Why Markdown?
Markdown is plain text with light marks for structure: # for headings, - for lists, | for tables. It's what note apps (Obsidian, Notion), documentation sites and code repositories use, and it's the cleanest way to give a document to an AI assistant: fewer tokens than a PDF, and the structure stays clear.
What is kept
- Headings, found from text size and weight: the largest text becomes #, smaller titles ## and ###.
- Paragraphs joined back together across line breaks, lists, links, bold and italic.
- Tables as Markdown tables.
- Columns read in order: a page layout model finds text columns, so two-column papers come out left column first, not mixed line by line.
Tick Leave out page headers, footers and page numbers to drop the text that repeats on every page, and Mark page breaks to keep a --- line between pages.
Limits
Scanned PDFs are pictures: run them through OCR PDF first. Pictures aren't included in the .md file; use Extract images to save them. For plain text without any marks, use PDF to Text.