Markdown and Mermaid Writing

Overview

This skill teaches you — and enforces a standard for — creating scientific documentation using markdown with embedded Mermaid diagrams as the default and canonical format.

The core bet: a relationship expressed as a Mermaid diagram inside a .md file is more valuable than any image. It is text, so it diffs cleanly in git. It requires no build step. It renders natively on GitHub, GitLab, Notion, VS Code, and any markdown viewer. It uses fewer tokens than a prose description of the same relationship. And it can always be converted to a polished image later — but the text version remains the source of truth.

"The more you get your reports and files in .md in just regular text, which mermaid is as well as being a simple 'script language'. This just helps with any downstream rendering and especially AI generated images (using mermaid instead of just long form text to describe relationships < tokens). Additionally mermaid can render along with markdown for easy use almost anywhere by humans or AI."

— Clayton Young (@borealBytes), K-Dense Discord, 2026-02-19

When to Use This Skill

Use this skill when:

• Creating any scientific document — reports, analyses, manuscripts, methods sections
• Writing any documentation — READMEs, how-tos, decision records, project docs
• Producing any diagram — workflows, data pipelines, architectures, timelines, relationships
• Generating any output that will be version-controlled — if it's going into git, it should be markdown
• Working with any other skill — this skill defines the documentation layer that wraps every other output
• Someone asks you to "add a diagram" or "visualize the relationship" — Mermaid first, always

Do NOT start with Python matplotlib, seaborn, or AI image generation for structural or relational diagrams. Those are Phase 2 and Phase 3 — only used when Mermaid cannot express what's needed (e.g., scatter plots with real data, photorealistic images).

🎨 The Source Format Philosophy

Why text-based diagrams win

The three-phase workflow

flowchart LR
    accTitle: Three-Phase Documentation Workflow
    accDescr: Phase 1 Mermaid in markdown is always required and is the source of truth. Phases 2 and 3 are optional downstream conversions for polished output.

    p1["📄 Phase 1<br/>Mermaid in Markdown<br/>(ALWAYS — source of truth)"]
    p2["🐍 Phase 2<br/>Python Generated<br/>(optional — data charts)"]
    p3["🎨 Phase 3<br/>AI Generated Visuals<br/>(optional — polish)"]
    out["📊 Final Deliverable"]

    p1 --> out
    p1 -.->|"when needed"| p2
    p1 -.->|"when needed"| p3
    p2 --> out
    p3 --> out

    classDef required fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#1e3a5f
    classDef optional fill:#fef9c3,stroke:#ca8a04,stroke-width:2px,color:#713f12
    classDef output fill:#dcfce7,stroke:#16a34a,stroke-width:2px,color:#14532d

    class p1 required
    class p2,p3 optional
    class out output

Phase 1 is mandatory. Even if you proceed to Phase 2 or 3, the Mermaid source stays committed.

What Mermaid can express

Mermaid covers 24 diagram types. Almost every scientific relationship fits one:

💡 Pick the right type, not the easy one. Don't default to flowcharts for everything. A timeline beats a flowchart for chronological events. A sequence beats a flowchart for service interactions. Scan the table and match.

🔧 Core workflow

Step 1: Identify the document type

Check if a template exists before writing from scratch:

Step 2: Read the style guide

Before writing any .md file: read references/markdown_style_guide.md.

Key rules to internalize:

• One H1 per document — the title. Never more.
• Emoji on H2 headings only — one emoji per H2, none in H3/H4
• Cite everything — every external claim gets a footnote [^N] with full URL
• Bold sparingly — max 2-3 bold terms per paragraph, never full sentences
• Horizontal rule after every </details> — mandatory
• Tables over prose for comparisons, configurations, structured data
• Diagrams over walls of text — if it describes flow, structure, or relationships, add Mermaid

Step 3: Pick the diagram type and read its guide

Before creating any Mermaid diagram: read references/mermaid_style_guide.md.

Then open the specific type file (e.g., references/diagrams/flowchart.md) for the exemplar, tips, and copy-paste template.

Mandatory rules for every diagram:

accTitle: Short Name 3-8 Words
accDescr: One or two sentences explaining what this diagram shows.

• **No `