docrev 0.11.0 → 0.11.2

package/types/index.d.ts

@@ -1,525 +1,531 @@
-/**
- * TypeScript type definitions for docrev
- */
-
-// ============================================
-// Annotations (lib/annotations.js)
-// ============================================
-
-export interface Annotation {
-  type: 'insert' | 'delete' | 'substitute' | 'comment' | 'highlight';
-  match: string;
-  content: string;
-  replacement?: string;
-  author?: string;
-  position: number;
-  line: number;
-  before?: string;
-  after?: string;
-}
-
-export interface Comment extends Annotation {
-  type: 'comment';
-  author: string;
-  resolved: boolean;
-}
-
-export interface AnnotationCounts {
-  inserts: number;
-  deletes: number;
-  substitutes: number;
-  comments: number;
-  total: number;
-}
-
-export interface StripOptions {
-  keepComments?: boolean;
-}
-
-export interface CommentFilterOptions {
-  pendingOnly?: boolean;
-  resolvedOnly?: boolean;
-}
-
-export function parseAnnotations(text: string): Annotation[];
-export function stripAnnotations(text: string, options?: StripOptions): string;
-export function applyDecision(text: string, annotation: Annotation, accept: boolean): string;
-export function getTrackChanges(text: string): Annotation[];
-export function getComments(text: string, options?: CommentFilterOptions): Comment[];
-export function setCommentStatus(text: string, comment: Comment, resolved: boolean): string;
-export function countAnnotations(text: string): AnnotationCounts;
-
-// ============================================
-// Build (lib/build.js)
-// ============================================
-
-export interface BuildConfig {
-  title?: string;
-  authors?: Author[];
-  sections?: string[];
-  bibliography?: string;
-  csl?: string;
-  crossref?: CrossrefConfig;
-  pdf?: PdfConfig;
-  docx?: DocxConfig;
-}
-
-export interface Author {
-  name: string;
-  affiliation?: string;
-  email?: string;
-  orcid?: string;
-}
-
-export interface CrossrefConfig {
-  figureTitle?: string;
-  tableTitle?: string;
-  figPrefix?: string | string[];
-  tblPrefix?: string | string[];
-}
-
-export interface PdfConfig {
-  documentclass?: string;
-  fontsize?: string;
-  geometry?: string;
-  linestretch?: number;
-  toc?: boolean;
-}
-
-export interface DocxConfig {
-  reference?: string;
-  keepComments?: boolean;
-  toc?: boolean;
-}
-
-export interface BuildResult {
-  format: string;
-  output: string;
-  success: boolean;
-  error?: string;
-}
-
-export function loadConfig(directory?: string): BuildConfig;
-export function findSections(directory: string, config: BuildConfig): string[];
-export function combineSections(files: string[], options?: object): string;
-export function build(formats?: string[], options?: object): Promise<BuildResult[]>;
-export function hasPandoc(): Promise<boolean>;
-export function hasPandocCrossref(): Promise<boolean>;
-
-// ============================================
-// Citations (lib/citations.js)
-// ============================================
-
-export interface Citation {
-  key: string;
-  line: number;
-  file: string;
-}
-
-export interface CitationValidation {
-  valid: Citation[];
-  missing: Citation[];
-  unused: string[];
-  duplicates: Array<{ key: string; count: number; locations: Citation[] }>;
-}
-
-export interface CitationStats {
-  totalCitations: number;
-  uniqueCited: number;
-  valid: number;
-  missing: number;
-  missingKeys: string[];
-  bibEntries: number;
-  unused: number;
-  unusedKeys: string[];
-}
-
-export function extractCitations(text: string, file?: string): Citation[];
-export function parseBibFile(bibPath: string): Set<string>;
-export function validateCitations(mdFiles: string[], bibPath: string): CitationValidation;
-export function getCitationStats(mdFiles: string[], bibPath: string): CitationStats;
-
-// ============================================
-// Crossref (lib/crossref.js)
-// ============================================
-
-export interface RefNumber {
-  num: number;
-  isSupp: boolean;
-  suffix: string | null;
-}
-
-export interface HardcodedRef {
-  type: 'fig' | 'tbl' | 'eq';
-  match: string;
-  numbers: RefNumber[];
-  position: number;
-}
-
-export interface DynamicRef {
-  type: 'fig' | 'tbl' | 'eq';
-  label: string;
-  match: string;
-  position: number;
-}
-
-export interface FigureInfo {
-  label: string;
-  num: number;
-  isSupp: boolean;
-  file: string;
-}
-
-export interface Registry {
-  figures: Map<string, FigureInfo>;
-  tables: Map<string, FigureInfo>;
-  equations: Map<string, FigureInfo>;
-  byNumber: {
-    fig: Map<number, string>;
-    figS: Map<number, string>;
-    tbl: Map<number, string>;
-    tblS: Map<number, string>;
-    eq: Map<number, string>;
-  };
-}
-
-export interface RefStatus {
-  dynamic: DynamicRef[];
-  hardcoded: HardcodedRef[];
-  anchors: { figures: number; tables: number; equations: number };
-}
-
-export function normalizeType(typeStr: string): 'fig' | 'tbl' | 'eq' | string;
-export function parseRefNumber(numStr: string, suffix?: string): RefNumber;
-export function parseReferenceList(listStr: string): RefNumber[];
-export function buildRegistry(directory: string, excludeFiles?: string[]): Registry;
-export function labelToDisplay(type: string, label: string, registry: Registry): string | null;
-export function numberToLabel(type: string, num: number, isSupp: boolean, registry: Registry): string | null;
-export function detectHardcodedRefs(text: string): HardcodedRef[];
-export function detectDynamicRefs(text: string): DynamicRef[];
-export function convertHardcodedRefs(text: string, registry: Registry): { converted: string; conversions: Array<{ from: string; to: string }>; warnings: string[] };
-export function getRefStatus(text: string, registry: Registry): RefStatus;
-
-// ============================================
-// DOI (lib/doi.js)
-// ============================================
-
-export interface BibEntry {
-  key: string;
-  type: string;
-  doi: string | null;
-  title: string;
-  authorRaw: string;
-  year: number | null;
-  journal: string;
-  skip: boolean;
-  expectDoi: boolean;
-  noDoi: boolean;
-  line: number;
-}
-
-export interface DoiCheckResult {
-  valid: boolean;
-  source?: 'crossref' | 'datacite';
-  metadata?: {
-    title: string;
-    authors: string[];
-    year: number;
-    journal: string;
-    type?: string;
-  };
-  error?: string;
-}
-
-export interface BibtexFetchResult {
-  success: boolean;
-  bibtex?: string;
-  error?: string;
-}
-
-export interface DoiLookupResult {
-  found: boolean;
-  doi?: string;
-  confidence?: 'low' | 'medium' | 'high';
-  score?: number;
-  metadata?: {
-    title: string;
-    authors: string[];
-    year: number;
-    journal: string;
-  };
-  alternatives?: Array<{
-    doi: string;
-    title: string;
-    score: number;
-  }>;
-  error?: string;
-}
-
-export interface BibCheckResult {
-  entries: Array<BibEntry & { status: string; message?: string; metadata?: object }>;
-  valid: number;
-  invalid: number;
-  missing: number;
-  skipped: number;
-}
-
-export function parseBibEntries(bibPath: string): BibEntry[];
-export function isValidDoiFormat(doi: string): boolean;
-export function checkDoi(doi: string): Promise<DoiCheckResult>;
-export function fetchBibtex(doi: string): Promise<BibtexFetchResult>;
-export function checkBibDois(bibPath: string, options?: { checkMissing?: boolean; parallel?: number }): Promise<BibCheckResult>;
-export function lookupDoi(title: string, author?: string, year?: number, journal?: string): Promise<DoiLookupResult>;
-export function lookupMissingDois(bibPath: string, options?: { parallel?: number; onProgress?: (current: number, total: number) => void }): Promise<Array<{ key: string; title: string; type: string; journal: string; result: DoiLookupResult }>>;
-export function addToBib(bibPath: string, bibtex: string): { success: boolean; key?: string; error?: string };
-
-// ============================================
-// Equations (lib/equations.js)
-// ============================================
-
-export interface Equation {
-  type: 'inline' | 'display';
-  content: string;
-  line: number;
-  file: string;
-}
-
-export interface EquationStats {
-  total: number;
-  display: number;
-  inline: number;
-  byFile: Array<{ file: string; display: number; inline: number }>;
-}
-
-export interface WordEquationResult {
-  success: boolean;
-  equations: Array<{
-    type: 'inline' | 'display' | 'unknown';
-    latex: string | null;
-    position: number;
-    line?: number;
-    raw?: string;
-    error?: string;
-  }>;
-  error?: string;
-}
-
-export function extractEquations(text: string, file?: string): Equation[];
-export function generateEquationSheet(equations: Equation[]): string;
-export function convertToWord(inputPath: string, outputPath: string, options?: { preserveLatex?: boolean }): Promise<{ success: boolean; message: string }>;
-export function createEquationsDoc(inputPath: string, outputPath: string): Promise<{ success: boolean; message: string; stats: { display: number; inline: number } | null }>;
-export function getEquationStats(files: string[]): EquationStats;
-export function extractEquationsFromWord(docxPath: string): Promise<WordEquationResult>;
-export function getWordEquationStats(docxPath: string): Promise<{ count: number; display: number; inline: number; converted: number; error?: string }>;
-
-// ============================================
-// Git (lib/git.js)
-// ============================================
-
-export interface FileChange {
-  added: number;
-  removed: number;
-  changes: Array<{ added: boolean; removed: boolean; value: string }>;
-}
-
-export interface CommitInfo {
-  hash: string;
-  date: string;
-  author: string;
-  message: string;
-}
-
-export function isGitRepo(directory?: string): boolean;
-export function getCurrentBranch(directory?: string): string | null;
-export function getDefaultBranch(directory?: string): string;
-export function getFileAtRef(filePath: string, ref: string): string | null;
-export function getChangedFiles(fromRef: string, toRef?: string): string[];
-export function getFileHistory(filePath: string, limit?: number): CommitInfo[];
-export function compareFileVersions(filePath: string, fromRef: string, toRef?: string): FileChange;
-export function getWordCountDiff(filePath: string, fromRef: string, toRef?: string): { before: number; after: number; diff: number };
-export function getRecentCommits(directory?: string, limit?: number): CommitInfo[];
-export function hasUncommittedChanges(directory?: string): boolean;
-export function getTags(directory?: string): string[];
-
-// ============================================
-// Journals (lib/journals.js)
-// ============================================
-
-export interface JournalProfile {
-  name: string;
-  url: string;
-  requirements: {
-    wordLimit?: { main: number; abstract?: number };
-    references?: { max?: number; doiRequired?: boolean };
-    figures?: { max?: number };
-    tables?: { max?: number };
-    sections?: string[];
-    formatting?: object;
-  };
-}
-
-export interface ValidationResult {
-  journal: string;
-  valid: boolean;
-  wordCount: { main: number; abstract: number; limit: { main: number; abstract: number } };
-  figures: { count: number; max: number };
-  tables: { count: number; max: number };
-  references: { count: number; max: number };
-  sections: { found: string[]; missing: string[]; required: string[] };
-  errors: string[];
-  warnings: string[];
-}
-
-export function listJournals(): Array<{ id: string; name: string; url: string }>;
-export function getJournalProfile(journalId: string): JournalProfile | null;
-export function validateManuscript(text: string, journalId: string, options?: { bibPath?: string }): ValidationResult;
-export function validateProject(directory: string, journalId: string): Promise<ValidationResult>;
-
-// ============================================
-// Merge (lib/merge.js)
-// ============================================
-
-export interface ReviewerChange {
-  reviewer: string;
-  type: 'insert' | 'delete' | 'replace';
-  start: number;
-  end: number;
-  oldText: string;
-  newText: string;
-}
-
-export interface Conflict {
-  start: number;
-  end: number;
-  original: string;
-  changes: ReviewerChange[];
-}
-
-export interface MergeResult {
-  merged: string;
-  conflicts: Conflict[];
-  stats: {
-    reviewers: number;
-    totalChanges: number;
-    nonConflicting: number;
-    conflicts: number;
-    comments: number;
-  };
-  originalText: string;
-}
-
-export function extractChanges(originalText: string, wordText: string, reviewer: string): ReviewerChange[];
-export function detectConflicts(allChanges: ReviewerChange[][]): { conflicts: Conflict[]; nonConflicting: ReviewerChange[] };
-export function applyChanges(originalText: string, changes: ReviewerChange[]): string;
-export function applyChangesAsAnnotations(originalText: string, changes: ReviewerChange[]): string;
-export function formatConflict(conflict: Conflict, originalText: string): string;
-export function mergeReviewerDocs(originalPath: string, reviewerDocs: Array<{ path: string; name: string }>, options?: { autoResolve?: boolean }): Promise<MergeResult>;
-export function resolveConflict(text: string, conflict: Conflict, choice: number, originalText: string): string;
-
-// ============================================
-// Sections (lib/sections.js)
-// ============================================
-
-export interface SectionConfig {
-  header: string;
-  aliases?: string[];
-  order?: number;
-}
-
-export interface SectionsConfig {
-  version: number;
-  description?: string;
-  sections: Record<string, SectionConfig>;
-}
-
-export interface ExtractedSection {
-  file: string;
-  header: string;
-  content: string;
-  matched: boolean;
-}
-
-export function extractHeader(filePath: string): string | null;
-export function generateConfig(directory: string, excludePatterns?: string[]): SectionsConfig;
-export function loadConfig(configPath: string): SectionsConfig;
-export function saveConfig(configPath: string, config: SectionsConfig): void;
-export function matchHeading(heading: string, sections: Record<string, SectionConfig>): { file: string; config: SectionConfig } | null;
-export function extractSectionsFromText(text: string, sections: Record<string, SectionConfig>): ExtractedSection[];
-export function splitAnnotatedPaper(paperContent: string, sections: Record<string, SectionConfig>): Map<string, string>;
-export function getOrderedSections(config: SectionsConfig): string[];
-
-// ============================================
-// Word (lib/word.js)
-// ============================================
-
-export interface WordComment {
-  id: string;
-  author: string;
-  date: string;
-  text: string;
-}
-
-export interface WordMetadata {
-  title?: string;
-  author?: string;
-  created?: string;
-  modified?: string;
-}
-
-export interface CommentAnchor {
-  text: string;
-  context: string;
-}
-
-export function extractWordComments(docxPath: string): Promise<WordComment[]>;
-export function extractCommentAnchors(docxPath: string): Promise<Map<string, CommentAnchor>>;
-export function extractTextFromWord(docxPath: string): Promise<string>;
-export function extractFromWord(docxPath: string): Promise<{ text: string; html: string }>;
-export function getWordMetadata(docxPath: string): Promise<WordMetadata>;
-export function isWordDocument(filePath: string): boolean;
-
-// ============================================
-// TrackChanges (lib/trackchanges.js)
-// ============================================
-
-export interface TrackChangeMarker {
-  type: 'insert' | 'delete';
-  start: number;
-  end: number;
-  content: string;
-}
-
-export function prepareForTrackChanges(text: string): { text: string; markers: TrackChangeMarker[] };
-export function applyTrackChangesToDocx(docxPath: string, markers: TrackChangeMarker[], author?: string): Promise<void>;
-export function buildWithTrackChanges(markdownPath: string, outputPath: string, options?: object): Promise<{ success: boolean; message: string }>;
-
-// ============================================
-// Spelling (lib/spelling.js)
-// ============================================
-
-export interface SpellingIssue {
-  word: string;
-  line: number;
-  column: number;
-  file?: string;
-  suggestions?: string[];
-}
-
-export interface SpellingResult {
-  misspelled: SpellingIssue[];
-  possibleNames: SpellingIssue[];
-}
-
-export function getGlobalDictPath(): string;
-export function getProjectDictPath(directory?: string): string;
-export function loadDictionaryFile(dictPath: string): Set<string>;
-export function saveDictionaryFile(words: Set<string>, dictPath: string): void;
-export function loadAllCustomWords(projectDir?: string): Set<string>;
-export function addWord(word: string, global?: boolean, projectDir?: string): boolean;
-export function removeWord(word: string, global?: boolean, projectDir?: string): boolean;
-export function listWords(global?: boolean, projectDir?: string): string[];
-export function getSpellchecker(projectDir?: string, lang?: 'en' | 'en-gb'): Promise<object>;
-export function clearCache(): void;
-export function extractWords(text: string): Array<{ word: string; line: number; column: number }>;
-export function checkSpelling(text: string, options?: { projectDir?: string; lang?: 'en' | 'en-gb' }): Promise<SpellingResult>;
-export function checkFile(filePath: string, options?: { projectDir?: string; lang?: 'en' | 'en-gb' }): Promise<SpellingResult>;
+/**
+ * TypeScript type definitions for docrev
+ */
+
+// ============================================
+// Annotations (lib/annotations.js)
+// ============================================
+
+export interface Annotation {
+  type: 'insert' | 'delete' | 'substitute' | 'comment' | 'highlight';
+  match: string;
+  content: string;
+  replacement?: string;
+  author?: string;
+  position: number;
+  line: number;
+  before?: string;
+  after?: string;
+}
+
+export interface Comment extends Annotation {
+  type: 'comment';
+  author: string;
+  resolved: boolean;
+}
+
+export interface AnnotationCounts {
+  inserts: number;
+  deletes: number;
+  substitutes: number;
+  comments: number;
+  total: number;
+}
+
+export interface StripOptions {
+  keepComments?: boolean;
+}
+
+export interface CommentFilterOptions {
+  pendingOnly?: boolean;
+  resolvedOnly?: boolean;
+}
+
+export function parseAnnotations(text: string): Annotation[];
+export function stripAnnotations(text: string, options?: StripOptions): string;
+export function applyDecision(text: string, annotation: Annotation, accept: boolean): string;
+export function getTrackChanges(text: string): Annotation[];
+export function getComments(text: string, options?: CommentFilterOptions): Comment[];
+export function setCommentStatus(text: string, comment: Comment, resolved: boolean): string;
+export function countAnnotations(text: string): AnnotationCounts;
+
+// ============================================
+// Build (lib/build.js)
+// ============================================
+
+export interface BuildConfig {
+  title?: string;
+  authors?: Author[];
+  sections?: string[];
+  bibliography?: string;
+  csl?: string;
+  crossref?: CrossrefConfig;
+  pdf?: PdfConfig;
+  docx?: DocxConfig;
+}
+
+export interface Author {
+  name: string;
+  affiliation?: string;
+  email?: string;
+  orcid?: string;
+}
+
+export interface CrossrefConfig {
+  figureTitle?: string;
+  tableTitle?: string;
+  figPrefix?: string | string[];
+  tblPrefix?: string | string[];
+}
+
+export interface PdfConfig {
+  documentclass?: string;
+  fontsize?: string;
+  geometry?: string;
+  linestretch?: number;
+  toc?: boolean;
+}
+
+export interface DocxConfig {
+  reference?: string;
+  keepComments?: boolean;
+  toc?: boolean;
+}
+
+export interface BuildResult {
+  format: string;
+  output: string;
+  success: boolean;
+  error?: string;
+}
+
+export function loadConfig(directory?: string): BuildConfig;
+export function findSections(directory: string, config: BuildConfig): string[];
+export function combineSections(files: string[], options?: object): string;
+export function build(formats?: string[], options?: object): Promise<BuildResult[]>;
+export function hasPandoc(): Promise<boolean>;
+export function hasPandocCrossref(): Promise<boolean>;
+
+// ============================================
+// Citations (lib/citations.js)
+// ============================================
+
+export interface Citation {
+  key: string;
+  line: number;
+  file: string;
+}
+
+export interface CitationValidation {
+  valid: Citation[];
+  missing: Citation[];
+  unused: string[];
+  duplicates: Array<{ key: string; count: number; locations: Citation[] }>;
+}
+
+export interface CitationStats {
+  totalCitations: number;
+  uniqueCited: number;
+  valid: number;
+  missing: number;
+  missingKeys: string[];
+  bibEntries: number;
+  unused: number;
+  unusedKeys: string[];
+}
+
+export function extractCitations(text: string, file?: string): Citation[];
+export function parseBibFile(bibPath: string): Set<string>;
+export function validateCitations(mdFiles: string[], bibPath: string): CitationValidation;
+export function getCitationStats(mdFiles: string[], bibPath: string): CitationStats;
+
+// ============================================
+// Crossref (lib/crossref.js)
+// ============================================
+
+export interface RefNumber {
+  num: number;
+  isSupp: boolean;
+  suffix: string | null;
+}
+
+export interface HardcodedRef {
+  type: 'fig' | 'tbl' | 'eq';
+  match: string;
+  numbers: RefNumber[];
+  position: number;
+}
+
+export interface DynamicRef {
+  type: 'fig' | 'tbl' | 'eq';
+  label: string;
+  match: string;
+  position: number;
+}
+
+export interface FigureInfo {
+  label: string;
+  num: number;
+  isSupp: boolean;
+  file: string;
+}
+
+export interface Registry {
+  figures: Map<string, FigureInfo>;
+  tables: Map<string, FigureInfo>;
+  equations: Map<string, FigureInfo>;
+  byNumber: {
+    fig: Map<number, string>;
+    figS: Map<number, string>;
+    tbl: Map<number, string>;
+    tblS: Map<number, string>;
+    eq: Map<number, string>;
+  };
+}
+
+export interface RefStatus {
+  dynamic: DynamicRef[];
+  hardcoded: HardcodedRef[];
+  anchors: { figures: number; tables: number; equations: number };
+}
+
+export function normalizeType(typeStr: string): 'fig' | 'tbl' | 'eq' | string;
+export function parseRefNumber(numStr: string, suffix?: string): RefNumber;
+export function parseReferenceList(listStr: string): RefNumber[];
+export function buildRegistry(directory: string, excludeFiles?: string[]): Registry;
+export function labelToDisplay(type: string, label: string, registry: Registry): string | null;
+export function numberToLabel(type: string, num: number, isSupp: boolean, registry: Registry): string | null;
+export function detectHardcodedRefs(text: string): HardcodedRef[];
+export function detectDynamicRefs(text: string): DynamicRef[];
+export function convertHardcodedRefs(text: string, registry: Registry): { converted: string; conversions: Array<{ from: string; to: string }>; warnings: string[] };
+export function getRefStatus(text: string, registry: Registry): RefStatus;
+
+// ============================================
+// DOI (lib/doi.js)
+// ============================================
+
+export interface BibEntry {
+  key: string;
+  type: string;
+  doi: string | null;
+  title: string;
+  authorRaw: string;
+  year: number | null;
+  journal: string;
+  skip: boolean;
+  expectDoi: boolean;
+  noDoi: boolean;
+  line: number;
+}
+
+export interface DoiCheckResult {
+  valid: boolean;
+  source?: 'crossref' | 'datacite';
+  metadata?: {
+    title: string;
+    authors: string[];
+    year: number;
+    journal: string;
+    type?: string;
+  };
+  error?: string;
+}
+
+export interface BibtexFetchResult {
+  success: boolean;
+  bibtex?: string;
+  error?: string;
+}
+
+export interface DoiLookupResult {
+  found: boolean;
+  doi?: string;
+  confidence?: 'low' | 'medium' | 'high';
+  score?: number;
+  metadata?: {
+    title: string;
+    authors: string[];
+    year: number;
+    journal: string;
+  };
+  alternatives?: Array<{
+    doi: string;
+    title: string;
+    score: number;
+  }>;
+  error?: string;
+}
+
+export interface BibCheckResult {
+  entries: Array<BibEntry & { status: string; message?: string; metadata?: object }>;
+  valid: number;
+  invalid: number;
+  missing: number;
+  skipped: number;
+}
+
+export function parseBibEntries(bibPath: string): BibEntry[];
+export function isValidDoiFormat(doi: string): boolean;
+export function checkDoi(doi: string): Promise<DoiCheckResult>;
+export function fetchBibtex(doi: string): Promise<BibtexFetchResult>;
+export function checkBibDois(bibPath: string, options?: { checkMissing?: boolean; parallel?: number }): Promise<BibCheckResult>;
+export function lookupDoi(title: string, author?: string, year?: number, journal?: string): Promise<DoiLookupResult>;
+export function lookupMissingDois(bibPath: string, options?: { parallel?: number; onProgress?: (current: number, total: number) => void }): Promise<Array<{ key: string; title: string; type: string; journal: string; result: DoiLookupResult }>>;
+export function addToBib(bibPath: string, bibtex: string): { success: boolean; key?: string; error?: string };
+
+// ============================================
+// Equations (lib/equations.js)
+// ============================================
+
+export interface Equation {
+  type: 'inline' | 'display';
+  content: string;
+  line: number;
+  file: string;
+}
+
+export interface EquationStats {
+  total: number;
+  display: number;
+  inline: number;
+  byFile: Array<{ file: string; display: number; inline: number }>;
+}
+
+export interface WordEquationResult {
+  success: boolean;
+  equations: Array<{
+    type: 'inline' | 'display' | 'unknown';
+    latex: string | null;
+    position: number;
+    line?: number;
+    raw?: string;
+    error?: string;
+  }>;
+  error?: string;
+}
+
+export function extractEquations(text: string, file?: string): Equation[];
+export function generateEquationSheet(equations: Equation[]): string;
+export function convertToWord(inputPath: string, outputPath: string, options?: { preserveLatex?: boolean }): Promise<{ success: boolean; message: string }>;
+export function createEquationsDoc(inputPath: string, outputPath: string): Promise<{ success: boolean; message: string; stats: { display: number; inline: number } | null }>;
+export function getEquationStats(files: string[]): EquationStats;
+export function extractEquationsFromWord(docxPath: string): Promise<WordEquationResult>;
+export function getWordEquationStats(docxPath: string): Promise<{ count: number; display: number; inline: number; converted: number; error?: string }>;
+
+// ============================================
+// Git (lib/git.js)
+// ============================================
+
+export interface FileChange {
+  added: number;
+  removed: number;
+  changes: Array<{ added: boolean; removed: boolean; value: string }>;
+}
+
+export interface CommitInfo {
+  hash: string;
+  date: string;
+  author: string;
+  message: string;
+}
+
+export function isGitRepo(directory?: string): boolean;
+export function getCurrentBranch(directory?: string): string | null;
+export function getDefaultBranch(directory?: string): string;
+export function getFileAtRef(filePath: string, ref: string): string | null;
+export function getChangedFiles(fromRef: string, toRef?: string): string[];
+export function getFileHistory(filePath: string, limit?: number): CommitInfo[];
+export function compareFileVersions(filePath: string, fromRef: string, toRef?: string): FileChange;
+export function getWordCountDiff(filePath: string, fromRef: string, toRef?: string): { before: number; after: number; diff: number };
+export function getRecentCommits(directory?: string, limit?: number): CommitInfo[];
+export function hasUncommittedChanges(directory?: string): boolean;
+export function getTags(directory?: string): string[];
+
+// ============================================
+// Journals (lib/journals.js)
+// ============================================
+
+export interface JournalProfile {
+  name: string;
+  url: string;
+  requirements: {
+    wordLimit?: { main: number; abstract?: number };
+    references?: { max?: number; doiRequired?: boolean };
+    figures?: { max?: number };
+    tables?: { max?: number };
+    sections?: string[];
+    formatting?: object;
+  };
+}
+
+export interface ValidationResult {
+  journal: string;
+  valid: boolean;
+  wordCount: { main: number; abstract: number; limit: { main: number; abstract: number } };
+  figures: { count: number; max: number };
+  tables: { count: number; max: number };
+  references: { count: number; max: number };
+  sections: { found: string[]; missing: string[]; required: string[] };
+  errors: string[];
+  warnings: string[];
+}
+
+export function listJournals(): Array<{ id: string; name: string; url: string }>;
+export function getJournalProfile(journalId: string): JournalProfile | null;
+export function validateManuscript(text: string, journalId: string, options?: { bibPath?: string }): ValidationResult;
+export function validateProject(directory: string, journalId: string): Promise<ValidationResult>;
+
+// ============================================
+// Merge (lib/merge.js)
+// ============================================
+
+export interface ReviewerChange {
+  reviewer: string;
+  type: 'insert' | 'delete' | 'replace';
+  start: number;
+  end: number;
+  oldText: string;
+  newText: string;
+}
+
+export interface Conflict {
+  start: number;
+  end: number;
+  original: string;
+  changes: ReviewerChange[];
+}
+
+export interface MergeResult {
+  merged: string;
+  conflicts: Conflict[];
+  stats: {
+    reviewers: number;
+    totalChanges: number;
+    nonConflicting: number;
+    conflicts: number;
+    comments: number;
+  };
+  originalText: string;
+}
+
+export function extractChanges(originalText: string, wordText: string, reviewer: string): ReviewerChange[];
+export function detectConflicts(allChanges: ReviewerChange[][]): { conflicts: Conflict[]; nonConflicting: ReviewerChange[] };
+export function applyChanges(originalText: string, changes: ReviewerChange[]): string;
+export function applyChangesAsAnnotations(originalText: string, changes: ReviewerChange[]): string;
+export function formatConflict(conflict: Conflict, originalText: string): string;
+export function mergeReviewerDocs(originalPath: string, reviewerDocs: Array<{ path: string; name: string }>, options?: { autoResolve?: boolean }): Promise<MergeResult>;
+export function resolveConflict(text: string, conflict: Conflict, choice: number, originalText: string): string;
+
+// ============================================
+// Sections (lib/sections.js)
+// ============================================
+
+export interface SectionConfig {
+  header: string;
+  aliases?: string[];
+  order?: number;
+}
+
+export interface SectionsConfig {
+  version: number;
+  description?: string;
+  sections: Record<string, SectionConfig>;
+}
+
+export interface ExtractedSection {
+  file: string;
+  header: string;
+  content: string;
+  matched: boolean;
+}
+
+export function extractHeader(filePath: string): string | null;
+export function generateConfig(directory: string, excludePatterns?: string[]): SectionsConfig;
+export function loadConfig(configPath: string): SectionsConfig;
+export function saveConfig(configPath: string, config: SectionsConfig): void;
+export function matchHeading(heading: string, sections: Record<string, SectionConfig>): { file: string; config: SectionConfig } | null;
+export function extractSectionsFromText(text: string, sections: Record<string, SectionConfig>): ExtractedSection[];
+export function splitAnnotatedPaper(paperContent: string, sections: Record<string, SectionConfig>): Map<string, string>;
+export function getOrderedSections(config: SectionsConfig): string[];
+
+// ============================================
+// Word (lib/word.js)
+// ============================================
+
+export interface WordComment {
+  id: string;
+  author: string;
+  date: string;
+  text: string;
+}
+
+export interface WordMetadata {
+  title?: string;
+  author?: string;
+  created?: string;
+  modified?: string;
+}
+
+export interface CommentAnchor {
+  text: string;
+  context: string;
+}
+
+export function extractWordComments(docxPath: string): Promise<WordComment[]>;
+export function extractCommentAnchors(docxPath: string): Promise<Map<string, CommentAnchor>>;
+export function extractTextFromWord(docxPath: string): Promise<string>;
+export function extractFromWord(docxPath: string): Promise<{ text: string; html: string }>;
+export function getWordMetadata(docxPath: string): Promise<WordMetadata>;
+export function isWordDocument(filePath: string): boolean;
+
+// ============================================
+// TrackChanges (lib/trackchanges.js)
+// ============================================
+
+export interface NativeTrackChangeStats {
+  insertions: number;
+  deletions: number;
+  substitutions: number;
+}
+
+export function criticToNativeTrackChanges(
+  text: string,
+  options?: { author?: string; date?: string }
+): { text: string; stats: NativeTrackChangeStats };
+export function enableTrackRevisions(docxPath: string): void;
+export function buildWithTrackChanges(
+  markdownPath: string,
+  outputPath: string,
+  options?: { author?: string; date?: string }
+): Promise<{ success: boolean; message: string; stats?: NativeTrackChangeStats }>;
+
+// ============================================
+// Spelling (lib/spelling.js)
+// ============================================
+
+export interface SpellingIssue {
+  word: string;
+  line: number;
+  column: number;
+  file?: string;
+  suggestions?: string[];
+}
+
+export interface SpellingResult {
+  misspelled: SpellingIssue[];
+  possibleNames: SpellingIssue[];
+}
+
+export function getGlobalDictPath(): string;
+export function getProjectDictPath(directory?: string): string;
+export function loadDictionaryFile(dictPath: string): Set<string>;
+export function saveDictionaryFile(words: Set<string>, dictPath: string): void;
+export function loadAllCustomWords(projectDir?: string): Set<string>;
+export function addWord(word: string, global?: boolean, projectDir?: string): boolean;
+export function removeWord(word: string, global?: boolean, projectDir?: string): boolean;
+export function listWords(global?: boolean, projectDir?: string): string[];
+export function getSpellchecker(projectDir?: string, lang?: 'en' | 'en-gb'): Promise<object>;
+export function clearCache(): void;
+export function extractWords(text: string): Array<{ word: string; line: number; column: number }>;
+export function checkSpelling(text: string, options?: { projectDir?: string; lang?: 'en' | 'en-gb' }): Promise<SpellingResult>;
+export function checkFile(filePath: string, options?: { projectDir?: string; lang?: 'en' | 'en-gb' }): Promise<SpellingResult>;