorrect path in `\input` or `\includegraphics` | Check file names (case-sensitive on Overleaf) |
+| `Overfull \hbox` | Content too wide for column | Resize figure, adjust text, or add `\sloppy` |
+| `Citation undefined` | BibTeX entry missing or key mismatch | Verify `.bib` entry key matches `\cite{}` |
+
+### Debugging Tips
+
+- Use **Recompile from scratch** (Ctrl+Shift+Enter) to clear cache
+- Check the **Logs and output files** panel for detailed error messages
+- Use `\listfiles` in preamble to see which packages are loaded
+- Overleaf uses TeX Live 2024; check package compatibility if using older templates
+
+## Submission Workflow
+
+### Preparing for Journal Submission
+
+1. **Flatten the project**: Some journals require a single `.tex` file.
+
+```bash
+# Use latexpand to flatten \input commands
+latexpand main.tex > submission.tex
+```
+
+2. **Check formatting**: Verify page limits, font sizes, margin requirements.
+3. **Download as zip**: Menu > Download > Source to get all files.
+4. **Convert figures**: Ensure all figures are in accepted formats (PDF, EPS, or high-res PNG/TIFF).
+5. **Clean up**: Remove TODO comments, author annotation commands, and debug code.
+
+```latex
+% Add to preamble for submission: disable all annotation commands
+\renewcommand{\alice}[1]{}
+\renewcommand{\bob}[1]{}
+\renewcommand{\todo}[1]{}
+```
+
+## Useful Overleaf Keyboard Shortcuts
+
+| Action | Shortcut (Mac) | Shortcut (Windows) |
+|--------|---------------|-------------------|
+| Compile | Cmd+Enter | Ctrl+Enter |
+| Bold | Cmd+B | Ctrl+B |
+| Italic | Cmd+I | Ctrl+I |
+| Comment toggle | Cmd+/ | Ctrl+/ |
+| Find & replace | Cmd+H | Ctrl+H |
+| Go to line | Cmd+Shift+L | Ctrl+Shift+L |
+| Toggle PDF | Cmd+Shift+O | Ctrl+Shift+O |