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feat: rename to paperspec and add the website

- Rename manuspec to paperspec everywhere outside pixi.toml: prose, the
  tools, provenance tool names and the fixture key derivations, so every
  fixture and vector is rebuilt.
- Move the namespace addresses under the site, mirroring the repository:
  schema $id https://paperspec.scient.ing/schemas/<file>, the JSON-LD
  context https://paperspec.scient.ing/context/scienting-1.jsonld, and
  term IRIs https://paperspec.scient.ing/vocab#<term>. Format
  identifiers (scienting-*) and URNs (urn:scienting:) are unchanged.
- tools/site.py (standard library only) builds _site/: every file of the
  repository at its own path, each Markdown file rendered as a page with
  sidebar navigation, heading anchors matching the forge's, folder
  listings, a vocabulary page for the context's IRIs, a heading search
  and a 404 page; light and dark themes.
- check.py builds the site and checks that every Markdown file has a
  page, every internal link and fragment resolves, no Markdown is left
  unrendered, and every $id, the context address and the vocabulary IRIs
  are files of the site.
- deploy/: a Caddyfile with the media types and CORS the data needs, and
  a guide; .gitea/workflows/site.yml builds on main and publishes with
  rsync when the SITE_* secrets are set.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

2026-10-14 21:27:21 -04:00

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18. Layers and annotations

Everything people and models add to a document is an annotation, and annotations are grouped in layers. scienting-layer/1 is the W3C Web Annotation Data Model with the anchor as a selector, so any Web Annotation tool can read it. The JSON-LD context is context/scienting-1.jsonld, published at https://paperspec.scient.ing/context/scienting-1.jsonld.

18.1 One rule decides what is a claim and what is a layer

If a statement is true independently of this paper, it belongs in a claim store as a claim, where it is checked and leveled. If it is about reading this paper, it belongs in a layer, where it is attributed and signed but not checked.

18.2 The layer

A layer is a folder with layer.json and annotations.jsonl. layer.json is an AnnotationCollection with the two contexts, format, an id of the form urn:scienting:layer:<store>/<record id>, a label, a purpose, an audience (novice, student, expert or mixed), a visibility (private, team or public), a license (CC BY 4.0 by default when public), its creator, created, its project, the docs it annotates and its total. A reader turns layers on and off, and the audience dial picks the level of glosses.

18.3 The annotation

Each line of annotations.jsonl is a W3C Annotation:

Property	Holds
`@context`	`["http://www.w3.org/ns/anno.jsonld", "https://paperspec.scient.ing/context/scienting-1.jsonld"]`.
`id`	`urn:scienting:annotation:<store>/<record id>` (4.6).
`type`, `layer`	`Annotation`, and the layer's ID.
`motivation`	A W3C motivation: `commenting`, `describing`, `linking`, `questioning`, `assessing`, `replying` and the others.
`creator`, `created`, `modified`	An agent `{id, type, name}`, with `type` `Person` or `Software`, and times.
`body`	One body (18.4).
`target`	A `SpecificResource` whose `source` is `urn:scienting:doc:<store>/<key>` and whose `selector` lists an `AnchorSelector` holding a `scienting-anchor/1`, optionally followed by a W3C `TextQuoteSelector` for tools that do not know ours; or, for a reply, a `SpecificResource` whose source is another annotation.
`status`	`proposed`, `confirmed`, `rejected` or `withdrawn`. A model's annotation is `proposed` until a person confirms it.
`receipt`	For a confirmed annotation, the receipt that covers it.

The TextQuoteSelector, when present, repeats the anchor quote's exact, prefix and suffix, with an empty string for a prefix or suffix the quote lacks. It is present only when the anchor's quote is plain text; an anchor whose quote is hashed or keyed (6.3) has none, so the fallback never shows text the anchor withholds.

An annotation's content hash is SHA-256 of the canonical JSON of the annotation without status, receipt and modified. A confirmed annotation is covered by its confirmer's receipt, which lists ["annotation", <record id>, <content hash>]. Replies are annotations that target annotations, so discussions are threads anchored to sentences.

18.4 Bodies

`kind`	W3C type	Adds	Says
`gloss`	`TextualBody`	`audience`	An explanation at `novice`, `student` or `expert` level.
`claim-link`	`SpecificResource`	`source` (`lode:<tag>`), `pin`, `role`	That the span `states`, `uses` or `disputes` a claim.
`symbol`	`SpecificResource`	`source`, `pin`, `symbol`	That this occurrence of a symbol is a symbol claim.
`comment`	`TextualBody`		A remark, opinion or interpretation.
`caveat`	`TextualBody`		A warning a reader should see.
`question`	`TextualBody`	`for`	A question for a `reader`, a `group` or the `authors`.
`exercise`	`TextualBody`	`exercise`	A task with a key and a rule (19).
`citation-context`	`TextualBody`	`reference`, `verdict`, `reason`	Why a sentence cites a reference, and whether it supports it.
`prerequisite`	`SpecificResource`	`source`	What to read or know first.
`crosslink`	`SpecificResource`	`source`, `selector`	That the span corresponds to a span in another document.
`translation`	`TextualBody`	`language`	The span in another language.
`description`	`TextualBody`	`role`	A description of a figure, panel or table for readers who cannot see it: `alt`, a short text equivalent, or `long`, a full description.
`generated`	`TextualBody`	`generator`	Text a model wrote about the span; never mistaken for source.

A textual body has a value, and optionally a format (text/plain or text/markdown) and a language. Nothing a model writes is ever stored as source text. A model may propose a description, and like any annotation it stays proposed until a person confirms it; an accessible export uses confirmed descriptions only, and a figure with none has no description. Other text a model writes about a span, such as a summary, is a generated annotation, which names its generator. fixtures/records/layer/ holds a layer with one annotation of each common kind and the receipt that confirms some of them.

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