AGENTS.md — Writings Workspace

Knowledge base for AI agents (Cursor, OpenCode) working in this scientific writings repository.

Workspace Overview

This repository contains all public writings by Daniel Burger: essays, papers, patents, and future books. Everything is written in LaTeX using a unified template system, with source code and compiled outputs version-controlled together.

Repository Structure

Writings/
├── 001_patents/                  # Patent applications (see Legal section)
│   └── YYYY/NNN_patent/          # Year/sequence organisation
│       ├── patent.tex            # Main LaTeX source
│       ├── figures/              # Images and diagrams
│       └── references/           # bibliography.bib
├── 002_papers/                   # Academic papers
│   └── YYYY/NNN_paper/           # Year/sequence organisation
│       ├── paper.tex             # Main LaTeX source
│       ├── figures/
│       └── references/
├── 003_books/                    # Book projects
│   └── book_slug/
│       ├── main.tex
│       └── chapters/
├── 004_essays/                   # Long-form essays
│   └── YYYY/NNN_essay/           # Year/sequence organisation
│       ├── essay.tex             # Main LaTeX source
│       ├── figures/
│       └── references/
├── _templates/                   # Shared LaTeX templates
│   ├── essay-preamble.tex        # Essays (single-column, 11pt)
│   ├── paper-preamble.tex        # Papers (two-column ready, 10pt)
│   ├── book-preamble.tex         # Books (memoir class, chapters)
│   ├── patent-preamble.tex       # Patents (double-spaced, numbered paras)
│   ├── preamble.tex              # Legacy (backwards compatibility)
│   ├── apa.bst                   # APA citation style
│   └── README.md                 # Template documentation
├── .agents/skills/               # Shared agent skills (Cursor + OpenCode)
├── .cursor/skills/               # Symlink → .agents/skills/ (Cursor compatibility)
├── .editorconfig                 # Editor formatting
└── AGENTS.md                     # This file

Content Types

Type	Template Variant	Purpose	Status
Patents	`patent`	Technical inventions	Active
Papers	`paper`	Academic papers, preprints	Active
Books	`book`	Extended works with chapter structure	Active
Essays	`essay`	Long-form scientific/philosophical writing	Active

Language & Style Guidelines

British English (Mandatory)

All content uses British English spelling, punctuation, and conventions:

American	British (Use This)
organize	organise
color	colour
center	centre
analyze	analyse
defense	defence
program	programme (except computing)
aluminum	aluminium
acknowledgment	acknowledgement

Punctuation:

Single quotes for emphasis: 'consciousness'
Double quotes for direct quotations: "Death is an engineering challenge"
Full stops inside quotation marks only when quoting complete sentences
Oxford comma: "neurons, synapses, and glia"

Academic Tone

Formal, precise, scholarly language
Active voice preferred when appropriate
First-person plural ("we propose") for collaborative works
Avoid hedging language when making strong claims backed by evidence
Technical terminology with clear definitions

Writing Philosophy

The author's writings are characterised by:

First-principles thinking — Build arguments from foundational definitions
Engineering pragmatism — Focus on tractable, testable approaches
Interdisciplinary synthesis — Bridge neuroscience, physics, philosophy, engineering
Intellectual boldness — Challenge conventional paradigms with rigorous alternatives

LaTeX Conventions

Template System

Personal Templates (for Drafting)

Separate preamble files for each document type:

% For essays (single-column, generous margins, 11pt)
\documentclass[11pt]{article}
\input{../../../_templates/essay-preamble.tex}

% For papers (two-column support, compact margins, 10pt)
\documentclass[10pt]{article}
\input{../../../_templates/paper-preamble.tex}

Template	Layout	Margins	Use Case
`essay-preamble.tex`	Single-column, 11pt	4cm L/R, generous	Essays, thought pieces
`paper-preamble.tex`	Two-column ready, 10pt	3cm L/R, compact	Papers, preprints
`preamble.tex`	Legacy unified	Conditional	Backwards compatibility

Submission Templates (for Journals/Conferences)

When submitting to journals or conferences, use their official templates:

Venue	Template	Notes
Springer LNCS	splncs04.cls	HCII, HCI conferences
IEEE	IEEEtran.cls	IEEE conferences/journals
ACM	acmart.cls	CHI, UIST, etc.
Elsevier	elsarticle.cls	Elsevier journals
Nature/Science	Word templates	Often require Word submission

Workflow:

Draft using personal templates (essay or paper variant)
Finalise content and structure
Convert to venue-specific template before submission (AI agents can assist)
Verify compliance with venue guidelines (page limits, formatting)

Document Structure

Standard LaTeX document organisation:

\begin{document}
\pagenumbering{roman}

% Frontmatter
\title{\textbf{Title Here}}
\author[1]{Author Name}
\affil[1]{\textbf{Institution}}
\date{\textit{Month DD, YYYY}}
\maketitle

% Abstract
\begin{abstract}
  Abstract text here.
\end{abstract}

% Preliminaries
\tableofcontents
\listoffigures
\pagenumbering{arabic}

% Main content
\section{Introduction}
\label{sec:introduction}

% Back matter
\bibliography{references/bibliography}
\bibliographystyle{../../../_templates/apa}
\end{document}

Section Markers

Use semantic markers for navigation:

% ! =====================
% ! # MARK: Section Name
% ! =====================

Custom Commands

Command	Usage	Output
`\floatcaption{title}{description}`	Enhanced captions	Title Description.
`\autoref{label}`	Smart references	"Figure 1", "Section 2"
`\cite{key}`	natbib citations	(Author, Year)
`\citet{key}`	Textual citation	Author (Year)

Figures

\begin{figure}[ht]
  \centering
  \includegraphics[width=\textwidth]{figures/filename.png}
  \floatcaption{Figure title}{Detailed description of what the figure shows.}
  \label{fig:descriptive-label}
\end{figure}

Tables

\begin{table}[ht]
  \centering
  \begin{tabular}{p{0.3\textwidth}p{0.6\textwidth}}
    \toprule
    \textbf{Column 1} & \textbf{Column 2} \\
    \midrule
    Content & Content \\
    \bottomrule
  \end{tabular}
  \caption{\textbf{Table title.} Description.}
  \label{tab:descriptive-label}
\end{table}

Code Listings

\begin{lstlisting}[language=Python, caption={Description.}, label={lst:example}]
def function():
    return "Hello, World!"
\end{lstlisting}

Mathematics

Use amsmath environments:

% Numbered equation
\begin{equation}
  \mathcal{C}(\mathcal{I}, [t_0, t_1]) \iff \forall t \in [t_0, t_1] : \left\| \frac{dS_{\text{crit}}}{dt}(t) \right\|_{\mathcal{S}} \le \Lambda_{\text{adapt}}(S_{\text{crit}}(t))
  \label{eq:continuity}
\end{equation}

% Inline: $S_{\text{crit}}(t) \in \mathcal{S}$

Convention: Use \text{} for subscript descriptors (e.g., S_{\text{crit}}).

Bibliography

BibTeX entries in references/bibliography.bib:

@article{author_keyword_year,
  title = {Article Title},
  author = {Last, First and Other, Author},
  journal = {Journal Name},
  volume = {1},
  number = {1},
  pages = {1--10},
  year = {2024},
  doi = {10.1000/example}
}

Key format: lastname_keyword_year (e.g., watanabe_biological_2022)

Workflow Guidelines

Creating New Documents

Create directory: NNN_type/YYYY/NNN_type/
Copy structure from existing document of same type
Update \input{} path to appropriate preamble (e.g., essay-preamble.tex, paper-preamble.tex)
Create figures/ and references/ subdirectories

Submodule Workflow (Work-in-Progress Documents)

Documents under active development live in separate private repositories and are linked here as Git submodules. Once a document reaches its final version, the submodule is replaced with the actual folder contents and the document is published to the public repository.

Adding a new WIP document as a submodule:

git submodule add <repo-url> 002_papers/2026/002_paper
git commit -m "Add paper/002 as submodule"

Promoting a finished document to a full folder:

# 1. Note the submodule path and remote URL
git submodule status

# 2. Remove the submodule
git submodule deinit -f 002_papers/2026/002_paper
git rm -f 002_papers/2026/002_paper
rm -rf .git/modules/002_papers/2026/002_paper

# 3. Clone the contents in its place
git clone <repo-url> 002_papers/2026/002_paper
rm -rf 002_papers/2026/002_paper/.git

# 4. Commit the expanded folder
git add 002_papers/2026/002_paper
git commit -m "Promote paper/002 from submodule to folder for publication"

Rules:

Submodules are private repos; they are never pushed to the public Writings remote until promoted.
Promotion happens only when the document is in its final, publishable state.
After promotion, push to the public remote: git push public main.

Compilation

# Single compilation
pdflatex essay.tex

# Full compilation with bibliography
latexmk -pdf essay.tex

# Clean auxiliary files
latexmk -c

Version Control

Commit:

Source files (.tex, .bib, .md)
Final PDFs (for easy access)
Template changes (separate from content)

Ignore (via .gitignore):

Auxiliary files (.aux, .log, .synctex.gz, etc.)
Intermediate compilation files

Branches:

main — Published/stable versions
essay/NNN — Work-in-progress essays
paper/NNN — Work-in-progress papers

Agent Instructions

For All Agents (Cursor, OpenCode, Claude Code)

When working in this repository:

Load relevant skills — Skills in .agents/skills/ provide specialised guidance
Understand template system — Check _templates/README.md before modifying preamble
Maintain consistency — Match existing document style in same category
Preserve semantic markers — Keep % ! # MARK: comments for navigation
Context awareness — This is a writings workspace, not a code repository
LaTeX focus — Primary files are .tex, not programming languages
British English — All generated text must use British spelling

Task Categories

Task Type	Approach
Drafting prose	Match author's voice; first-principles; bold but rigorous
LaTeX formatting	Follow template conventions; use custom commands
Bibliography	APA style; verify DOIs; consistent key format
Figures	Descriptive filenames; proper `\floatcaption` usage
Editing	Preserve meaning; improve clarity; maintain British English
Research assistance	Find citations; verify claims; suggest related work

Quality Checklist

Before completing any task:

British English spelling throughout
LaTeX compiles without errors
Cross-references (\autoref) resolve correctly
Bibliography entries complete
Figures have descriptive captions
Section markers present for major sections
Consistent formatting with existing documents

Legal & Publication Guidelines

Patents

CRITICAL: Patent documents in 001_patents/ have special handling:

Pre-submission: Content is confidential; do not discuss publicly
Post-provisional: Can be pushed to public repository only after provisional patent application filed
Publication timing: Coordinate with legal counsel before any public disclosure

Open Access

All other content (essays, papers, books) is intended for public access:

Repository is public after appropriate legal clearance
Contributions welcome via pull requests
Living documents — updates encouraged post-publication

Citation

When this work is cited:

@misc{burger_writings_2026,
  author = {Burger, Daniel},
  title = {Public Writings Repository},
  year = {2026},
  url = {https://github.com/[username]/Writings}
}

Available Skills

Skills provide specialised guidance for agents. Located in .agents/skills/.

Skill Overview

Skill	Purpose	When to Use
`writing-clearly-and-concisely`	Strunk's Elements of Style + AI pattern avoidance	Any prose for humans
`scientific-writing`	IMRAD structure, citations, reporting guidelines	Research papers, manuscripts
`scientific-critical-thinking`	Methodology critique, bias detection, evidence quality	Reviewing claims, research design
`scientific-brainstorming`	Research ideation, hypothesis generation	Creative problem-solving
`scientific-visualization`	Publication figures (matplotlib/seaborn/plotly)	Creating journal-ready plots
`latex-writing`	LaTeX best practices, semantic markup	Writing/editing .tex files
`mermaid-diagrams`	Software diagrams using Mermaid syntax	Flowcharts, sequence diagrams, ERDs

writing-clearly-and-concisely

Purpose: Apply Strunk's timeless rules for clearer, stronger writing. Avoid AI writing patterns.

Use when:

Writing documentation, explanations, any prose humans will read
Editing to improve clarity and conciseness
Avoiding AI-generated "slop" (puffery, empty phrases, promotional language)

Key principles:

Use active voice
Put statements in positive form
Use definite, specific, concrete language
Omit needless words
Keep related words together

Reference files: elements-of-style/ (grammar, composition, word choice), signs-of-ai-writing.md

scientific-writing

Purpose: Write scientific manuscripts with IMRAD structure, proper citations, and reporting guidelines.

Use when:

Writing any section of a scientific manuscript (abstract, introduction, methods, results, discussion)
Formatting citations (APA, AMA, Vancouver, Chicago, IEEE)
Applying reporting guidelines (CONSORT, STROBE, PRISMA)
Preparing manuscripts for journal submission

Critical principle: Always write in full paragraphs with flowing prose. Never submit bullet points. Use two-stage process:

Create section outlines with key points
Convert outlines to complete paragraphs

Reference files: imrad_structure.md, citation_styles.md, figures_tables.md, reporting_guidelines.md, writing_principles.md

scientific-critical-thinking

Purpose: Evaluate research rigor, assess methodology, detect biases, analyse statistical validity.

Use when:

Reviewing research papers or evaluating scientific claims
Assessing experimental design and methodology
Identifying biases and confounding factors
Applying GRADE or Cochrane risk of bias frameworks
Planning rigorous new studies

Core capabilities:

Methodology critique (study design, validity analysis)
Bias detection (cognitive, selection, measurement, analysis)
Statistical analysis evaluation (power, tests, p-values, effect sizes)
Evidence quality assessment (hierarchy, GRADE)
Logical fallacy identification

Reference files: scientific_method.md, common_biases.md, statistical_pitfalls.md, evidence_hierarchy.md, logical_fallacies.md, experimental_design.md

scientific-brainstorming

Purpose: Research ideation partner for generating hypotheses and exploring interdisciplinary connections.

Use when:

Generating novel research ideas or directions
Exploring interdisciplinary connections and analogies
Challenging assumptions in existing frameworks
Developing new methodological approaches
Overcoming creative blocks

Workflow phases:

Understanding context (research question, constraints)
Divergent exploration (cross-domain analogies, assumption reversal, scale shifting)
Connection making (patterns, themes, unexpected links)
Critical evaluation (feasibility, strengths, challenges)
Synthesis and next steps

Reference files: brainstorming_methods.md (SCAMPER, Six Thinking Hats, TRIZ, Biomimicry)

scientific-visualization

Purpose: Create publication-quality figures with matplotlib, seaborn, and plotly.

Use when:

Creating plots for scientific manuscripts
Preparing figures for journal submission (Nature, Science, Cell, PLOS)
Ensuring colorblind-friendly, accessible figures
Making multi-panel figures with consistent styling
Exporting at correct resolution and format (PDF/EPS/TIFF)

Key requirements:

Colorblind-safe palettes (Okabe-Ito recommended)
Proper resolution (300-600 DPI for raster, vector preferred)
Sans-serif fonts (Arial, Helvetica), minimum 6-7pt at final size
Error bars with statistical significance markers
Journal-specific dimensions

Reference files: publication_guidelines.md, color_palettes.md, journal_requirements.md, matplotlib_examples.md

Assets: color_palettes.py, *.mplstyle files (publication, nature, presentation)

Scripts: figure_export.py, style_presets.py

latex-writing

Purpose: Guide LaTeX authoring with semantic markup and best practices.

Use when:

Writing or editing .tex files
Reviewing LaTeX code quality
Working with literate programming (.nw) files

Key principles:

Semantic markup: Use environments matching content meaning, not visual appearance
Lists: Use description for term-definition pairs, not \textbf{Label:} in itemize
Cross-references: Always use \autoref{} (hyperref), never \S\ref{} or Figure~\ref{}
Emphasis: Use \emph{}, never ALL CAPITALS
Literate programming: Use [[code]] notation in .nw files, not \texttt{..._...}

Anti-patterns to avoid:

\textbf{Label:} in itemize → use \item[Label] in description
Section~\ref{sec:x} → use \autoref{sec:x}
ALL CAPS emphasis → use \emph{emphasis}

mermaid-diagrams

Purpose: Create professional software diagrams using Mermaid's text-based syntax.

Use when:

Creating flowcharts, sequence diagrams, class diagrams, or ERDs
Visualising system architecture (C4 diagrams)
Documenting user journeys, workflows, or state machines
Explaining code structure or application flows

Diagram types:

Type	Use Case
Class diagrams	Domain modelling, OOP design
Sequence diagrams	API flows, method calls
Flowcharts	Processes, algorithms, user journeys
ERDs	Database schemas
C4 diagrams	System/container/component architecture
State diagrams	State machines, lifecycles
Gantt charts	Project timelines

Key principles:

First line declares diagram type (classDiagram, sequenceDiagram, flowchart)
Use %% for comments
Diagrams are version-controllable text
Unknown words break diagrams; parameters fail silently

Future Extensions

This section documents planned additions to the workspace and agent capabilities.

Planned Document Types

Patents (001_patents/) — Technical invention disclosures ✓
Books (003_books/) — Extended works with chapter structure ✓
Presentations — Beamer slides for conferences
Grant proposals — Funding applications

Planned Skills (for agents)

Future skill modules to be added:

Skill	Purpose
`mathematics`	Equation formatting, proof structure, notation consistency
`bibliography-manager`	Citation verification, DOI lookup, reference formatting
`figure-design`	TikZ diagrams, scientific visualisation guidance
`patent-drafting`	Claims structure, legal language, prior art analysis

Integration Notes

Unified agent configuration:

.agents/skills/ provides skills for all compatible agents
Cursor, OpenCode, and Claude Code all discover skills from this location
AGENTS.md serves as the shared knowledge base

Editor compatibility:

Author uses Zed as primary editor
zed <FILE> opens files from CLI
This AGENTS.md is editor-agnostic

Quick Reference

Common Commands

# Compile document
latexmk -pdf document.tex

# Clean auxiliary files
latexmk -c

# Open in Zed
zed essay.tex

# Git workflow
git checkout -b essay/004
git add essay.tex references/bibliography.bib
git commit -m "Draft: consciousness continuity mechanisms"

LaTeX Snippets

% New section with marker
% ! ====================
% ! # MARK: Section Name
% ! ====================
\section{Section Name}
\label{sec:section-name}

% Figure with custom caption
\begin{figure}[ht]
  \centering
  \includegraphics[width=\textwidth]{figures/name.png}
  \floatcaption{Title}{Description.}
  \label{fig:name}
\end{figure}

% Inline citation
As demonstrated by \citet{author_keyword_year}, ...

% Parenthetical citation
... substrate independence \citep{author_keyword_year}.

File Naming

Figures: descriptive-name.png (lowercase, hyphens)
BibTeX keys: lastname_keyword_year
Labels: type:descriptive-name (e.g., fig:process-world-line, sec:introduction, eq:continuity)

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AGENTS.md — Writings Workspace

Workspace Overview

Repository Structure

Content Types

Language & Style Guidelines

British English (Mandatory)

Academic Tone

Writing Philosophy

LaTeX Conventions

Template System

Personal Templates (for Drafting)

Submission Templates (for Journals/Conferences)

Document Structure

Section Markers

Custom Commands

Figures

Tables

Code Listings

Mathematics

Bibliography

Workflow Guidelines

Creating New Documents

Submodule Workflow (Work-in-Progress Documents)

Compilation

Version Control

Agent Instructions

For All Agents (Cursor, OpenCode, Claude Code)

Task Categories

Quality Checklist

Legal & Publication Guidelines

Patents

Open Access

Citation

Available Skills

Skill Overview

writing-clearly-and-concisely

scientific-writing

scientific-critical-thinking

scientific-brainstorming

scientific-visualization

latex-writing

mermaid-diagrams

Future Extensions

Planned Document Types

Planned Skills (for agents)

Integration Notes

Quick Reference

Common Commands

LaTeX Snippets

File Naming