Your documentation architecture is wrong if you're storing PDFs in version control. Markdown should be your system of record. PDF should be your output format. This isn't a preference—it's infrastructure.
TL;DR – The Answer
📝 Markdown = Source of Truth (System of Record)
- • Version control friendly (Git diffs work)
- • Human-readable and editable
- • CI/CD pipeline compatible
- • Programmatically parsable
- • Future-proof (plain text)
📄 PDF = Output Format (Distribution)
- • Generate from Markdown via CI/CD
- • Distribute to clients/stakeholders
- • Archive final versions
- • Legal signatures and compliance
- • Never commit to version control
Exception: If you receive PDFs from external sources (contracts, research papers, vendor docs), convert them to Markdown immediately using BlazeDocs and store the Markdown.
Why This Decision Matters
Choosing between PDF and Markdown as your system of record isn't about file formats—it's about your entire documentation pipeline. Get this wrong and you'll fight tooling, lose history, and break automation.
✅ Good Architecture: Markdown as Source
docs/api-reference.md → Git commit → CI builds api-reference.pdf → Distribute to clients. Version history is semantic. Diffs show actual content changes. Automation works.
❌ Bad Architecture: PDF as Source
docs/api-reference.pdf → Git commit shows binary diff. Version history is useless. Can't search, can't parse, can't automate. You're debugging Word documents in 2025.
The format you choose as your system of record determines your workflow, your tooling, and your team's productivity. Choose wrong and you'll spend years compensating with brittle scripts and manual processes.
The Case for Markdown as System of Record
1. Version Control That Actually Works
Git was designed for plain text. Markdown is plain text. This isn't a coincidence—it's the entire point.
Markdown Git Diff
- API rate limit: 100 req/min + API rate limit: 200 req/min
You see exactly what changed. Semantic diffs. Merge conflicts are resolvable.
PDF Git Diff
Binary files differ.
Useless. You have no idea what changed. Download both versions, open side-by-side, squint.
2. Automation and CI/CD Integration
Modern documentation pipelines are code. Markdown enables this. PDF breaks it.
What You Can Automate with Markdown:
- • Lint documentation – Check for broken links, style violations, outdated sections
- • Generate API docs – Extract code examples, validate syntax, inject live data
- • Build multi-format outputs – PDF, HTML, DOCX from single source
- • Trigger reviews – Auto-assign reviewers when specific sections change
- • Validate compliance – Ensure required sections exist, templates followed
Try doing any of that with PDF as your source. You can't. PDF is a rendering format, not a data format. It's designed to look the same everywhere, not to be parsed and transformed.
3. Human Readability and Editability
Markdown is readable in vim, readable in GitHub, readable in Slack. No special tools required.
Editing Markdown
- • Any text editor works
- • Edit in browser (GitHub)
- • Edit via API
- • Edit via CLI
- • No proprietary software
Editing PDF
- • Requires Adobe Acrobat ($$$)
- • Or clunky alternatives
- • No programmatic editing
- • Results often broken
- • Formatting nightmares
4. Future-Proof and Portable
Markdown files from 2004 still render perfectly in 2025. Plain text is eternal. PDF spec has changed multiple times. Proprietary extensions break compatibility. Good luck opening a PDF from 1995 with modern JavaScript renderers.
The Case for PDF as Output Format
PDF isn't useless—it's just the wrong tool for version control. Here's where PDF excels:
📤 Distribution to Non-Technical Stakeholders
Clients, legal teams, executives—they want PDF. It looks professional, renders consistently, and doesn't require GitHub access. Generate PDF from Markdown in your CI pipeline, then distribute.
🔒 Legal Compliance and Signatures
Contracts, audit reports, regulatory submissions—these need PDF for signatures and tamper-evidence. But store the Markdown source, generate the PDF, sign the PDF.
📦 Archival and Long-Term Storage
PDF/A is designed for archival. If you need to preserve exact visual fidelity for decades, generate PDF/A from your Markdown source at milestone versions (v1.0, v2.0) and archive those.
🎨 Complex Layout and Typography
Marketing materials, branded reports, coffee table books—these need precise layout control. Use design tools to generate final PDF, but keep the content source in Markdown for reuse.
Key principle: PDF is a build artifact, like a compiled binary. You don't commit app.exe to Git—you commit source code and build it. Same logic applies to documentation.
Anti-Patterns That Break Your Pipeline
🚨 Anti-Pattern #1: Storing PDFs in Git
Why teams do this: "It's the source we received from the vendor/client/legal team."
Why it's wrong: You're storing binary blobs that can't be diffed, searched, or automated. Git LFS doesn't fix this—it just makes the problem slower.
Fix: Convert PDFs to Markdown with BlazeDocs immediately upon receipt. Store the Markdown. Keep the original PDF in S3/archive storage if needed for legal reasons.
🚨 Anti-Pattern #2: Manually Syncing PDF ↔ Markdown
Why teams do this: "We edit the Markdown for internal use, then manually update the PDF for clients."
Why it's wrong: Manual sync always drifts. The PDF becomes outdated. You waste hours reconciling differences.
Fix: Single source of truth (Markdown). Automate PDF generation via CI/CD. Use tools like pandoc, mdpdf, or LaTeX pipelines.
🚨 Anti-Pattern #3: Using Word/Google Docs as System of Record
Why teams do this: "Everyone knows how to use Word/Docs. Easy collaboration."
Why it's wrong: Proprietary formats. Poor version control. No automation. Export-to-PDF loses formatting. You're one API change away from losing access.
Fix: Write in Markdown, version in Git, render to HTML/PDF for distribution. Use BlazeDocs to convert legacy Word/Docs → Markdown for migration.
Modern Documentation Architecture
Here's how modern engineering teams structure their documentation pipeline:
The BlazeDocs Reference Architecture
Source: Write documentation in Markdown, store in Git alongside code
Ingest: When PDFs arrive (contracts, research, vendor docs), convert to Markdown with BlazeDocs API
Version Control: Commit Markdown to Git. Use semantic commits (docs: update API rate limits)
CI/CD: On merge to main, trigger pipeline that generates PDF, HTML, DOCX outputs
Distribution: Upload generated PDFs to S3, send to clients, publish HTML to docs site
Archive: Tag releases in Git (v2.1.0), store milestone PDFs in long-term storage
Example CI/CD Pipeline (GitHub Actions):
name: Build Docs
on:
push:
branches: [main]
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Convert MD to PDF
run: pandoc docs/*.md -o output.pdf
- name: Upload to S3
run: aws s3 cp output.pdf s3://docs-bucket/This is infrastructure. You're treating documentation as code. Markdown enables this. PDF does not.
How BlazeDocs Fits Into This Architecture
BlazeDocs isn't a "PDF to Markdown converter"—it's the bridge between legacy systems and modern infrastructure.
🔄 Ingestion Layer
External parties send you PDFs (contracts, research papers, vendor documentation). BlazeDocs converts these to Markdown automatically via API, so they enter your system as plain text—version-controllable and automatable.
Use case: Law firms receive 1000s of case PDFs → BlazeDocs API converts → Store as Markdown in Git → Full-text search, automated redaction, and compliance checks now work.
📚 Knowledge Base Migration
You have 10 years of documentation as PDFs. BlazeDocs batch-converts your entire archive to Markdown, preserving structure and formatting. Now you can index, search, and version-control your legacy knowledge.
Use case: Engineering consultancy migrating to Notion/Obsidian → BlazeDocs converts 5000 legacy PDFs → Import as Markdown → Searchable wiki instead of dead archive.
🤖 AI/LLM Pipeline Integration
RAG systems and AI agents need structured text, not PDFs. BlazeDocs extracts clean Markdown that embeds perfectly into vector databases without manual cleanup.
Use case: Support team builds internal AI assistant → BlazeDocs converts product manuals (PDF) → Markdown chunks embedded in Pinecone → AI answers questions from docs accurately.
🔁 Reverse Engineering Compliance
Regulatory bodies require PDF submissions, but you need to maintain those documents as code. Store Markdown source in Git, generate compliant PDFs on-demand.
Use case: Medical device company maintains IFU (Instructions For Use) → Markdown in Git with approval workflow → CI generates FDA-compliant PDF/A → BlazeDocs ensures legacy PDFs can be re-ingested if needed.
BlazeDocs = Infrastructure, Not a Tool
You don't "use BlazeDocs occasionally." You integrate BlazeDocs into your documentation pipeline as the PDF → Markdown normalization layer. It's infrastructure that ensures everything entering your system is version-controllable, searchable, and automatable.
View API Documentation →Frequently Asked Questions
What if I need to preserve exact visual fidelity?
Store Markdown as source. Generate pixel-perfect PDF via LaTeX or professional tooling. Version-control the LaTeX template, not the PDF output. This is how academic publishers work—.tex is source, .pdf is output.
Our legal team requires PDFs for contracts. How do we handle this?
Draft contracts in Markdown, version in Git, generate PDF for signature. After signing, store signed PDF in archive (S3/compliance system) but keep Markdown in Git for reference and future versions. When contracts arrive from external parties, convert to Markdown with BlazeDocs before storing.
What about diagrams, images, and complex layouts?
Reference images via Markdown syntax (). Store images in Git LFS or S3. For complex diagrams, use Mermaid (renders in Markdown) or commit SVG source files. Point is: everything should have a text-based source.
How do I migrate years of legacy PDFs to this architecture?
Batch convert with BlazeDocs API. Upload entire directories of PDFs, receive Markdown output with preserved structure. Then commit to Git with proper history (initial commit or squashed import). See our batch conversion guide.
What if my team insists on Word/Google Docs?
Compromise: Draft in Docs if needed, but export to Markdown before committing. Use Pandoc or BlazeDocs to convert DOCX → Markdown. Git becomes the source of truth. Docs/Word becomes a staging environment. This transition pattern works for most teams.
Can I still use Notion/Confluence if I want Markdown as source?
Yes. Notion and Confluence both support Markdown import/export. Store canonical Markdown in Git, sync to Notion/Confluence via their APIs for team consumption. Git remains system of record. See our Notion integration guide.
The Final Answer
Markdown is your system of record. It's version-controllable, automatable, human-readable, and future-proof. PDF is your output format—generated from Markdown via CI/CD and distributed to stakeholders who need visual fidelity or legal signatures.
If you're receiving PDFs from external sources, convert them to Markdown immediately with BlazeDocs and treat the Markdown as canonical. Don't let binary formats enter your version control system.
This isn't about file format preferences—it's about building documentation infrastructure that scales. Choose Markdown as your system of record and you'll thank yourself in 5 years.
Build Documentation Infrastructure That Scales
Convert legacy PDFs to Markdown. Integrate BlazeDocs into your CI/CD pipeline. Treat docs as code.
Infrastructure pricing. Pay per document. No subscription lock-in.