Clean text wins
Your retrieval system searches chunks, not whole PDFs. Good chunks come from clean text with stable source names, page numbers, and section titles.
If the text is messy, embeddings and prompts will also be messy. Prepare the documents before you build the index.
What to prepare
Use 3 to 6 sample documents for your first version. Pick documents with real value: college placement rules, club handbook, hostel FAQ, startup policy, product docs, or a small research note.
Keep originals in one folder. Store extracted text in another folder. This makes your repo easy to inspect later.