papilot 0.8.5 → 0.8.7

package/engine/src/web/style.css

@@ -968,6 +968,30 @@ kbd {
 .paper-clock {
   font-variant-numeric: tabular-nums;
 }
+/* Earlier pages are on screen while the complete PDF compiles; the notice
+   sits over the page's right margin rather than its text. */
+.paper-updating {
+  position: sticky;
+  top: 8px;
+  z-index: 3;
+  display: flex;
+  align-items: center;
+  gap: 8px;
+  width: fit-content;
+  margin: 0 8px 8px auto;
+  padding: 4px 12px;
+  border: 1px solid var(--line);
+  border-radius: 999px;
+  background: var(--bar);
+  box-shadow: var(--shadow);
+  color: var(--muted);
+  font-size: 13px;
+}
+.paper-updating .pulse {
+  width: 8px;
+  height: 8px;
+  margin: 0;
+}
 .waiting p {
   margin: 6px 0;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "papilot",
-  "version": "0.8.5",
+  "version": "0.8.7",
   "description": "A Cursor-like workspace for your papers: annotate and review PDFs directly without ever touching LaTeX.",
   "keywords": [
     "latex",

package/src/server/agents.ts

@@ -24,6 +24,8 @@ export interface AgentRuntime extends EventEmitter {
   // Whether the agent is present on this host (its CLI, SDK credentials or
   // key), checked without starting it. Agents that are not found are hidden.
   detect?(): boolean;
+  /** Loads an SDK this host already has, without starting the agent. */
+  preload?(): Promise<void>;
   start(): Promise<void>;
   request(method: string, params: any, timeout?: number): Promise<any>;
   respond(id: string | number, result: unknown): void;
@@ -192,6 +194,7 @@ export class ClaudeAgent extends Adapter {
     private findCli: () => string | null = () => findExecutable(process.env.PAPILOT_CLAUDE_BIN || 'claude'),
     private launch: Launch = (command, args, options) => spawn(command, args, { ...options, stdio: ['pipe', 'pipe', 'pipe'] })) { super(); }
   detect() { return Boolean(this.findCli()) || claudeConfigured(); }
+  async preload() { if (packageFile('@anthropic-ai/claude-agent-sdk')) await this.load(); }
   // The environment Claude Code runs with; undefined keeps Papilot's own.
   protected environment(): Record<string, string> | undefined { return undefined; }
   async start() {

package/src/server/annotated-pdf.ts

@@ -0,0 +1,392 @@
+import type * as Mupdf from 'mupdf';
+import { GROUP_COLORS, canonicalGroup, type NoteGroup } from '../note-groups.ts';
+
+type Rect = [number, number, number, number];
+// A note as the export draws it. Rectangles are fractions of the page, as the
+// PDF view stores them; a note without rects marks a region.
+export interface ExportNote { page: number; rect: Rect; rects?: Rect[]; comment: string; group?: NoteGroup; review?: boolean; author?: string }
+
+type Rgb = [number, number, number];
+const rgb = (hex: string): Rgb => [1, 3, 5].map(at => parseInt(hex.slice(at, at + 2), 16) / 255) as Rgb;
+const PANEL = rgb('#f7f6f3'), DIVIDER = rgb('#e4e1da'), CARD = rgb('#ffffff'), CARD_LINE = rgb('#e2dfd8');
+const TEXT = rgb('#1c1c1c'), AUTHOR = rgb('#6b6b6b');
+// The PDF view's colours: blue for a personal note, amber for an AI finding,
+// and each colour group's own swatch, with dark ink on yellow.
+function colors(note: ExportNote) {
+  if (note.group) {
+    const group = canonicalGroup(note.group), color = rgb(GROUP_COLORS[group]);
+    return { mark: color, tag: color, ink: rgb(group === 'yellow' ? '#422f00' : '#ffffff') };
+  }
+  if (note.review) return { mark: rgb('#d97706'), tag: rgb('#92400e'), ink: rgb('#ffffff') };
+  return { mark: rgb('#2563eb'), tag: rgb('#2563eb'), ink: rgb('#ffffff') };
+}
+
+// Latin, Greek and Cyrillic set in Nimbus Sans; anything it lacks (Chinese,
+// Japanese, Korean, most symbols) falls back to MuPDF's Droid Sans Fallback.
+type Style = 'regular' | 'bold';
+const FONT_NAMES: Record<Style | 'cjk', string> = { regular: 'Helvetica', bold: 'Helvetica-Bold', cjk: 'zh-Hans' };
+const RESOURCE: Record<Style | 'cjk', string> = { regular: 'PplR', bold: 'PplB', cjk: 'PplC' };
+interface Run { font: Style | 'cjk'; gids: number[]; width: number }
+
+class Type {
+  private fonts = new Map<Style | 'cjk', Mupdf.Font>();
+  readonly used = new Map<Style | 'cjk', Set<number>>();
+  private advances = new Map<string, { font: Style | 'cjk'; gid: number; advance: number } | null>();
+  constructor(private mupdf: typeof Mupdf) {}
+  font(kind: Style | 'cjk') {
+    let font = this.fonts.get(kind);
+    if (!font) { font = new this.mupdf.Font(FONT_NAMES[kind]); this.fonts.set(kind, font); }
+    return font;
+  }
+  private glyph(char: string, style: Style) {
+    const key = style + char;
+    if (!this.advances.has(key)) {
+      const code = char.codePointAt(0)!;
+      let found: { font: Style | 'cjk'; gid: number; advance: number } | null = null;
+      for (const kind of [style, 'cjk'] as const) {
+        const font = this.font(kind), gid = font.encodeCharacter(code);
+        if (gid > 0) { found = { font: kind, gid, advance: font.advanceGlyph(gid) }; break; }
+      }
+      this.advances.set(key, found);
+    }
+    return this.advances.get(key)!;
+  }
+  // The glyph runs for a line, one per font, with widths in points.
+  runs(text: string, style: Style, size: number): Run[] {
+    const runs: Run[] = [];
+    for (const char of text) {
+      const glyph = this.glyph(char, style) || this.glyph('?', style);
+      if (!glyph) continue;
+      let run = runs[runs.length - 1];
+      if (!run || run.font !== glyph.font) { run = { font: glyph.font, gids: [], width: 0 }; runs.push(run); }
+      run.gids.push(glyph.gid); run.width += glyph.advance * size;
+    }
+    return runs;
+  }
+  width(text: string, style: Style, size: number) { return this.runs(text, style, size).reduce((sum, run) => sum + run.width, 0); }
+  // Wraps at spaces, and between any two CJK characters, keeping closing
+  // punctuation on its line. Text past maxLines ends with an ellipsis.
+  wrap(text: string, style: Style, size: number, width: number, maxLines = Infinity) {
+    const lines: string[] = [];
+    for (const paragraph of text.replace(/\r\n?/g, '\n').split('\n')) {
+      const tokens: string[] = [];
+      for (const char of paragraph) {
+        const last = tokens[tokens.length - 1];
+        if (/\s/.test(char)) { if (last !== ' ') tokens.push(' '); }
+        else if (WIDE.test(char)) tokens.push(char);
+        else if (CLOSING.test(char) && last && last !== ' ') tokens[tokens.length - 1] += char;
+        else if (last && last !== ' ' && !WIDE.test(last.slice(-1))) tokens[tokens.length - 1] += char;
+        else tokens.push(char);
+      }
+      let line = '';
+      const push = () => { lines.push(line.trimEnd()); line = ''; };
+      for (const token of tokens) {
+        if (token === ' ') { if (line) line += ' '; continue; }
+        if (this.width(line + token, style, size) <= width) { line += token; continue; }
+        if (line.trim()) push();
+        // A word wider than the card breaks between letters.
+        for (const char of token) {
+          if (line && this.width(line + char, style, size) > width) push();
+          line += char;
+        }
+      }
+      if (line.trim() || !lines.length || paragraph.trim()) push();
+    }
+    while (lines.length > 1 && !lines[lines.length - 1]) lines.pop();
+    if (lines.length <= maxLines) return lines;
+    const kept = lines.slice(0, maxLines);
+    let last = kept[maxLines - 1].trimEnd();
+    while (last && this.width(last + '…', style, size) > width) last = [...last].slice(0, -1).join('').trimEnd();
+    kept[maxLines - 1] = last + '…';
+    return kept;
+  }
+  record(runs: Run[]) {
+    for (const run of runs) {
+      let set = this.used.get(run.font);
+      if (!set) { set = new Set(); this.used.set(run.font, set); }
+      for (const gid of run.gids) set.add(gid);
+    }
+  }
+}
+const WIDE = /[ᄀ-ᇿ⺀-⿿　-ヿ㄀-ㇿ㈀-鿿가-힯豈-﫿︰-﹏＀-￯]/u;
+const CLOSING = /[，。、！？；：）」』】〉》”’,.!?;:)\]}%]/u;
+
+// Content stream drawing in MuPDF's page space: points, origin at the page's
+// top-left corner, y growing downward.
+class Canvas {
+  private ops: string[] = [];
+  private state = '';
+  constructor(private type: Type) {}
+  private n = (value: number) => (Math.round(value * 1000) / 1000).toString();
+  private fill(color: Rgb) { this.ops.push(`${color.map(this.n).join(' ')} rg`); }
+  private stroke(color: Rgb) { this.ops.push(`${color.map(this.n).join(' ')} RG`); }
+  gs(name: string) { if (this.state !== name) { this.ops.push(`/${name} gs`); this.state = name; } }
+  rect(x: number, y: number, w: number, h: number, color: Rgb) { this.fill(color); this.ops.push(`${this.n(x)} ${this.n(y)} ${this.n(w)} ${this.n(h)} re f`); }
+  private rounded(x: number, y: number, w: number, h: number, r: number) {
+    r = Math.min(r, w / 2, h / 2);
+    const k = r * 0.4477, n = this.n;
+    this.ops.push(`${n(x + r)} ${n(y)} m ${n(x + w - r)} ${n(y)} l ${n(x + w - k)} ${n(y)} ${n(x + w)} ${n(y + k)} ${n(x + w)} ${n(y + r)} c`
+      + ` ${n(x + w)} ${n(y + h - r)} l ${n(x + w)} ${n(y + h - k)} ${n(x + w - k)} ${n(y + h)} ${n(x + w - r)} ${n(y + h)} c`
+      + ` ${n(x + r)} ${n(y + h)} l ${n(x + k)} ${n(y + h)} ${n(x)} ${n(y + h - k)} ${n(x)} ${n(y + h - r)} c`
+      + ` ${n(x)} ${n(y + r)} l ${n(x)} ${n(y + k)} ${n(x + k)} ${n(y)} ${n(x + r)} ${n(y)} c h`);
+  }
+  roundRect(x: number, y: number, w: number, h: number, r: number, fill: Rgb | null, line?: { color: Rgb; width: number }) {
+    this.rounded(x, y, w, h, r);
+    if (fill) this.fill(fill);
+    if (line) { this.stroke(line.color); this.ops.push(`${this.n(line.width)} w`); }
+    this.ops.push(fill && line ? 'B' : fill ? 'f' : 'S');
+  }
+  line(points: [number, number][], color: Rgb, width: number, curve = false) {
+    this.stroke(color); this.ops.push(`${this.n(width)} w 1 J`);
+    const [[x0, y0], ...rest] = points;
+    let path = `${this.n(x0)} ${this.n(y0)} m`;
+    if (curve && rest.length === 3) path += ` ${rest.flat().map(this.n).join(' ')} c`;
+    else for (const [x, y] of rest) path += ` ${this.n(x)} ${this.n(y)} l`;
+    this.ops.push(path + ' S');
+  }
+  text(text: string, x: number, baseline: number, style: Style, size: number, color: Rgb) {
+    const runs = this.type.runs(text, style, size);
+    this.type.record(runs);
+    this.fill(color);
+    this.ops.push(`BT 1 0 0 -1 ${this.n(x)} ${this.n(baseline)} Tm`);
+    for (const run of runs) this.ops.push(`/${RESOURCE[run.font]} ${this.n(size)} Tf <${run.gids.map(gid => gid.toString(16).padStart(4, '0')).join('')}> Tj`);
+    this.ops.push('ET');
+  }
+  // A number in a pill, centred on (x, y).
+  badge(label: string, x: number, y: number, size: number, fill: Rgb, ink: Rgb) {
+    const font = size * 0.6, width = Math.max(size, this.type.width(label, 'bold', font) + size * 0.62);
+    this.roundRect(x - width / 2, y - size / 2, width, size, size / 2, fill);
+    this.text(label, x - this.type.width(label, 'bold', font) / 2, y + font * 0.355, 'bold', font, ink);
+    return width;
+  }
+  toString() { return this.ops.join('\n'); }
+}
+
+interface Card { note: ExportNote; number: number; anchor: number; colors: ReturnType<typeof colors>; comment: string[]; author: string; top: number; height: number; cut: boolean }
+
+// Card typography, in points. The badge sits on the card's first row, the
+// author's name when there is one.
+const PAD = 7, COMMENT = 8.6, LEADING = 11.6, AUTHOR_SIZE = 7.4, GAP = 6, BADGE = 12, MAX_LINES = 24;
+const cardHeight = (lines: number, author: boolean) => PAD * 2 + ((author ? 1 : 0) + lines) * LEADING;
+
+// Cards sit beside their marks, pushed apart where they would overlap and
+// shortened, longest first, when a page has more comments than its margin can
+// hold. Shortened comments are printed in full at the end of the document.
+function layout(cards: Card[], top: number, bottom: number, type: Type, textWidth: number) {
+  const fits = () => cards.reduce((sum, card) => sum + card.height, 0) + GAP * Math.max(0, cards.length - 1) <= bottom - top;
+  while (!fits()) {
+    const longest = cards.reduce((a, b) => b.comment.length > a.comment.length ? b : a);
+    if (longest.comment.length <= 1) break;
+    longest.comment = type.wrap(longest.note.comment.trim(), 'regular', COMMENT, textWidth, longest.comment.length - 1);
+    longest.height = cardHeight(longest.comment.length, Boolean(longest.author));
+    longest.cut = true;
+  }
+  let next = top;
+  for (const card of cards) { card.top = Math.max(card.anchor - PAD - LEADING / 2, next); next = card.top + card.height + GAP; }
+  let limit = bottom;
+  for (const card of [...cards].reverse()) { card.top = Math.max(top, Math.min(card.top, limit - card.height)); limit = card.top - GAP; }
+}
+
+type Matrix = [number, number, number, number, number, number];
+const apply = (m: Matrix | number[], x: number, y: number) => [x * m[0] + y * m[2] + m[4], x * m[1] + y * m[3] + m[5]];
+const bounds = (m: Matrix | number[], [x0, y0, x1, y1]: number[]) => {
+  const points = [apply(m, x0, y0), apply(m, x1, y0), apply(m, x0, y1), apply(m, x1, y1)];
+  return [Math.min(...points.map(p => p[0])), Math.min(...points.map(p => p[1])), Math.max(...points.map(p => p[0])), Math.max(...points.map(p => p[1]))] as Rect;
+};
+const multiply = (a: number[], b: number[]): Matrix => [a[0] * b[0] + a[1] * b[2], a[0] * b[1] + a[1] * b[3], a[2] * b[0] + a[3] * b[2], a[2] * b[1] + a[3] * b[3], a[4] * b[0] + a[5] * b[2] + b[4], a[4] * b[1] + a[5] * b[3] + b[5]];
+
+// Returns a copy of the PDF with every note drawn on its page: marks over the
+// text, and the comment in a numbered card in a panel added to the right of
+// the page, joined to its mark's height. Links, bookmarks and text stay as
+// they were; notes without a comment are drawn as marks only. The marks show
+// what each comment is about, so cards do not repeat the quote.
+export function annotatePdf(mupdf: typeof Mupdf, input: Uint8Array, notes: ExportNote[]) {
+  const pdf = new mupdf.PDFDocument(input), type = new Type(mupdf);
+  try {
+    const count = pdf.countPages();
+    const placed = notes.filter(note => Number.isInteger(note.page) && note.page >= 0 && note.page < count);
+    if (!placed.length) return input;
+    const first = (note: ExportNote) => (note.rects?.length ? note.rects : [note.rect])[0];
+    const middle = (note: ExportNote) => (first(note)[1] + first(note)[3]) / 2;
+    // Numbers follow reading order: page, then line, then left to right.
+    const commented = placed.filter(note => note.comment.trim()).sort((a, b) => a.page - b.page || (Math.abs(middle(a) - middle(b)) > 0.006 ? middle(a) - middle(b) : first(a)[0] - first(b)[0]));
+    const numbers = new Map(commented.map((note, index) => [note, index + 1]));
+    const pages = new Map<number, ExportNote[]>();
+    for (const note of placed) pages.set(note.page, [...(pages.get(note.page) || []), note]);
+    // Every page gets the same panel so the pages stay one width in a viewer.
+    const firstPage = pdf.loadPage(0), [fx0, fy0, fx1, fy1] = firstPage.getBounds();
+    firstPage.destroy();
+    const panel = Math.round(Math.min(300, Math.max(210, (fx1 - fx0) * 0.4)));
+    const states = { mark: 'PplMark', box: 'PplBox', link: 'PplLink', solid: 'PplSolid' };
+
+    // Draw every page's marks and cards.
+    const drawn: { index: number; canvas: Canvas; toPdf: Matrix; box: Rect; cut: { card: Card; rect: Rect }[] }[] = [];
+    for (let index = 0; index < count; index++) {
+      const page = pdf.loadPage(index), [x0, y0, x1, y1] = page.getBounds(), w = x1 - x0, h = y1 - y0;
+      const ctm = mupdf.Matrix.invert(page.getTransform());
+      page.destroy();
+      const canvas = new Canvas(type);
+      canvas.gs(states.solid);
+      canvas.rect(w, 0, panel, h, PANEL);
+      canvas.rect(w, 0, 0.6, h, DIVIDER);
+      const list = pages.get(index) || [];
+      // Marks first, under every tag and line.
+      for (const note of list) {
+        const color = colors(note).mark;
+        if (note.rects?.length) {
+          canvas.gs(states.mark);
+          for (const [a, b, c, d] of note.rects) canvas.rect(a * w, b * h - 0.4, (c - a) * w, (d - b) * h + 0.8, color);
+        } else {
+          const [a, b, c, d] = note.rect;
+          canvas.gs(states.box); canvas.roundRect(a * w, b * h, (c - a) * w, (d - b) * h, 2.5, color);
+          canvas.gs(states.solid); canvas.roundRect(a * w, b * h, (c - a) * w, (d - b) * h, 2.5, null, { color, width: 1.1 });
+        }
+      }
+      const cardX = w + 20, cardWidth = panel - 32, textX = cardX + PAD + BADGE + 5, textWidth = cardX + cardWidth - PAD - textX;
+      const cards: Card[] = list.filter(note => numbers.has(note)).sort((a, b) => numbers.get(a)! - numbers.get(b)!).map(note => {
+        // A text mark's card meets its first line; a region's meets its top edge.
+        const [, top, , bottom] = first(note), anchor = note.rects?.length ? (top + bottom) / 2 * h : Math.min((top + bottom) / 2 * h, top * h + 9);
+        const all = type.wrap(note.comment.trim(), 'regular', COMMENT, textWidth), comment = all.length > MAX_LINES ? type.wrap(note.comment.trim(), 'regular', COMMENT, textWidth, MAX_LINES) : all;
+        const author = note.author?.trim() || '';
+        return { note, number: numbers.get(note)!, anchor, colors: colors(note), author, comment, top: 0, height: cardHeight(comment.length, Boolean(author)), cut: all.length > MAX_LINES };
+      });
+      layout(cards, 16, h - 16, type, textWidth);
+      // A dot on the margin's edge at the mark's height, joined to its card;
+      // the number appears once, on the card.
+      for (const card of cards) {
+        const badgeY = card.top + PAD + LEADING / 2, to = cardX;
+        canvas.gs(states.link);
+        canvas.line([[w, card.anchor], [w + (to - w) * 0.55, card.anchor], [to - (to - w) * 0.45, badgeY], [to, badgeY]], card.colors.tag, 0.7, true);
+        canvas.gs(states.solid);
+        canvas.roundRect(w - 2.2, card.anchor - 2.2, 4.4, 4.4, 2.2, card.colors.tag);
+      }
+      for (const card of cards) {
+        canvas.roundRect(cardX, card.top, cardWidth, card.height, 5, CARD, { color: CARD_LINE, width: 0.6 });
+        let y = card.top + PAD;
+        canvas.badge(String(card.number), cardX + PAD + BADGE / 2, y + LEADING / 2, BADGE, card.colors.tag, card.colors.ink);
+        if (card.author) { canvas.text(card.author, textX, y + LEADING / 2 + AUTHOR_SIZE * 0.355, 'bold', AUTHOR_SIZE, AUTHOR); y += LEADING; }
+        for (const line of card.comment) { canvas.text(line, textX, y + LEADING / 2 + COMMENT * 0.355, 'regular', COMMENT, TEXT); y += LEADING; }
+      }
+      // Drawing happens from the page's top-left corner; toPdf takes it to PDF
+      // space, whatever the page's rotation and origin.
+      const toPdf = multiply([1, 0, 0, 1, x0, y0], ctm);
+      drawn.push({ index, canvas, toPdf, box: bounds(toPdf, [0, 0, w + panel, h]), cut: cards.filter(card => card.cut).map(card => ({ card, rect: [cardX, card.top, cardX + cardWidth, card.top + card.height] as Rect })) });
+    }
+
+    // Comments shortened in the margin, in full, on pages after the paper.
+    const cut = drawn.flatMap(page => page.cut.map(entry => ({ ...entry, page: page.index })));
+    const extra: { canvas: Canvas; links: { rect: Rect; page: number; y: number }[] }[] = [];
+    const targets = new Map<Card, { page: number; y: number }>();
+    if (cut.length) {
+      const pageWidth = fx1 - fx0 + panel, pageHeight = fy1 - fy0, width = Math.min(440, pageWidth - 96), left = (pageWidth - width) / 2;
+      const textX = left + PAD + BADGE + 5;
+      let sheet: (typeof extra)[number] | undefined, y = 0;
+      const open = () => { sheet = { canvas: new Canvas(type), links: [] }; sheet.canvas.gs(states.solid); sheet.canvas.rect(0, 0, pageWidth, pageHeight, PANEL); extra.push(sheet); y = 56; };
+      for (const { card, page } of cut) {
+        // Where the note is, at the end of the first row: a page glyph and the
+        // page's number. The whole row links back to the mark.
+        const label = String(page + 1), chip = 9 + type.width(label, 'bold', AUTHOR_SIZE), textWidth = left + width - PAD - chip - 10 - textX;
+        let lines = type.wrap(card.note.comment.trim(), 'regular', COMMENT, textWidth), head = true;
+        while (lines.length) {
+          const author = head && Boolean(card.author);
+          if (!sheet || y + cardHeight(Math.min(lines.length, 3), author) > pageHeight - 56) open();
+          const room = Math.floor((pageHeight - 56 - y - PAD * 2) / LEADING) - (author ? 1 : 0);
+          const part = lines.slice(0, Math.max(1, room)), height = cardHeight(part.length, author);
+          const canvas = sheet!.canvas;
+          canvas.roundRect(left, y, width, height, 5, CARD, { color: CARD_LINE, width: 0.6 });
+          let row = y + PAD;
+          if (head) {
+            targets.set(card, { page: count + extra.length - 1, y });
+            canvas.badge(String(card.number), left + PAD + BADGE / 2, row + LEADING / 2, BADGE, card.colors.tag, card.colors.ink);
+            const end = left + width - PAD;
+            canvas.roundRect(end - chip, row + LEADING / 2 - 4, 6, 8, 1, null, { color: AUTHOR, width: 0.7 });
+            canvas.text(label, end - chip + 9, row + LEADING / 2 + AUTHOR_SIZE * 0.355, 'bold', AUTHOR_SIZE, AUTHOR);
+            sheet!.links.push({ rect: [left, y, left + width, y + height], page, y: card.anchor });
+            if (card.author) { canvas.text(card.author, textX, row + LEADING / 2 + AUTHOR_SIZE * 0.355, 'bold', AUTHOR_SIZE, AUTHOR); row += LEADING; }
+          }
+          for (const line of part) { canvas.text(line, textX, row + LEADING / 2 + COMMENT * 0.355, 'regular', COMMENT, TEXT); row += LEADING; }
+          y += height + GAP; lines = lines.slice(part.length); head = false;
+        }
+      }
+    }
+
+    // Our fonts, cut down to the glyphs we used in a scratch document so the
+    // paper's own fonts are never rewritten.
+    const scratch = new mupdf.PDFDocument(), fonts = new Map<Style | 'cjk', Mupdf.PDFObject>();
+    try {
+      const resources = scratch.newDictionary(), fontDict = scratch.newDictionary();
+      resources.put('Font', fontDict);
+      let content = 'BT\n';
+      for (const [kind, gids] of type.used) {
+        fontDict.put(RESOURCE[kind], scratch.addFont(type.font(kind)));
+        content += `/${RESOURCE[kind]} 10 Tf <${[...gids].map(gid => gid.toString(16).padStart(4, '0')).join('')}> Tj\n`;
+      }
+      scratch.insertPage(-1, scratch.addPage([0, 0, 100, 100], 0, resources, content + 'ET\n'));
+      scratch.subsetFonts();
+      for (const kind of type.used.keys()) fonts.set(kind, pdf.graftObject(fontDict.get(RESOURCE[kind])));
+    } finally { scratch.destroy(); }
+    const graphics = new Map<string, Mupdf.PDFObject>();
+    const state = (name: string, entries: Record<string, number | string>) => {
+      const dict = pdf.newDictionary(); dict.put('Type', pdf.newName('ExtGState'));
+      for (const [key, value] of Object.entries(entries)) dict.put(key, typeof value === 'string' ? pdf.newName(value) : value);
+      graphics.set(name, pdf.addObject(dict));
+    };
+    state(states.mark, { ca: 0.3, BM: 'Multiply' });
+    state(states.box, { ca: 0.1, BM: 'Multiply' });
+    state(states.link, { CA: 0.65, ca: 1 });
+    state(states.solid, { CA: 1, ca: 1, BM: 'Normal' });
+    const addResources = (resources: Mupdf.PDFObject) => {
+      const entry = (key: string) => {
+        let dict = resources.get(key);
+        if (!dict.isDictionary()) { dict = pdf.newDictionary(); resources.put(key, dict); }
+        return dict;
+      };
+      const fontDict = entry('Font'), stateDict = entry('ExtGState');
+      for (const [kind, ref] of fonts) fontDict.put(RESOURCE[kind], ref);
+      for (const [name, ref] of graphics) stateDict.put(name, ref);
+    };
+    const matrix = (m: number[]) => m.map(n => Math.round(n * 10000) / 10000).join(' ');
+
+    for (const { index, canvas, toPdf, box } of drawn) {
+      const page = pdf.loadPage(index), object = page.getObject();
+      // Grow the page to the right, in whichever PDF direction that is after rotation.
+      const array = () => { const value = pdf.newArray(); for (const n of box) value.push(n); return value; };
+      object.put('MediaBox', array());
+      object.put('CropBox', array());
+      for (const key of ['TrimBox', 'BleedBox', 'ArtBox']) object.delete(key);
+      let resources = object.getInheritable('Resources');
+      if (resources.isNull()) { resources = pdf.newDictionary(); object.put('Resources', resources); }
+      addResources(resources);
+      // Isolate the original page in q … Q, whatever state it leaves behind.
+      const contents = pdf.newArray(), old = object.get('Contents');
+      contents.push(pdf.addStream('q\n', pdf.newDictionary()));
+      if (old.isArray()) old.forEach(item => contents.push(item)); else if (!old.isNull()) contents.push(old);
+      contents.push(pdf.addStream(`Q\nq ${matrix(toPdf)} cm\n${canvas}\nQ\n`, pdf.newDictionary()));
+      object.put('Contents', contents);
+      page.destroy();
+    }
+    for (const sheet of extra) {
+      const resources = pdf.newDictionary();
+      addResources(resources);
+      const height = fy1 - fy0;
+      pdf.insertPage(-1, pdf.addPage([0, 0, fx1 - fx0 + panel, height], 0, resources, `q 1 0 0 -1 0 ${height} cm\n${sheet.canvas}\nQ\n`));
+    }
+    // Links between a shortened card and its full text, both ways. A link's
+    // area and destination are in the page's own space, after any rotation.
+    const drawing = (index: number) => index < count ? drawn[index].toPdf : [1, 0, 0, -1, 0, fy1 - fy0];
+    const link = (from: number, rect: Rect, to: number, y: number) => {
+      const source = pdf.loadPage(from), destination = pdf.loadPage(to);
+      try {
+        const area = bounds(source.getTransform(), bounds(drawing(from), rect));
+        const [, top] = apply(destination.getTransform(), ...apply(drawing(to), 0, Math.max(0, y - 24)) as [number, number]);
+        source.createLink(area, pdf.formatLinkURI({ type: 'XYZ', page: to, x: NaN, y: top, width: 0, height: 0, zoom: NaN, chapter: 0 }));
+      } finally { source.destroy(); destination.destroy(); }
+    };
+    for (const { card, page, rect } of cut) {
+      const full = targets.get(card);
+      if (full) link(page, rect, full.page, full.y);
+    }
+    extra.forEach((sheet, offset) => { for (const entry of sheet.links) link(count + offset, entry.rect, entry.page, entry.y); });
+    return pdf.saveToBuffer('compress,garbage=compact,objstms').asUint8Array();
+  } finally { pdf.destroy(); }
+}

package/src/server/annotation-placement.ts

@@ -48,15 +48,29 @@ export class AnnotationPages {
   }
 }
 
-export function placeAnnotation(note: Annotation, previous: AnnotationPages, current: AnnotationPages): AnnotationPlacement | null {
+// Reading a page's text or pixels takes milliseconds, and a search may read
+// every page of a long PDF, so the server answers other requests between pages.
+const breather = () => new Promise<void>(resolve => setImmediate(resolve));
+
+export async function placeAnnotation(note: Annotation, previous: AnnotationPages, current: AnnotationPages): Promise<AnnotationPlacement | null> {
   if (note.page < 0 || note.page >= previous.document.length) return null;
   const samePage = (page: number) => previous.hash(note.page) === current.hash(page);
-  if (note.page < current.document.length && samePage(note.page)) return { page: note.page, rect: note.rect, rects: note.rects };
+  if (note.page < current.document.length) {
+    // Each fingerprint renders a page, so they take turns with other requests.
+    previous.hash(note.page);
+    await breather();
+    if (samePage(note.page)) return { page: note.page, rect: note.rect, rects: note.rects };
+    await breather();
+  }
 
   // A box may contain a figure rather than text. Only move it automatically
   // when the entire original page still exists, exactly once, in the new PDF.
   if (!note.rects?.length) {
-    const pages = Array.from({ length: current.document.length }, (_, index) => index).filter(samePage);
+    const pages: number[] = [];
+    for (let index = 0; index < current.document.length; index++) {
+      if (index % 2 === 1) await breather();
+      if (samePage(index)) pages.push(index);
+    }
     return pages.length === 1 ? { page: pages[0], rect: note.rect, rects: note.rects } : null;
   }
 
@@ -71,6 +85,7 @@ export function placeAnnotation(note: Annotation, previous: AnnotationPages, cur
   const before = old.text.slice(Math.max(0, start - 32), start), after = old.text.slice(end, end + 32);
   const matches: { page: number; start: number }[] = [];
   for (let page = 0; page < current.document.length; page++) {
+    if (page % 2 === 1) await breather();
     const text = current.text(page).text;
     for (let from = 0; from <= text.length - needle.length;) {
       const found = text.indexOf(needle, from);

package/src/server/app.ts

@@ -8,8 +8,8 @@ import { randomUUID } from 'node:crypto';
 import { registerFrontend } from './frontend.ts';
 import type { Store } from './store.ts';
 import type { Workspace } from './workspace.ts';
-import { reviewClient, allowedReviewRoute, rewriteReviewHtml, rewriteReviewJson, confirmedReviewResponse, annotateReviewState } from './review.ts';
-import { fullPaperPdf } from './pdf.ts';
+import { reviewClient, allowedReviewRoute, rewriteReviewHtml, rewriteReviewJson, confirmedReviewResponse, annotateReviewState, taskRoute } from './review.ts';
+import { fullPaperPdf, nextPaperPass, paperPassPdf, preparePaper } from './pdf.ts';
 import { type ChangeAction, Changes } from './changes.ts';
 import { bibliography, confirmEntry } from './references.ts';
 import { type Manuscripts, annotationTask, gitAbortMerge, gitCommit, gitDiff, gitDiscard, gitFinishMerge, gitIgnore, gitRemote, gitStage, gitStatus } from './manuscript.ts';
@@ -31,6 +31,8 @@ import { registerAiReviewRoutes } from './ai-review-routes.ts';
 import { detectLatex } from './latex-installation.ts';
 
 const importsByWorkspace = new WeakMap<Workspace, PaperImports>();
+// Each workspace compiles predicted manuscripts once, however many listeners serve it.
+const predicting = new WeakSet<Workspace>();
 
 // Git writes to one repository run one at a time; each returns the new status.
 // Both listeners share one queue, so the owner and a collaborator take turns.
@@ -81,6 +83,39 @@ export async function buildApp(options: AppOptions) {
     if (id) projectRequests.set(request, workspace.enterProjectRequest(id));
   });
   app.addHook('onSend', async (request, _reply, payload) => { projectRequests.get(request)?.(); return payload; });
+  // Whatever may have written a paper's files compiles its manuscript right
+  // away: committing or applying a task, a Git action, a review decision. The
+  // PDF is on its way before anyone opens it, and a tree that did not change
+  // costs one snapshot.
+  const WRITES = /^\/api\/projects\/:id\/git\/|^\/api\/tasks\/:id\/(?:commit|apply|reconcile)$|^\/review\/:projectId\/(?:api\/changes\/(?:decide|undo)|\*)$/;
+  app.addHook('onResponse', async (request, reply) => {
+    if (request.method !== 'POST' || reply.statusCode >= 400 || !WRITES.test(request.routeOptions.url || '')) return;
+    const params = (request.params || {}) as Record<string, string>;
+    try {
+      const project = store.project(params.projectId ?? (request.routeOptions.url!.startsWith('/api/tasks/') ? store.task(params.id).projectId : params.id));
+      void manuscripts.refresh(project.id, project.path).catch(() => undefined);
+    } catch { /* The paper or task is gone. */ }
+  });
+  // A deferred task is applied as a whole once it is reviewed, so after each
+  // new round and each decision the manuscript it will produce compiles in
+  // the background.
+  const predict = async (taskId: string) => {
+    const task = store.task(taskId), project = store.project(task.projectId);
+    if (!task.deferred || task.mode === 'review' || task.delivery?.pending || task.status === 'deleting') return;
+    const client = await connectReview(project.path);
+    const preview = await client.get<{ files: Record<string, string | null> | null }>(`${taskRoute(task.name)}/preview`);
+    if (preview.files) await manuscripts.predict(project.id, project.path, Object.fromEntries(Object.entries(preview.files).map(([file, data]) => [file, data === null ? null : Buffer.from(data, 'base64')])));
+  };
+  if (!predicting.has(workspace)) {
+    predicting.add(workspace);
+    workspace.on('reviewed', (taskId: string) => void predict(taskId).catch(() => undefined));
+    // While a round compiles its changed chapters, the whole new version
+    // compiles too, for the review's full paper and often for the commit.
+    workspace.on('publishing', (taskId: string, revision: string) => {
+      try { preparePaper(store.project(store.task(taskId).projectId).path, revision, 'background'); }
+      catch { /* The task is gone. */ }
+    });
+  }
   app.addHook('onError', async request => { projectRequests.get(request)?.(); });
   await app.register(compress);
   app.setErrorHandler((error, _request, reply) => { reply.code((error as any).statusCode || 400).send({ error: (error as Error).message }); });
@@ -159,11 +194,16 @@ export async function buildApp(options: AppOptions) {
       if (viewer.listener !== 'account' || (event.userId !== viewer.user.id && event.sessionId !== viewer.session.id)) return;
       if (!accounts.session(cookie(request.headers.cookie, SESSION_COOKIE))) { reply.raw.write('event: change\ndata: {}\n\n'); reply.raw.end(); } else change();
     };
+    // A manuscript build started or finished: the open PDF view reloads now
+    // instead of at its next poll. The event names no paper.
+    let paperTimer: NodeJS.Timeout | undefined;
+    const paper = () => { paperTimer ??= setTimeout(() => { paperTimer = undefined; reply.raw.write('event: manuscript\ndata: {}\n\n'); }, 100); };
     workspace.on('change', change);
+    manuscripts.on('change', paper);
     accounts.on('revoked', revoked);
     const heartbeat = setInterval(() => reply.raw.write(': heartbeat\n\n'), 15000);
     reply.raw.on('close', () => {
-      clearInterval(heartbeat); if (timer) clearTimeout(timer); workspace.off('change', change); accounts.off('revoked', revoked);
+      clearInterval(heartbeat); if (timer) clearTimeout(timer); if (paperTimer) clearTimeout(paperTimer); workspace.off('change', change); manuscripts.off('change', paper); accounts.off('revoked', revoked);
       if (session) { const open = (streams.get(session) || 1) - 1; if (open) streams.set(session, open); else streams.delete(session); }
     });
   });
@@ -223,7 +263,7 @@ export async function buildApp(options: AppOptions) {
     const round = request.query.round === undefined ? task.review?.round : Number(request.query.round);
     const side = request.query.version || 'after';
     if (!round || !Number.isSafeInteger(round) || round < 1 || (side !== 'before' && side !== 'after')) return reply.code(400).send({ error: 'Select an existing review round and either the before or after PDF.' });
-    const pdf = await fullPaperPdf(project.path, task.name, round, side);
+    const pdf = await fullPaperPdf(connectReview, project.path, task.name, round, side);
     const filename = `papilot-${task.name}-r${round}-${side}.pdf`;
     return reply.type('application/pdf').header('Content-Disposition', `${request.query.download === '1' ? 'attachment' : 'inline'}; filename="${filename}"`).sendFile(path.basename(pdf), path.dirname(pdf), { cacheControl: false });
   });
@@ -407,11 +447,19 @@ export async function buildApp(options: AppOptions) {
     const words = await manuscripts.words(project.id, String(request.query.key || ''), Number(request.query.page));
     return reply.header('Cache-Control', 'private, max-age=31536000, immutable').send(words);
   });
+  const pdfName = (name: string, suffix = '') => (name.replace(/[^\w.-]+/g, '-').replace(/^-+|-+$/g, '') || 'manuscript') + suffix + '.pdf';
   app.get<{ Params: { id: string }; Querystring: { key?: string; download?: string } }>('/api/projects/:id/manuscript.pdf', project(), (request, reply) => {
     const project = store.project(request.params.id), pdf = manuscripts.pdf(project.id, String(request.query.key || ''));
-    const name = (project.name.replace(/[^\w.-]+/g, '-').replace(/^-+|-+$/g, '') || 'manuscript') + '.pdf';
     // Each key names one immutable build, so the viewer can cache and range-read it.
-    return reply.type('application/pdf').header('Content-Disposition', `${request.query.download === '1' ? 'attachment' : 'inline'}; filename="${name}"`).header('Cache-Control', 'private, max-age=31536000, immutable').sendFile(path.basename(pdf), path.dirname(pdf), { cacheControl: false });
+    return reply.type('application/pdf').header('Content-Disposition', `${request.query.download === '1' ? 'attachment' : 'inline'}; filename="${pdfName(project.name)}"`).header('Cache-Control', 'private, max-age=31536000, immutable').sendFile(path.basename(pdf), path.dirname(pdf), { cacheControl: false });
+  });
+  // The same build with the notes on it, as they are now.
+  app.get<{ Params: { id: string }; Querystring: { key?: string } }>('/api/projects/:id/manuscript/annotated.pdf', project(), async (request, reply) => {
+    const project = store.project(request.params.id), key = String(request.query.key || '');
+    const notes = store.annotations(project.id).filter(note => !note.taskId && !isTaskReviewNote(note) && note.key === key)
+      .map(note => ({ page: note.page, rect: note.rect, rects: note.rects, comment: note.comment, group: note.group, review: Boolean(note.aiReview), author: note.author?.name }));
+    const pdf = await manuscripts.annotatedPdf(project.id, key, notes);
+    return reply.type('application/pdf').header('Content-Disposition', `attachment; filename="${pdfName(project.name, '-annotated')}"`).header('Cache-Control', 'no-store').send(Buffer.from(pdf.buffer, pdf.byteOffset, pdf.byteLength));
   });
   app.post<{ Params: { id: string } }>('/api/requests/:id', { config: { access: { request: 'id' } } }, request => { workspace.answer(request.params.id, request.body as any); return { ok: true }; });
 
@@ -503,12 +551,20 @@ export async function buildApp(options: AppOptions) {
 
   // The complete PDF of a round's new version, for the review's full paper.
   // A round may compile only the changed chapters; this compiles them all once.
-  app.get<{ Params: { projectId: string; name: string; round: string } }>('/review/:projectId/pdf/:name/:round', { config: { access: { project: 'projectId' } } }, async (request, reply) => {
+  // While it compiles, `passes` names each earlier version that `?pass=`
+  // serves: the chapters the round compiled, then each TeX pass of the whole.
+  app.get<{ Params: { projectId: string; name: string; round: string }; Querystring: { pass?: string } }>('/review/:projectId/pdf/:name/:round', { config: { access: { project: 'projectId' } } }, async (request, reply) => {
     const project = store.project(request.params.projectId), name = request.params.name, round = Number(request.params.round);
-    if (!/^[a-z0-9-]+$/.test(name) || !Number.isSafeInteger(round) || round < 1) return reply.code(404).send({ error: 'Review resource not found.' });
-    const pdf = await fullPaperPdf(project.path, name, round, 'after');
+    const pass = request.query.pass === undefined ? null : Number(request.query.pass);
+    if (!/^[a-z0-9-]+$/.test(name) || !Number.isSafeInteger(round) || round < 1 || (pass !== null && (!Number.isSafeInteger(pass) || pass < 1))) return reply.code(404).send({ error: 'Review resource not found.' });
+    const pdf = pass === null ? await fullPaperPdf(connectReview, project.path, name, round, 'after') : await paperPassPdf(connectReview, project.path, name, round, pass);
     return reply.type('application/pdf').sendFile(path.basename(pdf), path.dirname(pdf), { cacheControl: false });
   });
+  app.get<{ Params: { projectId: string; name: string; round: string }; Querystring: { after?: string } }>('/review/:projectId/pdf/:name/:round/passes', { config: { access: { project: 'projectId' } } }, async (request, reply) => {
+    const project = store.project(request.params.projectId), name = request.params.name, round = Number(request.params.round), after = Number(request.query.after ?? 0);
+    if (!/^[a-z0-9-]+$/.test(name) || !Number.isSafeInteger(round) || round < 1 || !Number.isSafeInteger(after) || after < 0) return reply.code(404).send({ error: 'Review resource not found.' });
+    return nextPaperPass(connectReview, project.path, name, round, after);
+  });
   app.route<{ Params: { projectId: string; '*': string } }>({
     // The review page posts with the review engine's token rather than Papilot's.
     method: ['GET', 'POST'], url: '/review/:projectId/*', config: { access: { project: 'projectId' }, csrf: false }, handler: async (request, reply) => {
@@ -544,12 +600,14 @@ export async function buildApp(options: AppOptions) {
             if (task) {
               store.updateTask(task.id, { error: null });
               await workspace.refresh(task.id);
+              // A decision changes what applying the task will write.
+              workspace.emit('reviewed', task.id);
             }
           }
           // A round's new version as one complete PDF, which Papilot compiles,
           // lets the review show the changes in the whole paper.
           const round = request.method === 'GET' && response.ok ? /^\/api\/tasks\/([a-z0-9-]+)\/rounds\/(\d+)$/.exec(route) : null;
-          if (round) (value as { pdf?: string }).pdf = `${prefix}/pdf/${round[1]}/${round[2]}`;
+          if (round) Object.assign(value as object, { pdf: `${prefix}/pdf/${round[1]}/${round[2]}`, passes: `${prefix}/pdf/${round[1]}/${round[2]}/passes` });
           return rewriteReviewJson(value, prefix);
         }
         if (reviewTask && writesFiles) throw new Error('The review engine returned an unexpected response. Select Check status before continuing.');