Why does text from a PDF break onto so many lines?

A PDF stores where each line is drawn on the page rather than storing flowing paragraphs. When you copy it, every visual line becomes a real line break, which is why pasting into a document looks wrong.

What does rejoining hyphen-split words do?

Printed text often splits a word across two lines with a hyphen, like "sen-" and "tence". This option stitches those halves back into one word instead of leaving a stray hyphen.

Will it ruin my paragraph structure?

Not with Keep paragraph breaks on, which is the default. Blank lines between paragraphs are kept and only the breaks inside each paragraph are removed.

Can I do this to many files at once?

This page handles one paste at a time. For a folder of documents, or to save the cleanup as a reusable step, use the Text Workflow Mac app.