Who it is for

Save papers that keep their publication date

A saved paper without its publication date is a citation you have to reconstruct later. Clean Clipper reads the date from the page’s own metadata rather than from the running text, and when a page carries no date the field stays empty instead of being filled with today.

Where a saved paper loses its provenance

You read a preprint in the browser, save it, and three months later the note says nothing about when it was published or which version you read. The abstract page has moved on to v3, the reference links have become dead anchors pointing back at a page you left, and the author field reads “Skip to main content” because the clipper took the first bold string it found.

Dates are the worst of it, because the failure is silent. A clipper that stamps the note with the day you saved it produces a file that looks correct and is wrong. A year later you cannot tell which of two hundred notes carry a real publication date and which carry the date you happened to be reading – nothing in the file distinguishes them.

Text and thinking end up in different places. The reference manager holds the metadata, the notes app holds your comments, and neither holds the passage you were commenting on. At write-up time you go back to fetch it, and half the links resolve to a paywall you were reading through an institutional session that has since expired. Keeping the text itself, in the same file as your notes on it, removes that round trip entirely.

What the note records

• citation_date and citation_publication_date (the meta tags arXiv, PubMed and IEEE emit) are read directly.
• Also JSON-LD datePublished, article:published_time, time[datetime] and Unix timestamps, in that order of preference.
• No date on the page means an empty field – never today’s date.
• Reference links become [^1] footnotes with their definitions collected at the end of the note.
• The author field is filtered: section headings, journal names and button labels do not become bylines.
• The extraction field records the route: dom from the rendered page, jsonld-articlebody when the page never finished rendering.
• Publication date and capture date never merge – the page’s date is a frontmatter field, the day you clipped is {date} in the filename, and the two live in different places on purpose.
• Zero leftover HTML tags across 512 measured pages, so a passage pasted into a manuscript does not arrive carrying a stray span or a fragment of a figure caption.

---
title: "Attention Is All You Need"
source: "https://arxiv.org/abs/1706.03762"
author: "Ashish Vaswani, Noam Shazeer, Niki Parmar"
date: "2017-06-12"
extraction: "dom"
---

The dominant sequence transduction models are based on complex recurrent or
convolutional neural networks.[^1]

[^1]: Submitted 12 June 2017. Comments: 15 pages, 5 figures.

Setting it up for reading papers

The default settings are tuned for reading articles quickly. A reference folder wants the opposite – every metadata field kept, and a look at the result before it is filed.

1. Open Options from the extension icon and set the destination to the folder where the project’s sources live – sources/ beside the manuscript, or a folder inside your vault.
2. Leave the icon click as the preview window rather than “save to folder”. For papers the window earns its place – it is where you see whether the date and the authors actually came through, before the file exists.
3. Set the filename template to {domain}-{title}. A preprint server, a journal and a repository copy of the same paper are three different documents with the same title, and the domain is what tells them apart in a folder listing.
4. Turn on every frontmatter field, extraction included. That last one matters here more than anywhere – jsonld-articlebody means the text came from the page’s structured data rather than from what rendered, and the two are not always the same version.
5. Leave images as links. Figures are usually the argument, and a link at least says a figure was there; skipping them silently removes the fact that the paper had one.
6. Clip the abstract page and the full-text HTML separately when both exist. They carry different metadata – the abstract page usually holds the citation_date tag, the full text holds the references.
7. After the first clip from a publisher you have not used before, look at the date field. If it is empty, that site emits no date in its markup, and no setting will produce one.

Settings for a reference folder

The theme of this table is not speed. It is making sure that in two years the file still says where it came from and how it got there.

---
title: "Reproducibility of variant calling across sequencing platforms"
source: "https://example-journal.org/articles/vc-repro"
author: "M. Ilves, R. Okonkwo"
date: ""
extraction: "jsonld-articlebody"
---

## Abstract

Concordance between platforms fell below 0.90 for indels longer than eight
bases, while substitution calls agreed across all four pipelines tested.

Three ways it is used

A preprint that changes under the citation

You read v1 of a preprint in March and clip it. In September the abstract page serves v3, with a reworked results section and two new authors. You clip it again; the second file takes a numeric suffix rather than replacing the first.

Any diff tool now shows exactly which claims moved between the version you cited and the version a reader will find at that URL. Without the March file there is no way to establish that anything changed at all. The URL looks identical and the page shows only its current state.

Full text behind an institutional session

The article renders for you because you are on the campus network or logged in through your library. The extension reads what the browser rendered, so the full text clips like any other page, with the references becoming [^1] footnote definitions collected at the end of the note.

That matters six months later, when the session has expired and the same link asks for money. The passage, its authors and its date are in a file on your disk, and no part of that file depends on the subscription still being live.

Writing up, with the sources in the same folder

The manuscript is in paper/, the clipped sources in paper/sources/. Every quotation in the draft can be checked against the file it came from without opening a browser, and the URL and date needed for the reference list are two lines at the top of that file.

Because the files are plain text, grep across the folder answers the question a reference manager cannot – not which papers you saved, but which of them actually used a particular phrase.

Against the usual reading workflow

Most people already do two or three of these. The honest comparison is not that they fail but that they each drop something different.

When the metadata does not come through

The date field came out empty

The page emits no date the extension recognises. It looks for citation_date and citation_publication_date (the tags arXiv, PubMed and IEEE use) then JSON-LD datePublished, article:published_time, time[datetime] and Unix timestamps, in that order. When none of them is present the field stays empty rather than being filled with today, because a plausible wrong date in a reference folder is discovered at exactly the wrong moment.

The author field is empty on a paper that clearly has authors

Author extraction reads structured data and byline markup, then filters the usual false positives: section headings, journal names, “authority control” blocks and button labels. Some publishers put the author list in a JavaScript-rendered widget with no byline markup at all, and nothing survives the filter. An empty field is the deliberate outcome – “Skip to main content” in an author field has been the alternative on more than one clipper.

Only the abstract came across, not the paper

You clipped the abstract landing page, which for most preprint servers and journals genuinely contains only the abstract. The full text lives at a separate URL – usually a “full text”, “HTML” or “reader” link on the same page. Clip that one as well; the two pages carry different metadata and are worth keeping as two files.

The equations are missing

Mathematics rendered as images stays an image link, and if you have set images to “skip” it disappears entirely. Where a publisher renders formulae as text the characters come across. There is no conversion to LaTeX – the extension reads what the page rendered and does not reconstruct notation from a picture of it.

Honest limits

It reads HTML, not PDF – a paper that exists only as a PDF is not something the extension converts. It does not fetch BibTeX and writes no citation key. The frontmatter is metadata, not a bibliography entry. Mathematics rendered as images stays an image link. And some sites publish no date at all in their markup; on those the field is left blank rather than guessed, which is the honest answer but still an empty field.

Questions