Click Research in the sidebar to open Sources, your library of everything you cite. The arrow beside the row shows its two parts, Sources and Reading Room, and the switch at the top of the Research page moves between them too.

The library belongs to the vault you have open. Header keeps the list in Header Research/Research Sources.json, writes a source note for each entry into _sources/research, and copies imported PDFs into Research Sources/Papers. All three are ordinary files in your vault folder.

A lookup sends the text you typed or the identifier you pasted to the services in the table above. Importing a PDF can also look up a DOI printed on its first pages. Your notes, PDFs and other vault content are not uploaded. The first time you search, Header shows what it will send and to which services, and waits for your OK. For a title search, one approval covers the named services until you quit Header. A DOI, ISBN or link lookup asks again unless you approved one in the last two minutes or chose Don't ask again. Each request is recorded.

To stop title searches going to a particular service, switch it off under Research discovery: Search Semantic Scholar, Search Crossref and Search arXiv. All three start switched on.

Choose Enter Source Details Manually… from the Add Source menu. Fill in Title, Authors, separated by semicolons, Year and Type (Article, Book, Conference paper, Web source or Other). DOI, URL and Citekey are optional. Click Review Source to see it as a suggestion before adding it. Only the title is required.

Choose Import PDF or Citation File… and pick PDFs, BibTeX (.bib), RIS (.ris) or CSL JSON files. You can also drop them on the Smart Add field. PDFs are copied into Research Sources/Papers in your vault, so the original stays where it was.

A citation file imported this way is read once. If you later change the file, Header doesn't notice. To keep a library in step with a file that changes, watch it instead (next section).

If you keep your references in Zotero with the Better BibTeX plugin, set Better BibTeX to keep a .bib export up to date, then choose Connect BibTeX Library… from the Add Source menu (or Import & watch a BibTeX library… from More). Pick that file and click Watch. Header refreshes Sources whenever the file changes, and a status line shows the last sync and how many entries were added or removed.

• Resync BibTeX Library (Add Source menu) re-reads the file now.
• More → Change File points Header at a different export. Stop Watching File stops following it.
• More → Remove Watched Library from Header removes the references that came from that file. The .bib file itself isn't deleted.
• More → Clear Imported References from Header empties the library. Your notes, source notes and .bib files stay on disk.

Above the source list you can narrow it to All, Cited or Uncited, filter by type (Articles, Books, Web), and search. The Needs Attention menu turns orange when something needs fixing:

• Fix Missing Metadata opens Repair Source Metadata, one source at a time. Edit the fields yourself, or look the source up again by DOI, URL or title. Fetched values are shown for review and don't replace anything until you accept them, and fields you edited by hand are kept.
• Duplicate Citekeys shows sources that clash. On a duplicate, Compare & Merge lets you pick which record survives. Header writes a review and an undo backup first, and the other citekey keeps working as an alias.
• Broken Citations is covered below.

Every source gets a citekey when it's added. If that key is already taken, Header adds a letter (smith2024, then smith2024a). To choose your own, use manual entry. Repairing metadata later doesn't change the citekey, so your existing [@citekeys] keep working.

Each source has a source note in _sources/research, named after its citekey. The note's frontmatter holds the citation details, and the body starts with headings for Notes, Quotes, Claims, Connections and Used in Notes, followed by the BibTeX. It's an ordinary note, so you can write in it, link to it and search it.

The ⋯ button on a source holds the rest: Edit metadata, Open in browser, Read (or Attach PDF… if no file is linked yet), Create source note (opens the note), Copy citation (copies [@citekey]), Ask Header about this, and Remove from library.

Select a claim in your note, or put the cursor in the sentence, and choose Cite This Claim… from the This Note + AI part of the editor's ⋯ menu. The Assistant opens with a Cite this section. Click Find sources and Header matches the claim against your library on your Mac. Each match has Insert citation and Open source.

Rank with AI is optional. It reorders the matches using Apple Intelligence on your Mac when it's available, otherwise your cloud AI after the usual send preview. If you cancel, the local order stays. The command is greyed out until your library has at least one source.

Choose Needs Attention → Broken Citations in Sources. The panel lists each missing citekey with the note and line it appears on. For each one you can create a placeholder source, copy the [@citekey], or open the note. In a single note, the References tab lists unresolved citekeys with a Resolve… button.

Choose More → Citation Styles… in Sources. The bundled styles are APA 7, Chicago Author-Date, MLA 9, IEEE, Vancouver and Nature. Click Use next to one. The style you pick drives the citations in the editor, the manuscript preview and File → Export Note…. Export References writes its own fixed set of styles.

If your journal wants something else, download its .csl file and choose Import a CSL style…. Imported styles are drawn by Header's own CSL renderer, which handles a subset of CSL, so check the output against the style guide. Styles stay on your Mac; Header doesn't fetch them from a style repository.

For the note you're writing, open the Note Inspector's References tab. It lists every source the note cites; click one to jump to the citation, or right-click for Open PDF and Reveal PDF in Finder. Unresolved citekeys appear underneath with Resolve…. At the bottom, Export cited… starts an export with a bibliography, and Research library opens Sources.

A note with its bibliography. Choose File → Export Note… (⇧⌘E). When the note cites sources and you pick a format such as PDF, Word or HTML, a References section appears. Turn on Format cited sources to replace each citation and add a bibliography, using Header's built-in renderer; nothing else needs installing. Pick the Style there too. If the note has unresolved citekeys, they stay in the export as typed unless you turn on Omit unresolved citation markers. Markdown, Plain Text and Rich Text exports are the note's own text, so they don't offer this. Export cited… in the References tab opens the same sheet with formatting already on.

Your whole library. In Sources, click Export References. Header writes Header Research References as a PDF, a Markdown file and a .bib file into a Header Exports folder in your vault, then shows the PDF in Finder.

In Context → Ask, click Read This Paper. The assistant drafts its reading of the paper's argument, methods, limitations, related work and key terms. Each point comes with a quote from the paper. Header then checks the quote against the document itself and marks it Quote located with the page (or section, for Word), or Quote not located if it can't find that exact text. Anything the paper doesn't cover is listed as “Not stated in this paper”. Treat the points as the model's interpretation and check the quotes.

• Ask this paper. Type a question, such as “What is their baseline?”, and click Ask. If no matching passage turns up, Header says so rather than giving an answer tied to the source.
• Define a term. Select a short phrase (up to six words) and click Define “…”. A definition that doesn't come from the paper is labelled General knowledge.
• Send to Note. Select a passage, or use the button on a finding, to add it to the note you have open as a quoted excerpt. When the paper matches a library source, a selected passage carries its citekey, and so do findings and answers whose quote was located. With no note open, Header copies it to the clipboard instead. Save the note afterwards.
• Add to Library. If the document has a DOI that isn't in your library yet, the assistant offers to add it.

The assistant uses Apple Intelligence on your Mac when you've chosen to prefer on-device AI and it's available. Otherwise it uses the AI provider you set up (see Setting up AI). Small local models often can't produce the structured reading guide; if that happens Header says so and suggests a more capable model.

If a PDF has no selectable text, the Ask pane says “This looks like a scanned PDF”. Click Extract Text with OCR. Recognition runs on your Mac with no network, page by page, and you can cancel it. Afterwards the assistant works from the recognised text, so its quality depends on the scan.

Click a PDF or Word file in the sidebar or note list and it opens in Header's viewer. The PDF toolbar has page controls, zoom, Show page thumbnails, the highlights panel, Find in PDF, and Read with AI, which opens the document in the Reading Room. Word documents open in a reader view that simplifies complex layout; Open in Default App in its ⋯ menu shows the original.

• Highlight. Select text, then click a colour: yellow, green, blue, pink or purple. Click Note instead to highlight and attach a note.
• Review. The highlights panel lists each one with its page. Click the pencil to add or edit a note. The ⋯ on a highlight has Copy as Quote, a colour choice, and Delete Highlight. Copy as Quote copies a Markdown quote with a link back to the page, like > "…" — [[paper.pdf#page=4]].
• Extract. Click Extract in the panel (or ⋯ → Extract Highlights to Note). Header writes every highlight, with page links and your notes, into <file name> — Annotations.md beside the document.

For files in your vault, highlights are kept in the hidden .header/annotations folder of the vault, so the PDF or Word file itself isn't modified. For a document outside your vault that you open in the Reading Room, they're kept in Header's own folder on your Mac.