v1.20.1

Added

• An assistant connected through the MCP server can mark a paper. add_highlight highlights, underlines or strikes out a passage on a page, with a note if wanted; update_highlight rewrites a mark's note or colour; remove_highlight takes it off. list_highlights gives every mark the id these take. Marks are written into the PDF the way the reader writes its own, and a paper open in the reader shows them. The passage is found however its spacing, line breaks and hyphens fall, a passage that appears twice on the page is refused rather than guessed at, and an encrypted PDF is left alone.
• list_highlights says when each mark was made or last changed, who made it, and what its colour means.
• Every mark says who made it. The reader signs its marks with your name, an assistant signs with its own (the client's name, or one it gives), and marks from other apps keep theirs, in the PDF's standard author field. The notes rail and the notes file name the writer of any mark that is not yours.
• A highlighter can be added from the bar beside a selection: pick a colour, say what it means, and the selection takes it. add_highlighter does the same from an assistant.
• The Notes panel has a search field that narrows the list to marks whose passage or note contains the text. The Find bar lists matching notes among the PDF's own matches, and choosing one turns to its mark.
• The first screen links to Settings > Integrations, where an assistant is connected.

Changed

• A mark whose colour is none of your highlighters, one made in another app usually, is called a Note, in purple, rather than a Highlight nobody named.
• A notes file keeps its bookkeeping out of sight. The PaperShelf version and date, the PDF's path, when each mark was made and its colour are HTML comments, so rendered Markdown shows the title, quotations, notes and meanings only, and Settings > Notes chooses which of the four a file carries. Exported notes follow the same choices.
• The README and the website lead with what PaperShelf does, and say which tools can change files.

Fixed

• Find can be put away. Its close button and Escape left the rail showing an empty search whenever the paper had a table of contents; they now give the rail back as it was before Find opened it, hidden if it was hidden. ⌘F and the magnifier close Find as well as open it.
• Clicking the badge beside a mark with a note opens the notes rail on that mark, where the note can be read, edited or removed, instead of PDFKit's popup, whose Done button could not be read.
• v1.20.0 was tagged and never built, and nothing was published under it. A test of the note badge expected PDFKit to draw one on the macOS 26 release runner, where it does not. v1.20.0's changes are in this release.

Full Changelog: v1.19.1...v1.20.1