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Best Practice Guidelines for Prompt Markdown Instructions (.md Files)
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Markdown-Instructions-for-AI--and-humans.md

Best Practice Guidelines for Prompt Markdown Instructions (.md Files)

When creating Markdown (.md) files to standardize prompt instructions or best practices, clarity, consistency, and structure are paramount. Below is a comprehensive guideline on how to structure these files and what to do-and avoid-when authoring them.

Key Principles

  • Clarity: Use Markdown to make prompts and instructions easy to read, both for humans and AI models[6][8].
  • Consistency: Stick to a single Markdown flavor (e.g., CommonMark, GitHub Flavored Markdown) throughout your project[5].
  • Explicitness: Clearly state roles, expected outputs, and formatting requirements[6][7].

Recommended Structure for Prompt Guidelines in Markdown

  1. Front Matter (Optional but Recommended)

    • Use YAML front matter for metadata (title, author, date, description)[2].
    • Example: 
      ---
title: Prompt Engineering Best Practices
author: Jane Doe
date: 2025-04-30
description: Guidelines for structuring prompt instructions in Markdown.
---

  2. Title and Introduction

    • Start with a single H1 heading that matches the filename or topic[4].
    • Provide a concise introduction (1–3 sentences) explaining the document’s purpose[4].

  3. Table of Contents (TOC)

    • Add [TOC] after the introduction if your platform supports it, to enhance navigation for longer documents[4].

  4. Sectioned Content Using Headings

    • Use H2 (##) for main sections and H3 (###) for subsections[4][8].
    • Example: 
      ## Structuring Prompts
### Step-by-Step Instructions

  5. Best Practices and Examples

    • Use bulleted lists for unordered items and numbered lists for ordered steps[3][5][8].
    • Highlight key points with bold (**text**) or italics (*text*)[3][8].
    • Include fenced code blocks for sample prompts or output, specifying the language if relevant[5].
    • Example: 
      **Do:**
- Use clear section headings.
- Specify expected output format.
- Break down complex instructions into steps.

**Don't:**
- Mix Markdown with other document formats.
- Overcomplicate with unnecessary detail.

  6. Formatting and Accessibility

    • Use horizontal rules (---) to separate major sections[8].
    • Add alt text to images for accessibility[3].
    • Keep lines at or below 80 characters for readability, except for links or tables[4].

  7. References and Further Reading

    • End with a “See Also” or “References” section for additional resources[4].

Do’s and Don’ts for Prompt Markdown Files

Do’s Don’ts
Use a single H1 title per document[4] Use multiple H1 headings
Start with a short, clear introduction[4] Skip context or purpose
Add a TOC after the intro for long docs[4] Place TOC at the end or in the middle
Use clear, descriptive section headings[4][8] Use ambiguous or generic headings
Prefer bulleted/numbered lists for clarity[3][5][8] Use long, dense paragraphs
Provide sample prompts and expected outputs[6][7] Leave instructions vague or open-ended
Specify formatting/output requirements[6][7] Assume the reader/model knows your preferred format
Keep instructions concise and explicit[6][7] Overload with unnecessary details
Use fenced code blocks for examples[5] Mix code and prose in the same block
Use bold/italics for emphasis[3][8] Overuse formatting, making text hard to read
Maintain consistent Markdown flavor and style[5] Mix different Markdown syntaxes
Organize files in a logical directory structure[5] Scatter related files across unrelated directories

Example Template

---
title: Prompt Engineering Best Practices
author: Jane Doe
date: 2025-04-30
description: Guidelines for structuring prompt instructions in Markdown.
---

# Prompt Engineering Best Practices

A concise guide to creating clear, effective prompt instructions using Markdown.

[TOC]

## Structuring Your Prompt

- **Start with context:** Briefly explain the task or goal.
- **Specify roles:** e.g., “You are an expert editor...”
- **Break down steps:** Use numbered lists for step-by-step instructions.
- **Define output format:** e.g., “Respond in Markdown table format.”

## Do’s

- Use headings to separate sections.
- Provide sample input and expected output.
- Keep instructions concise and explicit.

## Don’ts

- Don’t mix Markdown with other document formats.
- Don’t skip specifying output format.
- Don’t use multiple H1 headings.

## Sample Prompt

Task

Summarize the following text as a bullet point list.

Text: """ {Insert text here} """

Output Format

  • Point 1
  • Point 2

## See Also

- [OpenAI Prompt Engineering Guide]
- [Markdown Style Guide]

Additional Tips

  • Preview your Markdown files to catch formatting errors before sharing[3].
  • Escape special characters when needed (e.g., \* for a literal asterisk)[2].
  • Use descriptive link text, not just “click here”[2].
  • Keep document structure logical and easy to navigate[5].

By following these guidelines, your prompt instruction Markdown files will be clear, maintainable, and effective for both humans and AI models[4][5][6][7][8].

Sources [1] Prompting: Experimenting with Markdown (with Example of Multi ... https://www.linkedin.com/pulse/prompting-experimenting-markdown-example-test-data-generation-verma-toiuf [2] Best practices and tips in markdown https://technicalwritingmp.com/docs/markdown-course/best-practices-and-tips-in-markdown/ [3] 13 must-know Markdown tips and tricks - TechTarget https://www.techtarget.com/searchsoftwarequality/tip/Must-know-Markdown-tips-and-tricks [4] Markdown style guide | styleguide - Google https://google.github.io/styleguide/docguide/style.html [5] Markdown Best Practices for Documentation https://www.markdowntoolbox.com/blog/markdown-best-practices-for-documentation/ [6] How To Write Effective AI Prompts (Updated) - Daniel Miessler https://danielmiessler.com/blog/how-i-write-prompts [7] Best practices for prompt engineering with the OpenAI API https://help.openai.com/en/articles/6654000-best-practices-for-prompt-engineering-with-the-openai-api [8] Streamline Your Prompts with Markdown: A Quick Guide for Better ... https://nfps.ai/tutorials/prompt-with-markdown/ [9] Ultimate Markdown guide: 5 rules to know - TechTarget https://www.techtarget.com/searchsoftwarequality/tip/Ultimate-Markdown-guide-Rules-to-know [10] 10 Markdown Tips for Creating Beautiful Product Documentation in ... https://dev.to/auden/10-markdown-tips-for-creating-beautiful-product-documentation-in-2025-5ek4 [11] Understanding Prompt Structure: Key Parts of a Prompt https://learnprompting.org/docs/basics/prompt_structure [12] Do you write your prompts in Markdown? : r/PromptEngineering https://www.reddit.com/r/PromptEngineering/comments/17aktzb/do_you_write_your_prompts_in_markdown/ [13] 10 Quick Tips About A Great Markdown Editor - Froala https://froala.com/blog/editor/10-quick-tips-about-a-great-markdown-editor/ [14] (opinionated) Simple (and obvious) best practices for the Prompt https://community.openai.com/t/opinionated-simple-and-obvious-best-practices-for-the-prompt/984955 [15] Markdown Cheat Sheet https://www.markdownguide.org/cheat-sheet/ [16] What is the best practice for code runner for markdown files? #6629 squidfunk/mkdocs-material#6629 [17] Creating Instructions with Markdown Syntax - Skillable https://docs.skillable.com/docs/creating-instructions-with-markdown-syntax [18] Markdown Blocks Tips and Tricks - NocoBase https://www.nocobase.com/en/tutorials/clever-uses-of-markdown-blocks [19] Creating Beautiful Markdown Files in GitHub. - DEV Community https://dev.to/danishzayan/creating-beautiful-markdown-files-in-github-5ga3 [20] Basic writing and formatting syntax - GitHub Docs https://docs.github.com/github/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax [21] Novel organizer for markdown files : r/linuxquestions - Reddit https://www.reddit.com/r/linuxquestions/comments/18eam63/novel_organizer_for_markdown_files/ [22] Markdown Guide https://www.markdownguide.org [23] Markdown style guide - Gruntwork Docs https://docs.gruntwork.io/guides/style/markdown-style-guide/ [24] What is the right way to arrange the content folder and md files - HUGO https://discourse.gohugo.io/t/what-is-the-right-way-to-arrange-the-content-folder-and-md-files/45276 [25] Extended Syntax - Markdown Guide https://www.markdownguide.org/extended-syntax/ [26] How to maintain a good folder structure? : r/ObsidianMD - Reddit https://www.reddit.com/r/ObsidianMD/comments/16ebwaz/how_to_maintain_a_good_folder_structure/ [27] Markdown for Technical Writers: Tips, Tricks, and Best Practices https://israelmitolu.hashnode.dev/markdown-for-technical-writers-tips-tricks-and-best-practices [28] Markdown - Wikipedia https://en.wikipedia.org/wiki/Markdown [29] Is the best digital workplace just a bunch of Markdown files? https://luhr.co/blog/2024/09/02/markdown-files-as-the-digital-workplace/ [30] Basic Syntax - Markdown Guide https://www.markdownguide.org/basic-syntax/ [31] Prompts with Markdown format are better? : r/ChatGPT - Reddit https://www.reddit.com/r/ChatGPT/comments/1gfgvhc/prompts_with_markdown_format_are_better/ [32] Getting Started | Markdown Guide https://www.markdownguide.org/getting-started/ [33] How To Write Better & Cleaner Markdown: The Definitive Guide https://dev.to/soumikdhar/how-to-write-better-cleaner-markdown-the-definitive-guide-3fif [34] How to Organize Your Writing with Markdown https://redeemingproductivity.com/markdown/ [35] Introductory Guide to Markdown for Documentation Writers https://document360.com/blog/introductory-guide-to-markdown-for-documentation-writers/

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Prompt Documentation Best Practices: A Comprehensive Markdown Guide

Effective prompt documentation is essential for maintaining, sharing, and scaling AI prompt engineering efforts across teams. This guide outlines best practices for creating well-structured markdown (.md) files for prompt documentation, focusing on organization, formatting, and content standards that ensure clarity, consistency, and usability.

Introduction to Prompt Documentation

Prompt documentation ensures AI systems deliver accurate and consistent results. It involves recording the instructions given to language models (LLMs) in a systematic way, including task details, context, formatting rules, and version history[6]. Well-documented prompts are easier to maintain, share, and improve over time.

Why Document Prompts?

Not having a well-organized prompt library can lead to several problems:

  • Lost Knowledge: Valuable intellectual property or institutional knowledge disappears when prompts aren't documented[17]
  • Redundancies: Without centralization, teams create duplicate prompts, leading to inefficiencies[17]
  • Information Silos: Undocumented prompts create barriers to knowledge sharing across teams[17]
  • Compliance Breaches: Unmanaged prompts might inadvertently violate organizational or legal regulations[17]

File Structure and Organization

Creating a logical, consistent file structure forms the foundation of good prompt documentation.

Folder Structure Best Practices

DO:

  • Store prompts in a shared, centralized repository (not on personal devices)[21]
  • Group prompts by category, function, or use case[21]
  • Implement a clear, consistent folder hierarchy[20]
  • Use descriptive folder names that indicate contents[20]

DON'T:

  • Mix business and personal prompt files[21]
  • Create overly complex nested folder structures (aim for 3-4 levels maximum)[21]
  • Use ambiguous folder names that require opening to understand contents[21]

Recommended Folder Structure

/prompts
  /templates          # Reusable prompt templates
  /use-cases          # Prompts organized by business function
    /content-creation
    /customer-support
    /data-analysis
  /components         # Reusable prompt components
  /examples           # Example prompts with outputs
  /archived           # Retired or superseded prompts
  README.md           # Overview of the prompt library

Markdown Formatting Standards

Consistent formatting improves readability and usability of prompt documentation.

Heading Structure

DO:

  • Use a single level-one heading (#) for the document title[2][3]
  • Implement a logical heading hierarchy (# for title, ## for sections, ### for subsections)[2]
  • Ensure heading levels are sequential without skipping levels[1]
  • Use descriptive headings that clearly indicate section contents[4]

DON'T:

  • Use multiple level-one headings in a single document[2]
  • Skip heading levels (like going from ## to ####)[1]
  • Use headings that don't accurately describe content[4]

Text Formatting

DO:

  • Use bold for important information and key terms[3][4]
  • Use italics for emphasis and supplementary notes[3][4]
  • Use strikethrough to indicate deprecated features or removed content[3]
  • Use consistent spacing and indentation patterns[1]

DON'T:

  • Overuse text formatting, which reduces its effectiveness[5]
  • Mix formatting styles inconsistently[1]
  • Use decorative formatting that doesn't add meaning[5]

Prompt Documentation Template

Every prompt document should follow a consistent template structure for maximum clarity and usability.

Basic Template Structure

# [Prompt Name]

## Purpose
Brief description of what this prompt does and when to use it.

## Parameters
| Parameter | Type | Required | Description |
|-----------|------|----------|-------------|
| input1    | text | Yes      | Description of input1 |
| input2    | text | No       | Description of input2 |

## Template

Configuration (optional)

provider: openai
model: gpt-4o
temperature: 0.7
max_tokens: 4000

[Prompt text goes here. Use {{variables}} for dynamic inputs]


## Example Input

[Example of how to use this prompt with sample values]


## Example Output

[Example of expected output]


## Notes
Additional information, caveats, or best practices.

## Version History
| Version | Date | Changes | Author |
|---------|------|---------|--------|
| 1.0     | 2025-04-30 | Initial version | Jane Doe |

Content Components for Effective Documentation

Effective prompt documentation includes several key components that provide context and guidance.

Essential Components

DO:

  • Include clear purpose statements that explain what the prompt does[10]
  • Specify required inputs and expected outputs[10][15]
  • Provide usage examples that demonstrate the prompt in action[10][15]
  • Document any assumptions or limitations[6]
  • Include version history to track changes over time[6]

DON'T:

  • Omit context necessary for understanding how the prompt works[5]
  • Use vague descriptions that don't clearly communicate purpose[5]
  • Skip examples, which are crucial for understanding proper usage[5][6]

Advanced Documentation Elements

For more sophisticated prompts, consider including:

  • Step-by-step instructions for multi-part prompts[18]
  • Role clarification for prompts requiring specific AI personas[18]
  • Format specifications for structured outputs (tables, JSON, etc.)[5]
  • Chain of thought examples for complex reasoning tasks[16]
  • Prompt variants for different use cases or contexts[16]

YAML Front Matter for Metadata

Using YAML front matter can enhance prompt documentation with structured metadata.

DO:

  • Include essential prompt parameters in YAML format[14]
  • Document model selection, temperature, and token limits[14]
  • Use consistent parameter naming conventions[14]

DON'T:

  • Include sensitive information in YAML metadata[14]
  • Omit critical parameters needed for reproduction[14]

Example YAML Front Matter

---
title: Customer Support Response Generator
author: John Smith
version: 1.2
date: 2025-04-30
model: gpt-4o
temperature: 0.7
max_tokens: 2000
description: Generates empathetic customer support responses based on issue description
tags: [customer-support, response-generation, tone-management]
---

Version Control and Maintenance

Proper version control ensures prompt documentation remains accurate and up-to-date.

DO:

  • Use a version control system like Git for tracking changes[6][23]
  • Implement semantic versioning (MAJOR.MINOR.PATCH) for prompts[23]
  • Document changes in a changelog or version history section[6]
  • Schedule regular reviews to ensure documentation quality and accuracy[6]

DON'T:

  • Maintain multiple versions of the same prompt without clear versioning[23]
  • Make undocumented changes to prompt templates[6]
  • Neglect to update documentation when prompts are refined[6]

Documentation Review Checklist

Before finalizing prompt documentation, use this checklist to ensure quality and completeness:

Accuracy:

  • Verify all prompt text is correct and properly formatted[25]
  • Check that examples work as expected[24]
  • Confirm all parameters are accurately described[24]

Completeness:

  • Ensure all required sections are included[25]
  • Verify all necessary context is provided[25]
  • Check that version history is up-to-date[26]

Usability:

  • Confirm documentation is clear and readable[24]
  • Verify formatting is consistent throughout[24]
  • Ensure examples are helpful and relevant[25]

Examples of Well-Structured Prompt Documentation

Basic Instruction Prompt

# Product Feature Summarizer

## Purpose
Creates concise summaries of product features for marketing materials.

## Parameters
| Parameter | Type | Required | Description |
|-----------|------|----------|-------------|
| product_name | text | Yes | Name of the product |
| feature_list | text | Yes | Comma-separated list of features |
| tone | text | No | Desired tone (default: professional) |

## Template

model: gpt-4o
temperature: 0.7

You are a skilled marketing copywriter specializing in clear, compelling product descriptions.

Create a concise summary of the key features for {{product_name}}. Focus on these features: {{feature_list}}.

Write in a {{tone}} tone, emphasizing benefits alongside features. Limit to 2-3 sentences per feature.


## Example Input

product_name: EcoWash Dishwasher
feature_list: Energy Star certified, Half-load option, Quiet operation (45dB)
tone: enthusiastic


## Example Output

The EcoWash Dishwasher revolutionizes kitchen cleanup with its Energy Star certification, slashing your utility bills while protecting the environment! Its innovative Half-load option delivers perfect results when you're short on dishes, saving valuable water and electricity without compromising cleanliness. You'll barely notice it's running thanks to whisper-quiet 45dB operation, making it perfect for open-concept homes where conversation flows as freely as your evening!


## Notes
- Adjust temperature lower (0.5) for more factual descriptions
- Increase temperature (0.8) for more creative variations

## Version History
| Version | Date | Changes | Author |
|---------|------|---------|--------|
| 1.0 | 2025-04-15 | Initial version | Alex Wong |
| 1.1 | 2025-04-30 | Added tone parameter | Alex Wong |

Complex Multi-Part Prompt

# Customer Complaint Analysis and Response Generator

## Purpose
Analyzes customer complaints to identify key issues, sentiment, and generates appropriate response templates.

## Parameters
| Parameter | Type | Required | Description |
|-----------|------|----------|-------------|
| complaint_text | text | Yes | Customer complaint in full |
| product_line | text | Yes | Product line being referenced |
| customer_history | text | No | Previous interactions summary |
| response_type | text | No | Options: empathetic, solution-focused, or escalation (default: solution-focused) |

## Template

model: gpt-4o
temperature: 0.4
max_tokens: 4000

Your Role

You are a customer experience specialist with expertise in analyzing complaints and generating appropriate responses.

Task Details

You will:

  1. Analyze the customer complaint
  2. Identify key issues and sentiment
  3. Generate an appropriate response template

Customer Complaint

{{complaint_text}}

Product Information

Product Line: {{product_line}}

Customer History

{{customer_history}}

Response Type

{{response_type}}

Analysis Instructions

First, analyze the complaint to identify:

  • Primary issues (list up to 3)
  • Customer sentiment (frustrated, angry, disappointed, etc.)
  • Issue severity (low, medium, high)

Response Instructions

Based on your analysis, create a response template that:

  • Acknowledges the customer's feelings
  • Addresses each identified issue
  • Provides clear next steps or solutions
  • Maintains brand voice while being authentic
  • Follows the specified response type approach

## Example Input

complaint_text: I've been waiting for my order (XJ-5539) for three weeks now, and customer service keeps telling me it's "being processed." This is ridiculous! I paid extra for expedited shipping and have received nothing but excuses. I'm about to dispute the charge with my credit card company.
product_line: Premium Kitchen Appliances
customer_history: Frequent customer, 5+ purchases in last year, no previous complaints
response_type: empathetic


## Example Output

Analysis

Primary Issues:

  1. Extended delay in order delivery (3+ weeks)
  2. Perceived lack of resolution from previous customer service contacts
  3. Paid for expedited shipping that wasn't honored

Customer Sentiment: Frustrated and angry

Issue Severity: High (customer threatening chargeback)

Response Template

Dear Valued Customer,

I'm truly sorry to hear about your frustrating experience with order XJ-5539. I completely understand your disappointment, especially as someone who has consistently chosen our Premium Kitchen Appliances. The delay you've experienced, particularly after paying for expedited shipping, is absolutely not the experience we want for you.

I've personally looked into your order and can see the difficulties you've encountered. Rather than offer explanations, I want to take immediate action:

  1. I've expedited your order with our highest priority status - it will ship within 24 hours with overnight delivery
  2. We're refunding your expedited shipping fee plus an additional 15% off your entire order
  3. I'm sending you a direct contact line to reach me personally if you have any questions before delivery

As a valued customer who has supported us with multiple purchases, your experience matters tremendously to us. I'm genuinely sorry we've disappointed you, and we're committed to making this right.

May I ask if these solutions address your concerns, or is there something else you feel would better resolve this situation?

Sincerely,
[Your Name]
Customer Experience Specialist
[Direct Contact Information]


## Notes
- Adjust analysis depth based on complaint complexity
- For high-severity issues, always include a direct contact method
- Response types dramatically change approach - review examples of each

## Version History
| Version | Date | Changes | Author |
|---------|------|---------|--------|
| 1.0 | 2025-03-10 | Initial version | Maya Johnson |
| 1.1 | 2025-04-02 | Added customer history parameter | Maya Johnson |
| 1.2 | 2025-04-18 | Added response type options | Chris Lee |

Conclusion

Creating effective prompt documentation in Markdown requires attention to structure, content, and formatting. By following these best practices, you can build a valuable prompt library that enhances collaboration, preserves institutional knowledge, and improves the consistency of AI outputs across your organization.

Remember that good documentation is an ongoing process, not a one-time effort. Regularly review and update your prompt documentation to reflect new insights, techniques, and use cases. By investing in quality documentation now, you'll create a foundation for sustainable AI prompt engineering practices that grow with your organization's needs.

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