PDF review markup, in both directions.

{
  "entries": [
    { "page": 1,
      "type": "highlight",
      "quote": "interpretable in practice",
      "comment": "Key claim. Interpretable to whom?
                  Cite the evaluation." },
    { "page": 2,
      "type": "replace",
      "quote": "No attempt was made to preserve the
                original ordering of the samples.",
      "replacement": "Samples were processed in
                      random order.",
      "comment": "Say what was done, not what was not." },
    { "page": 2,
      "type": "underline",
      "quote": "small but consistent",
      "comment": "Give the effect size and the
                  number of runs." }
  ]
}

$ railmark sample.pdf --apply-markup plan.json
Applied 3/3 markup entries (3 added).

$ railmark sample-marked.pdf -o notes.md

# Annotations: sample-marked.pdf

| Section      | Text markup | Notes |
|--------------|-------------|-------|
| Introduction | 1           | 0     |
| Results      | 2           | 0     |

## Introduction

> The model described here is **interpretable in
> practice**, which is the point of the exercise.
>
> **Comment:** Key claim. Interpretable to whom?
> Cite the evaluation.
>
> *(p. 1, highlight)*

## Results

> ~~No attempt was made to preserve the original
> ordering of the samples.~~ → **Samples were
> processed in random order.**
>
> **Comment:** Say what was done, not what was not.
>
> *(p. 2, suggested replacement)*

> <u>small but consistent</u>
>
> **Comment:** Give the effect size and the number
> of runs.
>
> *(p. 2, underline)*

$ railmark sample-marked.pdf --format json -o -

{
  "source": "sample-marked.pdf",
  "annotations": [
    {
      "page": 1,
      "type": "highlight",
      "id": "9dc67a3b-6d9e-47c5-bf13-4a29694ce950",
      "quote": "interpretable in practice",
      "comment": "Key claim. Interpretable to whom?
                  Cite the evaluation.",
      "color": "#FFFF00",
      "author": "AI Reviewer",
      "heading": "Introduction"
    },
    {
      "page": 2,
      "type": "replace",
      "id": "7741ff74-bf65-4f59-ab88-db7498ce69f3",
      "quote": "No attempt was made to preserve the
                original ordering of the samples.",
      "replacement": "Samples were processed in random order.",
      "color": "#0066FF",
      "author": "AI Reviewer",
      "heading": "Results"
    },
    …
  ]
}