docrev 0.8.1 → 0.8.5

package/lib/build.ts

@@ -0,0 +1,1013 @@
+/**
+ * Build system - combines sections → paper.md → PDF/DOCX/TEX
+ *
+ * Features:
+ * - Reads rev.yaml config
+ * - Combines section files into paper.md (persisted)
+ * - Strips annotations appropriately per output format
+ * - Runs pandoc with crossref filter
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import { execSync, spawn, ChildProcess } from 'child_process';
+import YAML from 'yaml';
+import { stripAnnotations } from './annotations.js';
+import { buildRegistry, labelToDisplay, detectDynamicRefs, resolveForwardRefs } from './crossref.js';
+import { processVariables, hasVariables } from './variables.js';
+import { processSlideMarkdown, hasSlideSyntax } from './slides.js';
+import { generatePptxTemplate, templateNeedsRegeneration, injectMediaIntoPptx, injectSlideNumbers, applyThemeFonts, applyCentering, applyBuildupColors } from './pptx-template.js';
+import { getThemePath, getThemeNames, PPTX_THEMES } from './pptx-themes.js';
+import { runPostprocess } from './postprocess.js';
+import { hasPandoc, hasPandocCrossref, hasLatex } from './dependencies.js';
+import { buildImageRegistry, writeImageRegistry } from './image-registry.js';
+import type { Author } from './types.js';
+
+// =============================================================================
+// Constants
+// =============================================================================
+
+/** Supported output formats */
+const SUPPORTED_FORMATS = ['pdf', 'docx', 'tex', 'beamer', 'pptx'] as const;
+
+/** Maximum title length for output filename */
+const MAX_TITLE_FILENAME_LENGTH = 50;
+
+// =============================================================================
+// Interfaces
+// =============================================================================
+
+export interface CrossrefConfig {
+  figureTitle?: string;
+  tableTitle?: string;
+  figPrefix?: string | string[];
+  tblPrefix?: string | string[];
+  secPrefix?: string | string[];
+  linkReferences?: boolean;
+}
+
+export interface PdfConfig {
+  template?: string | null;
+  documentclass?: string;
+  fontsize?: string;
+  geometry?: string;
+  linestretch?: number;
+  numbersections?: boolean;
+  toc?: boolean;
+}
+
+export interface DocxConfig {
+  reference?: string | null;
+  keepComments?: boolean;
+  toc?: boolean;
+}
+
+export interface TexConfig {
+  standalone?: boolean;
+}
+
+export interface BeamerConfig {
+  theme?: string;
+  colortheme?: string | null;
+  fonttheme?: string | null;
+  aspectratio?: string | null;
+  navigation?: string | null;
+  section?: boolean;
+  notes?: string | false;
+  fit_images?: boolean;
+}
+
+export interface PptxConfig {
+  theme?: string;
+  reference?: string | null;
+  media?: string | null;
+  colors?: {
+    default?: string;
+    title?: string;
+  };
+  buildup?: {
+    grey?: string;
+    accent?: string;
+    enabled?: boolean;
+  };
+}
+
+export interface TablesConfig {
+  nowrap?: string[];
+}
+
+export interface PostprocessConfig {
+  pdf?: string | null;
+  docx?: string | null;
+  tex?: string | null;
+  pptx?: string | null;
+  beamer?: string | null;
+  all?: string | null;
+  [key: string]: string | null | undefined;
+}
+
+export interface BuildConfig {
+  title: string;
+  authors: (string | Author)[];
+  sections: string[];
+  bibliography: string | null;
+  csl: string | null;
+  crossref: CrossrefConfig;
+  pdf: PdfConfig;
+  docx: DocxConfig;
+  tex: TexConfig;
+  beamer: BeamerConfig;
+  pptx: PptxConfig;
+  tables: TablesConfig;
+  postprocess: PostprocessConfig;
+  _configPath?: string | null;
+}
+
+export interface BuildResult {
+  format: string;
+  success: boolean;
+  outputPath?: string;
+  error?: string;
+}
+
+interface BuildOptions {
+  verbose?: boolean;
+  config?: BuildConfig;
+  outputPath?: string;
+  crossref?: boolean;
+  _refsAutoInjected?: boolean;
+  _forwardRefsResolved?: number;
+}
+
+interface CombineOptions extends BuildOptions {
+  _refsAutoInjected?: boolean;
+}
+
+interface VariablesContext {
+  sectionContents: string[];
+}
+
+interface PandocResult {
+  outputPath: string;
+  success: boolean;
+  error?: string;
+}
+
+interface FullBuildResult {
+  results: BuildResult[];
+  paperPath: string;
+  warnings: string[];
+  forwardRefsResolved: number;
+  refsAutoInjected?: boolean;
+}
+
+interface DynamicRef {
+  type: string;
+  label: string;
+  match: string;
+  position: number;
+}
+
+interface Registry {
+  figures: Map<string, unknown>;
+  tables: Map<string, unknown>;
+  equations: Map<string, unknown>;
+  byNumber: {
+    fig?: Map<number, string>;
+    figS?: Map<number, string>;
+    tbl?: Map<number, string>;
+    tblS?: Map<number, string>;
+    eq?: Map<number, string>;
+  };
+}
+
+/**
+ * Default rev.yaml configuration
+ */
+export const DEFAULT_CONFIG: BuildConfig = {
+  title: 'Untitled Document',
+  authors: [],
+  sections: [],
+  bibliography: null,
+  csl: null,
+  crossref: {
+    figureTitle: 'Figure',
+    tableTitle: 'Table',
+    figPrefix: ['Fig.', 'Figs.'],
+    tblPrefix: ['Table', 'Tables'],
+    secPrefix: ['Section', 'Sections'],
+    linkReferences: true,
+  },
+  pdf: {
+    template: null,
+    documentclass: 'article',
+    fontsize: '12pt',
+    geometry: 'margin=1in',
+    linestretch: 1.5,
+    numbersections: false,
+    toc: false,
+  },
+  docx: {
+    reference: null,
+    keepComments: true,
+    toc: false,
+  },
+  tex: {
+    standalone: true,
+  },
+  // Slide formats
+  beamer: {
+    theme: 'default',
+    colortheme: null,
+    fonttheme: null,
+    aspectratio: null, // '169' for 16:9, '43' for 4:3
+    navigation: null, // 'horizontal', 'vertical', 'frame', 'empty'
+    section: true, // section divider slides
+    notes: 'show', // 'show' (presenter view), 'only' (notes only), 'hide', or false
+    fit_images: true, // scale images to fit within slide bounds
+  },
+  pptx: {
+    theme: 'default', // Built-in theme: default, dark, academic, minimal, corporate
+    reference: null, // Custom reference-doc (overrides theme)
+    media: null, // directory with logo images (e.g., logo-left.png, logo-right.png)
+  },
+  // Table formatting
+  tables: {
+    nowrap: [], // Column headers to apply nowrap formatting (converts Normal() → $\mathcal{N}()$ etc.)
+  },
+  // Postprocess scripts
+  postprocess: {
+    pdf: null,
+    docx: null,
+    tex: null,
+    pptx: null,
+    beamer: null,
+    all: null, // Runs after any format
+  },
+};
+
+// =============================================================================
+// Public API
+// =============================================================================
+
+/**
+ * Load rev.yaml config from directory
+ * @param directory - Project directory path
+ * @returns Merged config with defaults
+ * @throws {TypeError} If directory is not a string
+ * @throws {Error} If rev.yaml exists but cannot be parsed
+ */
+export function loadConfig(directory: string): BuildConfig {
+  if (typeof directory !== 'string') {
+    throw new TypeError(`directory must be a string, got ${typeof directory}`);
+  }
+
+  const configPath = path.join(directory, 'rev.yaml');
+
+  if (!fs.existsSync(configPath)) {
+    return { ...DEFAULT_CONFIG, _configPath: null };
+  }
+
+  try {
+    const content = fs.readFileSync(configPath, 'utf-8');
+    const userConfig = YAML.parse(content) || {};
+
+    // Deep merge with defaults
+    const config: BuildConfig = {
+      ...DEFAULT_CONFIG,
+      ...userConfig,
+      crossref: { ...DEFAULT_CONFIG.crossref, ...userConfig.crossref },
+      pdf: { ...DEFAULT_CONFIG.pdf, ...userConfig.pdf },
+      docx: { ...DEFAULT_CONFIG.docx, ...userConfig.docx },
+      tex: { ...DEFAULT_CONFIG.tex, ...userConfig.tex },
+      beamer: { ...DEFAULT_CONFIG.beamer, ...userConfig.beamer },
+      pptx: { ...DEFAULT_CONFIG.pptx, ...userConfig.pptx },
+      tables: { ...DEFAULT_CONFIG.tables, ...userConfig.tables },
+      postprocess: { ...DEFAULT_CONFIG.postprocess, ...userConfig.postprocess },
+      _configPath: configPath,
+    };
+
+    return config;
+  } catch (err) {
+    const error = err as Error;
+    throw new Error(`Failed to parse rev.yaml: ${error.message}`);
+  }
+}
+
+/**
+ * Find section files in directory
+ * @param directory - Project directory path
+ * @param configSections - Sections from rev.yaml (optional)
+ * @returns Ordered list of section file names
+ * @throws {TypeError} If directory is not a string
+ */
+export function findSections(directory: string, configSections: string[] = []): string[] {
+  if (typeof directory !== 'string') {
+    throw new TypeError(`directory must be a string, got ${typeof directory}`);
+  }
+
+  // If sections specified in config, use that order
+  if (configSections.length > 0) {
+    const sections: string[] = [];
+    for (const section of configSections) {
+      const filePath = path.join(directory, section);
+      if (fs.existsSync(filePath)) {
+        sections.push(section);
+      } else {
+        console.warn(`Warning: Section file not found: ${section}`);
+      }
+    }
+    return sections;
+  }
+
+  // Try sections.yaml
+  const sectionsYamlPath = path.join(directory, 'sections.yaml');
+  if (fs.existsSync(sectionsYamlPath)) {
+    try {
+      const sectionsConfig = YAML.parse(fs.readFileSync(sectionsYamlPath, 'utf-8'));
+      if (sectionsConfig.sections) {
+        return Object.entries(sectionsConfig.sections)
+          .sort((a: [string, any], b: [string, any]) => (a[1].order ?? 999) - (b[1].order ?? 999))
+          .map(([file]) => file)
+          .filter((f) => fs.existsSync(path.join(directory, f)));
+      }
+    } catch (e) {
+      if (process.env.DEBUG) {
+        const error = e as Error;
+        console.warn('build: YAML parse error in sections.yaml:', error.message);
+      }
+    }
+  }
+
+  // Default: find all .md files except special ones
+  const exclude = ['paper.md', 'readme.md', 'claude.md'];
+  const files = fs.readdirSync(directory).filter((f) => {
+    if (!f.endsWith('.md')) return false;
+    if (exclude.includes(f.toLowerCase())) return false;
+    return true;
+  });
+
+  // Sort alphabetically as fallback
+  return files.sort();
+}
+
+/**
+ * Combine section files into paper.md
+ */
+export function combineSections(directory: string, config: BuildConfig, options: CombineOptions = {}): string {
+  const sections = findSections(directory, config.sections);
+
+  if (sections.length === 0) {
+    throw new Error('No section files found. Create .md files or specify sections in rev.yaml');
+  }
+
+  const parts: string[] = [];
+
+  // Add YAML frontmatter
+  const frontmatter = buildFrontmatter(config);
+  parts.push('---');
+  parts.push(YAML.stringify(frontmatter).trim());
+  parts.push('---');
+  parts.push('');
+
+  // Read all section contents for variable processing
+  const sectionContents: string[] = [];
+
+  // Check if we need to auto-inject references before supplementary
+  // Pandoc places refs at the end by default, which breaks when supplementary follows
+  const hasRefsSection = sections.some(s =>
+    s.toLowerCase().includes('reference') || s.toLowerCase().includes('refs')
+  );
+  const suppIndex = sections.findIndex(s =>
+    s.toLowerCase().includes('supp') || s.toLowerCase().includes('appendix')
+  );
+  const hasBibliography = config.bibliography && fs.existsSync(path.join(directory, config.bibliography));
+
+  // Track if we find an explicit refs div in any section
+  let hasExplicitRefsDiv = false;
+
+  // Combine sections
+  for (let i = 0; i < sections.length; i++) {
+    const section = sections[i];
+    if (!section) continue;
+    const filePath = path.join(directory, section);
+    let content = fs.readFileSync(filePath, 'utf-8');
+
+    // Remove any existing frontmatter from section files
+    content = stripFrontmatter(content);
+    sectionContents.push(content);
+
+    // Check if this section has an explicit refs div
+    if (content.includes('::: {#refs}') || content.includes(':::  {#refs}')) {
+      hasExplicitRefsDiv = true;
+    }
+
+    // Auto-inject references before supplementary if needed
+    if (i === suppIndex && hasBibliography && !hasRefsSection && !hasExplicitRefsDiv) {
+      parts.push('# References\n');
+      parts.push('::: {#refs}');
+      parts.push(':::');
+      parts.push('');
+      parts.push('');
+      options._refsAutoInjected = true;
+    }
+
+    parts.push(content.trim());
+    parts.push('');
+    parts.push(''); // Double newline between sections
+  }
+
+  let paperContent = parts.join('\n');
+
+  // Process template variables if any exist
+  if (hasVariables(paperContent)) {
+    paperContent = processVariables(paperContent, config as any, { sectionContents });
+  }
+
+  // Resolve forward references (refs that appear before their anchor definition)
+  // This fixes pandoc-crossref limitation with multi-file documents
+  if (hasPandocCrossref()) {
+    const registry = buildRegistry(directory, sections);
+    const { text, resolved } = resolveForwardRefs(paperContent, registry);
+    if (resolved.length > 0) {
+      paperContent = text;
+      // Store resolved count for optional reporting
+      options._forwardRefsResolved = resolved.length;
+    }
+  }
+
+  const paperPath = path.join(directory, 'paper.md');
+
+  fs.writeFileSync(paperPath, paperContent, 'utf-8');
+
+  return paperPath;
+}
+
+/**
+ * Build YAML frontmatter from config
+ */
+function buildFrontmatter(config: BuildConfig): Record<string, unknown> {
+  const fm: Record<string, unknown> = {};
+
+  if (config.title) fm.title = config.title;
+
+  if (config.authors && config.authors.length > 0) {
+    fm.author = config.authors;
+  }
+
+  if (config.bibliography) {
+    fm.bibliography = config.bibliography;
+  }
+
+  if (config.csl) {
+    fm.csl = config.csl;
+  }
+
+  return fm;
+}
+
+/**
+ * Strip YAML frontmatter from content
+ */
+function stripFrontmatter(content: string): string {
+  const match = content.match(/^---\r?\n([\s\S]*?)\r?\n---\r?\n/);
+  if (match) {
+    return content.slice(match[0].length);
+  }
+  return content;
+}
+
+/**
+ * Process markdown tables to apply nowrap formatting to specified columns.
+ * Converts distribution notation (Normal, Student-t, Gamma) to LaTeX math.
+ * @param content - Markdown content
+ * @param tablesConfig - tables config from rev.yaml
+ * @param format - output format (pdf, docx, etc.)
+ * @returns processed content
+ */
+export function processTablesForFormat(content: string, tablesConfig: TablesConfig, format: string): string {
+  // Only process for PDF/TeX output
+  if (format !== 'pdf' && format !== 'tex') {
+    return content;
+  }
+
+  // Check if we have nowrap columns configured
+  if (!tablesConfig?.nowrap?.length) {
+    return content;
+  }
+
+  const nowrapPatterns = tablesConfig.nowrap.map((p) => p.toLowerCase());
+
+  // Match pipe tables: header row, separator row, body rows
+  // Header: | Col1 | Col2 | Col3 |
+  // Separator: |:-----|:-----|:-----|
+  // Body: | val1 | val2 | val3 |
+  const tableRegex = /^(\|[^\n]+\|\r?\n\|[-:| ]+\|\r?\n)((?:\|[^\n]+\|\r?\n?)+)/gm;
+
+  return content.replace(tableRegex, (match, headerAndSep, body) => {
+    // Split header from separator
+    const lines = headerAndSep.split(/\r?\n/);
+    const headerLine = lines[0] ?? '';
+
+    // Parse header cells to find nowrap column indices
+    const headerCells = headerLine
+      .split('|')
+      .slice(1, -1)
+      .map((c: string) => c.trim().toLowerCase());
+
+    const nowrapCols: number[] = [];
+    headerCells.forEach((cell: string, i: number) => {
+      if (nowrapPatterns.some((p) => cell.includes(p))) {
+        nowrapCols.push(i);
+      }
+    });
+
+    // If no nowrap columns found in this table, return unchanged
+    if (nowrapCols.length === 0) {
+      return match;
+    }
+
+    // Process body rows
+    const bodyLines = body.split(/\r?\n/).filter((l: string) => l.trim());
+    const processedBody = bodyLines
+      .map((row: string) => {
+        // Split row into cells, keeping the pipe structure
+        const cells = row.split('|');
+        // cells[0] is empty (before first |), cells[last] is empty (after last |)
+
+        nowrapCols.forEach((colIdx) => {
+          const cellIdx = colIdx + 1; // Account for empty first element
+          if (cells[cellIdx] !== undefined) {
+            const cellContent = cells[cellIdx].trim();
+
+            // Skip if empty, already math, or already has LaTeX commands
+            if (!cellContent || cellContent.startsWith('$') || cellContent.startsWith('\\')) {
+              return;
+            }
+
+            // Convert distribution notation to LaTeX math
+            // Order matters: compound names (Half-Normal) must come before simple names (Normal)
+            let processed = cellContent;
+
+            // Half-Normal(x) → $\text{Half-Normal}(x)$ (must come before Normal)
+            processed = processed.replace(/Half-Normal\(([^)]+)\)/g, '$\\text{Half-Normal}($1)$');
+
+            // Normal(x, y) → $\mathcal{N}(x, y)$
+            processed = processed.replace(/Normal\(([^)]+)\)/g, '$\\mathcal{N}($1)$');
+
+            // Student-t(df, loc, scale) → $t_{df}(loc, scale)$
+            processed = processed.replace(/Student-t\((\d+),\s*([^)]+)\)/g, '$t_{$1}($2)$');
+
+            // Gamma(a, b) → $\text{Gamma}(a, b)$
+            processed = processed.replace(/Gamma\(([^)]+)\)/g, '$\\text{Gamma}($1)$');
+
+            // Exponential(x) → $\text{Exp}(x)$
+            processed = processed.replace(/Exponential\(([^)]+)\)/g, '$\\text{Exp}($1)$');
+
+            // Update cell with padding
+            cells[cellIdx] = ` ${processed} `;
+          }
+        });
+
+        return cells.join('|');
+      })
+      .join('\n');
+
+    return headerAndSep + processedBody + '\n';
+  });
+}
+
+/**
+ * Prepare paper.md for specific output format
+ */
+export function prepareForFormat(
+  paperPath: string,
+  format: string,
+  config: BuildConfig,
+  options: BuildOptions = {}
+): string {
+  const directory = path.dirname(paperPath);
+  let content = fs.readFileSync(paperPath, 'utf-8');
+
+  // Build crossref registry for reference conversion
+  // Pass sections from config to ensure correct file ordering
+  const registry = buildRegistry(directory, config.sections);
+
+  if (format === 'pdf' || format === 'tex') {
+    // Strip all annotations for clean output
+    content = stripAnnotations(content);
+
+    // Process tables for nowrap columns (convert Normal() → $\mathcal{N}()$ etc.)
+    content = processTablesForFormat(content, config.tables, format);
+  } else if (format === 'docx') {
+    // Strip track changes, optionally keep comments
+    content = stripAnnotations(content, { keepComments: config.docx.keepComments });
+
+    // Convert @fig:label to "Figure 1" for Word readers
+    content = convertDynamicRefsToDisplay(content, registry);
+  } else if (format === 'beamer' || format === 'pptx') {
+    // Strip annotations for slide output
+    content = stripAnnotations(content);
+
+    // Process slide syntax (::: step, ::: notes)
+    if (hasSlideSyntax(content)) {
+      content = processSlideMarkdown(content, format);
+    }
+  }
+
+  // Write to temporary file
+  const preparedPath = path.join(directory, `.paper-${format}.md`);
+  fs.writeFileSync(preparedPath, content, 'utf-8');
+
+  return preparedPath;
+}
+
+/**
+ * Convert @fig:label references to display format (Figure 1)
+ */
+function convertDynamicRefsToDisplay(text: string, registry: Registry): string {
+  const refs = detectDynamicRefs(text);
+
+  // Process in reverse order to preserve positions
+  let result = text;
+  for (let i = refs.length - 1; i >= 0; i--) {
+    const ref = refs[i];
+    if (!ref) continue;
+    const display = labelToDisplay(ref.type, ref.label, registry as any);
+
+    if (display) {
+      result = result.slice(0, ref.position) + display + result.slice(ref.position + ref.match.length);
+    }
+  }
+
+  return result;
+}
+
+/**
+ * Build pandoc arguments for format
+ */
+export function buildPandocArgs(format: string, config: BuildConfig, outputPath: string): string[] {
+  const args: string[] = [];
+
+  // Output format
+  if (format === 'tex') {
+    args.push('-t', 'latex');
+    if (config.tex.standalone) {
+      args.push('-s');
+    }
+  } else if (format === 'pdf') {
+    args.push('-t', 'pdf');
+  } else if (format === 'docx') {
+    args.push('-t', 'docx');
+  } else if (format === 'beamer') {
+    args.push('-t', 'beamer');
+  } else if (format === 'pptx') {
+    args.push('-t', 'pptx');
+  }
+
+  // Output file (use basename since we set cwd to directory in runPandoc)
+  args.push('-o', path.basename(outputPath));
+
+  // Crossref filter (if available) - skip for slides
+  if (hasPandocCrossref() && format !== 'beamer' && format !== 'pptx') {
+    args.push('--filter', 'pandoc-crossref');
+  }
+
+  // Bibliography
+  if (config.bibliography) {
+    args.push('--citeproc');
+  }
+
+  // Format-specific options
+  if (format === 'pdf') {
+    if (config.pdf.template) {
+      args.push('--template', config.pdf.template);
+    }
+    args.push('-V', `documentclass=${config.pdf.documentclass}`);
+    args.push('-V', `fontsize=${config.pdf.fontsize}`);
+    args.push('-V', `geometry:${config.pdf.geometry}`);
+    if (config.pdf.linestretch !== 1) {
+      args.push('-V', `linestretch=${config.pdf.linestretch}`);
+    }
+    if (config.pdf.numbersections) {
+      args.push('--number-sections');
+    }
+    if (config.pdf.toc) {
+      args.push('--toc');
+    }
+  } else if (format === 'docx') {
+    if (config.docx.reference) {
+      args.push('--reference-doc', config.docx.reference);
+    }
+    if (config.docx.toc) {
+      args.push('--toc');
+    }
+  } else if (format === 'beamer') {
+    // Beamer slide options
+    const beamer = config.beamer || {};
+    if (beamer.theme) {
+      args.push('-V', `theme=${beamer.theme}`);
+    }
+    if (beamer.colortheme) {
+      args.push('-V', `colortheme=${beamer.colortheme}`);
+    }
+    if (beamer.fonttheme) {
+      args.push('-V', `fonttheme=${beamer.fonttheme}`);
+    }
+    if (beamer.aspectratio) {
+      args.push('-V', `aspectratio=${beamer.aspectratio}`);
+    }
+    if (beamer.navigation) {
+      args.push('-V', `navigation=${beamer.navigation}`);
+    }
+    // Speaker notes - default to 'show' which creates presenter view PDF
+    // Options: 'show' (dual screen), 'only' (notes only), 'hide' (no notes), false (disabled)
+    const notesMode = beamer.notes !== undefined ? beamer.notes : 'show';
+    if (notesMode && notesMode !== 'hide') {
+      args.push('-V', `classoption=notes=${notesMode}`);
+    }
+    // Fit images within slide bounds (default: true)
+    if (beamer.fit_images !== false) {
+      const fitImagesHeader = `\\makeatletter
+\\def\\maxwidth{\\ifdim\\Gin@nat@width>\\linewidth\\linewidth\\else\\Gin@nat@width\\fi}
+\\def\\maxheight{\\ifdim\\Gin@nat@height>0.75\\textheight 0.75\\textheight\\else\\Gin@nat@height\\fi}
+\\makeatother
+\\setkeys{Gin}{width=\\maxwidth,height=\\maxheight,keepaspectratio}`;
+      args.push('-V', `header-includes=${fitImagesHeader}`);
+    }
+    // Slides need standalone
+    args.push('-s');
+  } else if (format === 'pptx') {
+    // PowerPoint options - handled separately in preparePptxTemplate
+    // Reference doc is set by caller after template generation
+  }
+
+  return args;
+}
+
+/**
+ * Write crossref.yaml if needed
+ */
+function ensureCrossrefConfig(directory: string, config: BuildConfig): void {
+  const crossrefPath = path.join(directory, 'crossref.yaml');
+
+  if (!fs.existsSync(crossrefPath) && hasPandocCrossref()) {
+    fs.writeFileSync(crossrefPath, YAML.stringify(config.crossref), 'utf-8');
+  }
+}
+
+/**
+ * Get install instructions for missing dependency
+ */
+function getInstallInstructions(tool: string): string {
+  const instructions: Record<string, string> = {
+    pandoc: 'https://pandoc.org/installing.html',
+    latex: 'https://www.latex-project.org/get/',
+  };
+  return instructions[tool] || 'Check documentation';
+}
+
+/**
+ * Run pandoc build
+ */
+export async function runPandoc(
+  inputPath: string,
+  format: string,
+  config: BuildConfig,
+  options: BuildOptions = {}
+): Promise<PandocResult> {
+  const directory = path.dirname(inputPath);
+  const baseName = config.title
+    ? config.title.toLowerCase().replace(/[^a-z0-9]+/g, '-').slice(0, 50)
+    : 'paper';
+
+  // Map format to file extension
+  const extMap: Record<string, string> = {
+    tex: '.tex',
+    pdf: '.pdf',
+    docx: '.docx',
+    beamer: '.pdf', // beamer outputs PDF
+    pptx: '.pptx',
+  };
+  const ext = extMap[format] || '.pdf';
+
+  // For beamer, use -slides suffix to distinguish from regular PDF
+  const suffix = format === 'beamer' ? '-slides' : '';
+  // Allow custom output path via options
+  const outputPath = options.outputPath || path.join(directory, `${baseName}${suffix}${ext}`);
+
+  // Ensure crossref.yaml exists
+  ensureCrossrefConfig(directory, config);
+
+  const args = buildPandocArgs(format, config, outputPath);
+
+  // Handle PPTX reference template and themes
+  let pptxMediaDir: string | null = null;
+  if (format === 'pptx') {
+    const pptx = config.pptx || {};
+
+    // Determine media directory (default: pptx/media or slides/media)
+    let mediaDir = pptx.media;
+    if (!mediaDir) {
+      if (fs.existsSync(path.join(directory, 'pptx', 'media'))) {
+        mediaDir = path.join(directory, 'pptx', 'media');
+      } else if (fs.existsSync(path.join(directory, 'slides', 'media'))) {
+        mediaDir = path.join(directory, 'slides', 'media');
+      }
+    } else if (!path.isAbsolute(mediaDir)) {
+      mediaDir = path.join(directory, mediaDir);
+    }
+    pptxMediaDir = mediaDir || null;
+
+    // Determine reference doc: custom reference overrides theme
+    let referenceDoc: string | null = null;
+    if (pptx.reference && fs.existsSync(path.join(directory, pptx.reference))) {
+      // Custom reference doc takes precedence
+      referenceDoc = path.join(directory, pptx.reference);
+    } else {
+      // Use built-in theme (default: 'default')
+      const themeName = pptx.theme || 'default';
+      const themePath = getThemePath(themeName);
+      if (themePath && fs.existsSync(themePath)) {
+        referenceDoc = themePath;
+      }
+    }
+
+    if (referenceDoc) {
+      args.push('--reference-doc', referenceDoc);
+    }
+
+    // Add color filter for PPTX (handles [text]{color=#RRGGBB} syntax)
+    const colorFilterPath = path.join(path.dirname(new URL(import.meta.url).pathname.replace(/^\/([A-Z]:)/, '$1')), 'pptx-color-filter.lua');
+    if (fs.existsSync(colorFilterPath)) {
+      args.push('--lua-filter', colorFilterPath);
+    }
+  }
+
+  // Add crossref metadata file if exists (skip for slides - they don't use crossref)
+  if (format !== 'beamer' && format !== 'pptx') {
+    const crossrefPath = path.join(directory, 'crossref.yaml');
+    if (fs.existsSync(crossrefPath) && hasPandocCrossref()) {
+      // Use basename since we set cwd to directory
+      args.push('--metadata-file', 'crossref.yaml');
+    }
+  }
+
+  // Input file (use basename since we set cwd to directory)
+  args.push(path.basename(inputPath));
+
+  return new Promise((resolve) => {
+    const pandoc: ChildProcess = spawn('pandoc', args, {
+      cwd: directory,
+      stdio: ['ignore', 'pipe', 'pipe'],
+    });
+
+    let stderr = '';
+    pandoc.stderr?.on('data', (data) => {
+      stderr += data.toString();
+    });
+
+    pandoc.on('close', async (code) => {
+      if (code === 0) {
+        // For PPTX, post-process to add slide numbers, buildup colors, and logos
+        if (format === 'pptx') {
+          try {
+            // Inject slide numbers into content slides only
+            await injectSlideNumbers(outputPath);
+          } catch (e) {
+            // Slide number injection failed but output was created
+          }
+          try {
+            // Apply colors (default text color, title color, buildup greying)
+            const pptxConfig = config.pptx || {};
+            const colorsConfig = pptxConfig.colors || {};
+            const buildupConfig = pptxConfig.buildup || {};
+            // Merge colors and buildup config for applyBuildupColors
+            const colorConfig = {
+              default: colorsConfig.default,
+              title: colorsConfig.title,
+              grey: buildupConfig.grey,
+              accent: buildupConfig.accent,
+              enabled: buildupConfig.enabled
+            };
+            await applyBuildupColors(outputPath, colorConfig);
+          } catch (e) {
+            // Color application failed but output was created
+          }
+          // Inject logos into cover slide (if media dir configured)
+          if (pptxMediaDir) {
+            try {
+              await injectMediaIntoPptx(outputPath, pptxMediaDir);
+            } catch (e) {
+              // Logo injection failed but output was created
+            }
+          }
+        }
+
+        // Run user postprocess scripts
+        const postResult = await runPostprocess(outputPath, format, config as unknown as Parameters<typeof runPostprocess>[2], options);
+        if (!postResult.success && options.verbose) {
+          console.error(`Postprocess warning: ${postResult.error}`);
+        }
+
+        resolve({ outputPath, success: true });
+      } else {
+        resolve({ outputPath, success: false, error: stderr || `Exit code ${code}` });
+      }
+    });
+
+    pandoc.on('error', (err) => {
+      resolve({ outputPath, success: false, error: err.message });
+    });
+  });
+}
+
+/**
+ * Full build pipeline
+ */
+export async function build(
+  directory: string,
+  formats: string[] = ['pdf', 'docx'],
+  options: BuildOptions = {}
+): Promise<FullBuildResult> {
+  const warnings: string[] = [];
+  let forwardRefsResolved = 0;
+
+  // Check pandoc
+  if (!hasPandoc()) {
+    const instruction = getInstallInstructions('pandoc');
+    throw new Error(`Pandoc not found. Install with: ${instruction}\nOr run: rev doctor`);
+  }
+
+  // Check LaTeX if PDF is requested
+  if ((formats.includes('pdf') || formats.includes('all')) && !hasLatex()) {
+    warnings.push(`LaTeX not found - PDF generation may fail. Install with: ${getInstallInstructions('latex')}`);
+  }
+
+  // Check pandoc-crossref
+  if (!hasPandocCrossref()) {
+    warnings.push('pandoc-crossref not found - figure/table numbering will not work');
+  }
+
+  // Load config (use passed config if provided, otherwise load from file)
+  const config = options.config || loadConfig(directory);
+
+  // Combine sections → paper.md
+  const buildOptions: CombineOptions = { ...options };
+  const paperPath = combineSections(directory, config, buildOptions);
+  forwardRefsResolved = buildOptions._forwardRefsResolved || 0;
+  const refsAutoInjected = buildOptions._refsAutoInjected || false;
+
+  // Expand 'all' to all formats
+  if (formats.includes('all')) {
+    formats = ['pdf', 'docx', 'tex'];
+  }
+
+  // Build and save image registry when DOCX is being built
+  // This allows import to restore proper image syntax from Word documents
+  if (formats.includes('docx')) {
+    const paperContent = fs.readFileSync(paperPath, 'utf-8');
+    const crossrefReg = buildRegistry(directory, config.sections);
+    const imageReg = buildImageRegistry(paperContent, crossrefReg as any);
+    if ((imageReg as any).figures?.length > 0) {
+      writeImageRegistry(directory, imageReg);
+    }
+  }
+
+  const results: BuildResult[] = [];
+
+  for (const format of formats) {
+    // Prepare format-specific version
+    const preparedPath = prepareForFormat(paperPath, format, config, options);
+
+    // Run pandoc
+    const result = await runPandoc(preparedPath, format, config, options);
+    results.push({ format, ...result });
+
+    // Clean up temp file
+    try {
+      fs.unlinkSync(preparedPath);
+    } catch {
+      // Ignore cleanup errors
+    }
+  }
+
+  return { results, paperPath, warnings, forwardRefsResolved, refsAutoInjected };
+}
+
+/**
+ * Get build status summary
+ */
+export function formatBuildResults(results: BuildResult[]): string {
+  const lines: string[] = [];
+
+  for (const r of results) {
+    if (r.success) {
+      lines.push(`  ${r.format.toUpperCase()}: ${path.basename(r.outputPath!)}`);
+    } else {
+      lines.push(`  ${r.format.toUpperCase()}: FAILED - ${r.error}`);
+    }
+  }
+
+  return lines.join('\n');
+}