@ncukondo/reference-manager 0.5.1 → 0.5.3

package/dist/chunks/index-Bl_mOQRe.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index-Bl_mOQRe.js","sources":["../../src/features/operations/update.ts","../../src/config/csl-styles.ts","../../src/features/import/cache.ts","../../src/features/import/normalizer.ts","../../src/features/import/detector.ts","../../src/features/import/rate-limiter.ts","../../src/features/import/fetcher.ts","../../src/features/import/parser.ts","../../src/features/import/importer.ts","../../src/features/operations/add.ts","../../src/features/format/pretty.ts","../../src/features/format/bibtex.ts","../../src/features/format/citation-fallback.ts","../../src/features/format/citation-csl.ts","../../src/features/operations/cite.ts","../../src/features/operations/list.ts","../../src/features/operations/remove.ts","../../src/features/operations/search.ts","../../src/server/routes/add.ts","../../src/server/routes/cite.ts","../../src/server/routes/health.ts","../../src/server/routes/list.ts","../../src/server/routes/references.ts","../../src/server/routes/search.ts","../../src/server/index.ts"],"sourcesContent":["import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../core/library-interface.js\";\n\n/**\n * Options for updateReference operation\n */\nexport interface UpdateOperationOptions {\n  /** Reference ID or UUID */\n  identifier: string;\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType;\n  /** Partial updates to apply to the reference */\n  updates: Partial<CslItem>;\n  /** How to handle ID collision: 'fail' (default) or 'suffix' */\n  onIdCollision?: \"fail\" | \"suffix\";\n}\n\n/**\n * Result of updateReference operation\n */\nexport interface UpdateOperationResult {\n  /** Whether the update was successful */\n  updated: boolean;\n  /** The updated item (if successful) */\n  item?: CslItem;\n  /** True if ID collision occurred (only when updated=false and onIdCollision='fail') */\n  idCollision?: boolean;\n  /** True if the ID was changed due to collision resolution */\n  idChanged?: boolean;\n  /** The new ID after collision resolution (only when idChanged=true) */\n  newId?: string;\n}\n\n/**\n * Update a reference in the library.\n *\n * @param library - The library to update\n * @param options - Update options including identifier, updates, and collision handling\n * @returns Result indicating success and the updated item\n */\nexport async function updateReference(\n  library: ILibrary,\n  options: UpdateOperationOptions\n): Promise<UpdateOperationResult> {\n  const { identifier, idType = \"id\", updates, onIdCollision = \"fail\" } = options;\n\n  // Update the reference using unified update() method\n  const updateResult = await library.update(identifier, updates, { idType, onIdCollision });\n\n  if (!updateResult.updated) {\n    const result: UpdateOperationResult = { updated: false };\n    if (updateResult.idCollision) {\n      result.idCollision = true;\n    }\n    return result;\n  }\n\n  // Save the library\n  await library.save();\n\n  // Build result from UpdateResult (item is now included)\n  const result: UpdateOperationResult = { updated: true };\n\n  if (updateResult.item) {\n    result.item = updateResult.item;\n  }\n\n  if (updateResult.idChanged && updateResult.newId) {\n    result.idChanged = true;\n    result.newId = updateResult.newId;\n  }\n\n  return result;\n}\n","/**\n * CSL Style Management\n *\n * Handles resolution and loading of CSL (Citation Style Language) style files.\n *\n * Style Resolution Order:\n * 1. --csl-file <path> (exact file path)\n * 2. Built-in style matching --style <name>\n * 3. Search in csl_directory paths (in array order)\n * 4. Default style from config (default_style)\n * 5. \"apa\" (hardcoded default)\n */\n\nimport * as fs from \"node:fs\";\nimport * as path from \"node:path\";\n\n/**\n * Built-in styles available in @citation-js/plugin-csl\n * These can be used directly without loading external files\n */\nexport const BUILTIN_STYLES = [\"apa\", \"vancouver\", \"harvard\"] as const;\n\nexport type BuiltinStyleName = (typeof BUILTIN_STYLES)[number];\n\n/**\n * Check if a style name is a built-in style\n */\nexport function isBuiltinStyle(styleName: string): styleName is BuiltinStyleName {\n  return BUILTIN_STYLES.includes(styleName as BuiltinStyleName);\n}\n\nexport interface StyleResolutionOptions {\n  /**\n   * Exact path to CSL file (from --csl-file option)\n   * Takes highest priority\n   */\n  cslFile?: string;\n\n  /**\n   * Style name to resolve (from --style option)\n   */\n  style?: string;\n\n  /**\n   * Directory or directories to search for custom CSL files\n   * (from csl_directory config)\n   * Can be a single string or array of strings\n   */\n  cslDirectory?: string | string[];\n\n  /**\n   * Default style to use if specified style not found\n   * (from default_style config)\n   */\n  defaultStyle?: string;\n}\n\nexport interface StyleResolution {\n  /**\n   * Type of resolution: \"builtin\" for citation-js built-in styles,\n   * \"custom\" for external CSL files\n   */\n  type: \"builtin\" | \"custom\";\n\n  /**\n   * The resolved style name (for built-in) or identifier (for custom)\n   */\n  styleName: string;\n\n  /**\n   * CSL XML content (only for custom styles)\n   */\n  styleXml?: string;\n}\n\n/**\n * Expand tilde (~) in path to home directory\n */\nfunction expandTilde(filePath: string): string {\n  if (filePath.startsWith(\"~/\")) {\n    const home = process.env.HOME || process.env.USERPROFILE || \"\";\n    return path.join(home, filePath.slice(2));\n  }\n  return filePath;\n}\n\n/**\n * Load CSL style file content from the given path\n *\n * @param stylePath - Path to the CSL style file\n * @returns Content of the CSL style file (XML string)\n * @throws Error if file cannot be read\n */\nexport function loadCSLStyleFile(stylePath: string): string {\n  return fs.readFileSync(stylePath, \"utf-8\");\n}\n\n/**\n * Resolve the style based on resolution options\n *\n * Resolution order:\n * 1. cslFile (exact path) - throws if doesn't exist\n * 2. Built-in style matching style name\n * 3. Search in csl_directory paths (in order)\n * 4. Default style (defaultStyle) - if built-in\n * 5. \"apa\" (hardcoded fallback)\n *\n * @param options - Style resolution options\n * @returns StyleResolution with type, styleName, and optional styleXml\n * @throws Error if cslFile is specified but doesn't exist\n */\nexport function resolveStyle(options: StyleResolutionOptions): StyleResolution {\n  const { cslFile, style, cslDirectory, defaultStyle } = options;\n\n  // 1. If cslFile is specified, use it (highest priority)\n  if (cslFile) {\n    if (!fs.existsSync(cslFile)) {\n      throw new Error(`CSL file '${cslFile}' not found`);\n    }\n    const styleXml = loadCSLStyleFile(cslFile);\n    const styleName = path.basename(cslFile, \".csl\");\n    return {\n      type: \"custom\",\n      styleName,\n      styleXml,\n    };\n  }\n\n  // Determine which style name to try\n  const styleToResolve = style || defaultStyle || \"apa\";\n\n  // 2. Check if it's a built-in style\n  if (isBuiltinStyle(styleToResolve)) {\n    return {\n      type: \"builtin\",\n      styleName: styleToResolve,\n    };\n  }\n\n  // 3. Search in csl_directory paths\n  if (cslDirectory) {\n    const directories = Array.isArray(cslDirectory) ? cslDirectory : [cslDirectory];\n\n    for (const dir of directories) {\n      const expandedDir = expandTilde(dir);\n      const stylePath = path.join(expandedDir, `${styleToResolve}.csl`);\n\n      if (fs.existsSync(stylePath)) {\n        const styleXml = loadCSLStyleFile(stylePath);\n        return {\n          type: \"custom\",\n          styleName: styleToResolve,\n          styleXml,\n        };\n      }\n    }\n  }\n\n  // 4. Fall back to default style if it's built-in\n  if (defaultStyle && isBuiltinStyle(defaultStyle)) {\n    return {\n      type: \"builtin\",\n      styleName: defaultStyle,\n    };\n  }\n\n  // 5. Fall back to apa (hardcoded default)\n  return {\n    type: \"builtin\",\n    styleName: \"apa\",\n  };\n}\n","/**\n * Response cache for PMID and DOI metadata\n *\n * In-memory cache with TTL to avoid redundant API calls.\n * - Per ADR-001: No persistent cache files on disk\n * - Cache is warm during interactive sessions (server mode)\n * - CLI invocations start fresh\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\n\n/** Default TTL: 1 hour */\nconst DEFAULT_TTL_MS = 60 * 60 * 1000;\n\n/**\n * Cache configuration\n */\nexport interface CacheConfig {\n  /** Time-to-live in milliseconds (default: 1 hour) */\n  ttlMs?: number;\n}\n\n/**\n * Cache entry with timestamp and TTL\n */\ninterface CacheEntry {\n  item: CslItem;\n  cachedAt: number;\n  ttlMs: number;\n}\n\n/** PMID cache: Map<pmid, CacheEntry> */\nconst pmidCache = new Map<string, CacheEntry>();\n\n/** DOI cache: Map<doi, CacheEntry> */\nconst doiCache = new Map<string, CacheEntry>();\n\n/** ISBN cache: Map<isbn, CacheEntry> */\nconst isbnCache = new Map<string, CacheEntry>();\n\n/**\n * Check if a cache entry is still valid\n */\nfunction isEntryValid(entry: CacheEntry): boolean {\n  const now = Date.now();\n  return now - entry.cachedAt < entry.ttlMs;\n}\n\n/**\n * Get item from cache if valid\n */\nfunction getFromCache(cache: Map<string, CacheEntry>, key: string): CslItem | undefined {\n  const entry = cache.get(key);\n  if (!entry) {\n    return undefined;\n  }\n  if (!isEntryValid(entry)) {\n    cache.delete(key);\n    return undefined;\n  }\n  return entry.item;\n}\n\n/**\n * Store item in cache\n */\nfunction storeInCache(\n  cache: Map<string, CacheEntry>,\n  key: string,\n  item: CslItem,\n  config?: CacheConfig\n): void {\n  const ttlMs = config?.ttlMs ?? DEFAULT_TTL_MS;\n  cache.set(key, {\n    item,\n    cachedAt: Date.now(),\n    ttlMs,\n  });\n}\n\n/**\n * Get cached PMID result\n */\nexport function getPmidFromCache(pmid: string): CslItem | undefined {\n  return getFromCache(pmidCache, pmid);\n}\n\n/**\n * Cache PMID result\n */\nexport function cachePmidResult(pmid: string, item: CslItem, config?: CacheConfig): void {\n  storeInCache(pmidCache, pmid, item, config);\n}\n\n/**\n * Get cached DOI result\n */\nexport function getDoiFromCache(doi: string): CslItem | undefined {\n  return getFromCache(doiCache, doi);\n}\n\n/**\n * Cache DOI result\n */\nexport function cacheDoiResult(doi: string, item: CslItem, config?: CacheConfig): void {\n  storeInCache(doiCache, doi, item, config);\n}\n\n/**\n * Get cached ISBN result\n */\nexport function getIsbnFromCache(isbn: string): CslItem | undefined {\n  return getFromCache(isbnCache, isbn);\n}\n\n/**\n * Cache ISBN result\n */\nexport function cacheIsbnResult(isbn: string, item: CslItem, config?: CacheConfig): void {\n  storeInCache(isbnCache, isbn, item, config);\n}\n\n/**\n * Reset all caches (for test isolation)\n */\nexport function resetCache(): void {\n  pmidCache.clear();\n  doiCache.clear();\n  isbnCache.clear();\n}\n","/**\n * DOI normalizer module\n *\n * Normalizes DOI identifiers by:\n * - Removing URL prefixes (doi.org, dx.doi.org)\n * - Trimming whitespace\n */\n\n/**\n * URL prefixes to remove from DOI\n */\nconst DOI_URL_PREFIXES = [\n  \"https://doi.org/\",\n  \"http://doi.org/\",\n  \"https://dx.doi.org/\",\n  \"http://dx.doi.org/\",\n];\n\n/**\n * Normalize a DOI identifier\n *\n * @param doi - DOI string, possibly with URL prefix\n * @returns Normalized DOI (10.xxx/xxx format)\n */\nexport function normalizeDoi(doi: string): string {\n  // Trim whitespace\n  const trimmed = doi.trim();\n\n  if (!trimmed) {\n    return \"\";\n  }\n\n  // Check for URL prefixes (case-insensitive)\n  const lowerInput = trimmed.toLowerCase();\n\n  for (const prefix of DOI_URL_PREFIXES) {\n    if (lowerInput.startsWith(prefix.toLowerCase())) {\n      // Remove the prefix while preserving the original case of the DOI\n      return trimmed.slice(prefix.length);\n    }\n  }\n\n  // No prefix found, return as-is\n  return trimmed;\n}\n\n/**\n * Normalizes a PMID by removing the optional \"PMID:\" prefix and trimming whitespace.\n *\n * Supported formats:\n * - \"12345678\" -> \"12345678\"\n * - \"PMID:12345678\" -> \"12345678\"\n * - \"pmid:12345678\" -> \"12345678\"\n * - \"PMID: 12345678\" -> \"12345678\" (space after colon)\n *\n * @param pmid - The PMID string to normalize\n * @returns The normalized PMID (digits only) or empty string if invalid\n */\nexport function normalizePmid(pmid: string): string {\n  // Trim whitespace\n  const trimmed = pmid.trim();\n\n  if (!trimmed) {\n    return \"\";\n  }\n\n  // Remove \"PMID:\" prefix (case-insensitive, optional whitespace after colon)\n  const normalized = trimmed.replace(/^pmid:\\s*/i, \"\");\n\n  return normalized.trim();\n}\n\n/**\n * Normalizes an ISBN by removing the \"ISBN:\" prefix, hyphens, spaces, and uppercasing X.\n *\n * Supported formats:\n * - \"ISBN:978-4-00-000000-0\" -> \"9784000000000\"\n * - \"isbn:4-00-000000-0\" -> \"4000000000\"\n * - \"ISBN: 978 4 00 000000 0\" -> \"9784000000000\"\n * - \"ISBN:400000000x\" -> \"400000000X\" (uppercase X)\n *\n * @param isbn - The ISBN string to normalize\n * @returns The normalized ISBN (digits only, X uppercase at end for ISBN-10) or empty string if invalid\n */\nexport function normalizeIsbn(isbn: string): string {\n  // Trim whitespace\n  const trimmed = isbn.trim();\n\n  if (!trimmed) {\n    return \"\";\n  }\n\n  // Check for ISBN: prefix (case-insensitive)\n  if (!/^isbn:/i.test(trimmed)) {\n    return \"\";\n  }\n\n  // Remove \"ISBN:\" prefix (case-insensitive, optional whitespace after colon)\n  let normalized = trimmed.replace(/^isbn:\\s*/i, \"\");\n\n  // Remove hyphens and spaces\n  normalized = normalized.replace(/[-\\s]/g, \"\");\n\n  // Uppercase X (for ISBN-10 check digit)\n  normalized = normalized.toUpperCase();\n\n  return normalized;\n}\n","/**\n * Format detection module for multi-format import\n *\n * Detects input format based on:\n * - File extension (.json, .bib, .ris)\n * - Content patterns (JSON, BibTeX, RIS)\n * - Identifier patterns (PMID, DOI)\n * - Multiple whitespace-separated identifiers\n */\n\nimport { normalizeIsbn, normalizePmid } from \"./normalizer.js\";\n\n/**\n * Supported input formats\n */\nexport type InputFormat =\n  | \"json\"\n  | \"bibtex\"\n  | \"ris\"\n  | \"pmid\"\n  | \"doi\"\n  | \"isbn\"\n  | \"identifiers\"\n  | \"unknown\";\n\n/**\n * Extension to format mapping\n */\nconst EXTENSION_MAP: Record<string, InputFormat> = {\n  \".json\": \"json\",\n  \".bib\": \"bibtex\",\n  \".ris\": \"ris\",\n};\n\n/**\n * DOI URL prefixes to strip\n */\nconst DOI_URL_PREFIXES = [\n  \"https://doi.org/\",\n  \"http://doi.org/\",\n  \"https://dx.doi.org/\",\n  \"http://dx.doi.org/\",\n];\n\n/**\n * Detect the format of the given input\n *\n * @param input - File path, identifier, or empty string for stdin\n * @param content - Optional content to analyze (for stdin or unknown extension)\n * @returns Detected format\n */\nexport function detectFormat(input: string, content?: string): InputFormat {\n  // 1. Try extension-based detection first\n  const extFormat = detectByExtension(input);\n  if (extFormat !== \"unknown\") {\n    return extFormat;\n  }\n\n  // 2. If content provided, try content-based detection\n  if (content !== undefined) {\n    const contentFormat = detectByContent(content);\n    if (contentFormat !== \"unknown\") {\n      return contentFormat;\n    }\n  }\n\n  // 3. Try identifier detection on input string\n  if (input.length > 0) {\n    const identifierFormat = detectIdentifier(input);\n    if (identifierFormat !== \"unknown\") {\n      return identifierFormat;\n    }\n  }\n\n  return \"unknown\";\n}\n\n/**\n * Detect format based on file extension\n */\nexport function detectByExtension(input: string): InputFormat {\n  if (!input) return \"unknown\";\n\n  // Extract extension (last dot and onwards)\n  const dotIndex = input.lastIndexOf(\".\");\n  if (dotIndex === -1 || dotIndex === input.length - 1) {\n    return \"unknown\";\n  }\n\n  const ext = input.slice(dotIndex).toLowerCase();\n  return EXTENSION_MAP[ext] ?? \"unknown\";\n}\n\n/**\n * Detect format based on content patterns\n */\nexport function detectByContent(content: string): InputFormat {\n  const trimmed = content.trim();\n  if (!trimmed) return \"unknown\";\n\n  // JSON: starts with [ or {\n  if (trimmed.startsWith(\"[\") || trimmed.startsWith(\"{\")) {\n    return \"json\";\n  }\n\n  // BibTeX: starts with @\n  if (trimmed.startsWith(\"@\")) {\n    return \"bibtex\";\n  }\n\n  // RIS: starts with TY  - (tag format)\n  if (trimmed.startsWith(\"TY  -\")) {\n    return \"ris\";\n  }\n\n  // Check if content is multiple identifiers\n  return detectIdentifier(trimmed);\n}\n\n/**\n * Detect if input is an identifier (PMID, DOI, ISBN) or multiple identifiers\n */\nfunction detectIdentifier(input: string): InputFormat {\n  // Split by whitespace\n  const parts = input.split(/\\s+/).filter((p) => p.length > 0);\n\n  if (parts.length === 0) {\n    return \"unknown\";\n  }\n\n  // Check each part\n  const formats: (\"pmid\" | \"doi\" | \"isbn\")[] = [];\n  for (const part of parts) {\n    const format = detectSingleIdentifier(part);\n    if (format === \"unknown\") {\n      // If any part is not a valid identifier, return unknown\n      return \"unknown\";\n    }\n    formats.push(format);\n  }\n\n  // Single identifier returns its specific format\n  if (formats.length === 1) {\n    // formats[0] is guaranteed to exist when length === 1\n    return formats[0] as \"pmid\" | \"doi\" | \"isbn\";\n  }\n\n  // Multiple valid identifiers\n  return \"identifiers\";\n}\n\n/**\n * Detect if a single string is a PMID, DOI, or ISBN\n */\nexport function detectSingleIdentifier(input: string): \"pmid\" | \"doi\" | \"isbn\" | \"unknown\" {\n  // DOI: starts with 10. or is a DOI URL\n  if (isDoi(input)) {\n    return \"doi\";\n  }\n\n  // ISBN: requires ISBN: prefix\n  if (isIsbn(input)) {\n    return \"isbn\";\n  }\n\n  // PMID: numeric only (must be after ISBN check to avoid conflicts)\n  if (isPmid(input)) {\n    return \"pmid\";\n  }\n\n  return \"unknown\";\n}\n\n/**\n * Check if string is a valid DOI\n */\nexport function isDoi(input: string): boolean {\n  // Check DOI URL formats\n  for (const prefix of DOI_URL_PREFIXES) {\n    if (input.toLowerCase().startsWith(prefix.toLowerCase())) {\n      const remainder = input.slice(prefix.length);\n      return isDoiFormat(remainder);\n    }\n  }\n\n  // Check standard DOI format (10.xxx/xxx)\n  return isDoiFormat(input);\n}\n\n/**\n * Check if string is a valid DOI format (10.xxx/xxx)\n */\nfunction isDoiFormat(input: string): boolean {\n  // DOI starts with 10. followed by registrant code and suffix\n  // Pattern: 10.{registrant}/{suffix}\n  if (!input.startsWith(\"10.\")) {\n    return false;\n  }\n\n  // Must have content after 10.\n  if (input.length <= 3) {\n    return false;\n  }\n\n  // Must have a slash after registrant code\n  const slashIndex = input.indexOf(\"/\");\n  if (slashIndex === -1 || slashIndex <= 3) {\n    return false;\n  }\n\n  return true;\n}\n\n/**\n * Check if string is a valid PMID (numeric only)\n */\nexport function isPmid(input: string): boolean {\n  if (!input || input.length === 0) {\n    return false;\n  }\n\n  // Normalize input (removes PMID: prefix if present)\n  const normalized = normalizePmid(input);\n\n  if (!normalized) {\n    return false;\n  }\n\n  // PMID is all digits\n  return /^\\d+$/.test(normalized);\n}\n\n/**\n * Check if string is a valid ISBN (requires ISBN: prefix)\n *\n * ISBN must have ISBN: prefix and be either:\n * - ISBN-13: 13 digits\n * - ISBN-10: 10 digits (last may be X)\n */\nexport function isIsbn(input: string): boolean {\n  if (!input || input.length === 0) {\n    return false;\n  }\n\n  // Normalize input (removes ISBN: prefix if present, hyphens, spaces)\n  const normalized = normalizeIsbn(input);\n\n  if (!normalized) {\n    return false;\n  }\n\n  // Check length: ISBN-10 (10 chars) or ISBN-13 (13 chars)\n  if (normalized.length !== 10 && normalized.length !== 13) {\n    return false;\n  }\n\n  // ISBN-10: 9 digits + (digit or X)\n  if (normalized.length === 10) {\n    // First 9 must be digits, last can be digit or X\n    if (!/^\\d{9}[\\dX]$/.test(normalized)) {\n      return false;\n    }\n    return true;\n  }\n\n  // ISBN-13: all digits\n  if (!/^\\d{13}$/.test(normalized)) {\n    return false;\n  }\n\n  return true;\n}\n","/**\n * Rate limiter module for API calls\n *\n * Uses factory + lazy initialization singleton pattern:\n * - RateLimiter class: Delay-based rate limiting with configurable requests/second\n * - getRateLimiter(api, config): Returns singleton per API type\n * - resetRateLimiters(): Clears singletons for test isolation\n */\n\n/**\n * API types supported by the rate limiter\n */\nexport type ApiType = \"pubmed\" | \"crossref\" | \"isbn\";\n\n/**\n * Configuration for rate limiter\n */\nexport interface RateLimiterConfig {\n  pubmedApiKey?: string;\n}\n\n/**\n * Rate limiter interface\n */\nexport interface RateLimiter {\n  readonly requestsPerSecond: number;\n  readonly intervalMs: number;\n  readonly lastRequestTime: number;\n  acquire(): Promise<void>;\n}\n\n/**\n * Rate limit settings per API type\n */\nconst RATE_LIMITS = {\n  pubmed: {\n    withoutApiKey: 3, // 3 req/sec\n    withApiKey: 10, // 10 req/sec\n  },\n  crossref: 50, // 50 req/sec\n  isbn: 10, // 10 req/sec (conservative for Google Books API daily limit)\n} as const;\n\n/**\n * Internal rate limiter implementation\n */\nclass RateLimiterImpl implements RateLimiter {\n  readonly requestsPerSecond: number;\n  readonly intervalMs: number;\n  private _lastRequestTime = 0;\n  private _pending: Promise<void> = Promise.resolve();\n\n  constructor(requestsPerSecond: number) {\n    this.requestsPerSecond = requestsPerSecond;\n    this.intervalMs = 1000 / requestsPerSecond;\n  }\n\n  get lastRequestTime(): number {\n    return this._lastRequestTime;\n  }\n\n  async acquire(): Promise<void> {\n    // Chain onto pending promise to ensure sequential processing\n    this._pending = this._pending.then(() => this._acquireInternal());\n    return this._pending;\n  }\n\n  private async _acquireInternal(): Promise<void> {\n    const now = Date.now();\n    const elapsed = now - this._lastRequestTime;\n    const waitTime = Math.max(0, this.intervalMs - elapsed);\n\n    if (waitTime > 0 && this._lastRequestTime > 0) {\n      await this._delay(waitTime);\n    }\n\n    this._lastRequestTime = Date.now();\n  }\n\n  private _delay(ms: number): Promise<void> {\n    return new Promise((resolve) => setTimeout(resolve, ms));\n  }\n}\n\n/**\n * Singleton storage for rate limiters by API type\n */\nconst limiters = new Map<ApiType, RateLimiter>();\n\n/**\n * Create a new rate limiter instance\n */\nexport function createRateLimiter(options: {\n  requestsPerSecond: number;\n}): RateLimiter {\n  return new RateLimiterImpl(options.requestsPerSecond);\n}\n\n/**\n * Get singleton rate limiter for the specified API type\n *\n * Note: Configuration is only used on first call. Subsequent calls\n * return the existing singleton regardless of config changes.\n */\nexport function getRateLimiter(api: ApiType, config: RateLimiterConfig): RateLimiter {\n  const existing = limiters.get(api);\n  if (existing) {\n    return existing;\n  }\n\n  const requestsPerSecond = getRequestsPerSecond(api, config);\n  const limiter = createRateLimiter({ requestsPerSecond });\n  limiters.set(api, limiter);\n\n  return limiter;\n}\n\n/**\n * Determine requests per second based on API type and configuration\n */\nfunction getRequestsPerSecond(api: ApiType, config: RateLimiterConfig): number {\n  switch (api) {\n    case \"pubmed\":\n      return config.pubmedApiKey ? RATE_LIMITS.pubmed.withApiKey : RATE_LIMITS.pubmed.withoutApiKey;\n    case \"crossref\":\n      return RATE_LIMITS.crossref;\n    case \"isbn\":\n      return RATE_LIMITS.isbn;\n  }\n}\n\n/**\n * Reset all rate limiter singletons (for test isolation)\n */\nexport function resetRateLimiters(): void {\n  limiters.clear();\n}\n","/**\n * Fetcher module for PMID and DOI metadata retrieval\n *\n * - PMID: Uses PMC Citation Exporter API (returns CSL-JSON directly)\n * - DOI: Uses citation-js plugin-doi (Cite.async)\n */\n\nimport { Cite } from \"@citation-js/core\";\nimport \"@citation-js/plugin-doi\";\nimport \"@citation-js/plugin-isbn\";\nimport { type CslItem, CslItemSchema } from \"../../core/csl-json/types.js\";\nimport { getRateLimiter } from \"./rate-limiter.js\";\n\n/** PMC Citation Exporter API base URL */\nconst PMC_API_BASE = \"https://pmc.ncbi.nlm.nih.gov/api/ctxp/v1/pubmed/\";\n\n/** Default timeout for API requests (10 seconds) */\nconst DEFAULT_TIMEOUT_MS = 10000;\n\n/** DOI pattern for validation */\nconst DOI_PATTERN = /^10\\.\\d{4,}(?:\\.\\d+)*\\/\\S+$/;\n\n/**\n * PubMed configuration for API requests\n */\nexport interface PubmedConfig {\n  email?: string;\n  apiKey?: string;\n}\n\n/**\n * Result of fetching a single identifier\n */\nexport type FetchResult = { success: true; item: CslItem } | { success: false; error: string };\n\n/**\n * Result of fetching a PMID (includes pmid for tracking)\n */\nexport type PmidFetchResult =\n  | { pmid: string; success: true; item: CslItem }\n  | { pmid: string; success: false; error: string };\n\n/**\n * Results of fetching multiple PMIDs\n */\nexport type FetchResults = PmidFetchResult[];\n\n/**\n * Build PMC API URL with query parameters\n */\nfunction buildPmcUrl(pmids: string[], config: PubmedConfig): string {\n  const url = new URL(PMC_API_BASE);\n  url.searchParams.set(\"format\", \"csl\");\n\n  // Add each PMID as separate id parameter\n  for (const pmid of pmids) {\n    url.searchParams.append(\"id\", pmid);\n  }\n\n  if (config.email) {\n    url.searchParams.set(\"email\", config.email);\n  }\n  if (config.apiKey) {\n    url.searchParams.set(\"api_key\", config.apiKey);\n  }\n\n  return url.toString();\n}\n\n/**\n * Extract PMID from CSL-JSON item id field\n * PMC API returns id like \"pmid:12345678\"\n */\nfunction extractPmidFromId(id: string | undefined): string | undefined {\n  if (!id) return undefined;\n  const match = id.match(/^pmid:(\\d+)$/);\n  return match?.[1];\n}\n\n/**\n * Fetch metadata for multiple PMIDs from PMC Citation Exporter API\n *\n * Uses batch API endpoint: /api/ctxp/v1/pubmed/?format=csl&id=1&id=2\n */\n\n/**\n * Parse raw API items and build maps of found items and validation errors\n */\nfunction parseRawItems(rawItems: unknown[]): {\n  foundItems: Map<string, CslItem>;\n  validationErrors: Map<string, string>;\n} {\n  const foundItems = new Map<string, CslItem>();\n  const validationErrors = new Map<string, string>();\n\n  for (const rawItem of rawItems) {\n    const parseResult = CslItemSchema.safeParse(rawItem);\n    if (parseResult.success) {\n      const pmid = extractPmidFromId(parseResult.data.id);\n      if (pmid) {\n        foundItems.set(pmid, parseResult.data);\n      }\n    } else {\n      // Try to extract pmid even from invalid data for error reporting\n      const maybeId = (rawItem as { id?: string })?.id;\n      const pmid = extractPmidFromId(maybeId);\n      if (pmid) {\n        validationErrors.set(pmid, parseResult.error.message);\n      }\n    }\n  }\n\n  return { foundItems, validationErrors };\n}\n\n/**\n * Build fetch result for a single PMID\n */\nfunction buildPmidResult(\n  pmid: string,\n  foundItems: Map<string, CslItem>,\n  validationErrors: Map<string, string>\n): PmidFetchResult {\n  const item = foundItems.get(pmid);\n  if (item) {\n    return { pmid, success: true as const, item };\n  }\n  const validationError = validationErrors.get(pmid);\n  if (validationError) {\n    return {\n      pmid,\n      success: false as const,\n      error: `Invalid CSL-JSON data: ${validationError}`,\n    };\n  }\n  return {\n    pmid,\n    success: false as const,\n    error: `PMID ${pmid} not found`,\n  };\n}\n\nexport async function fetchPmids(pmids: string[], config: PubmedConfig): Promise<FetchResults> {\n  // Return empty array for empty input\n  if (pmids.length === 0) {\n    return [];\n  }\n\n  // Apply rate limiting\n  const rateLimiterConfig = config.apiKey ? { pubmedApiKey: config.apiKey } : {};\n  const rateLimiter = getRateLimiter(\"pubmed\", rateLimiterConfig);\n  await rateLimiter.acquire();\n\n  const url = buildPmcUrl(pmids, config);\n\n  try {\n    const response = await fetch(url, {\n      method: \"GET\",\n      signal: AbortSignal.timeout(DEFAULT_TIMEOUT_MS),\n    });\n\n    if (!response.ok) {\n      // Return error for all PMIDs\n      const errorMsg = `HTTP ${response.status}: ${response.statusText}`;\n      return pmids.map((pmid) => ({\n        pmid,\n        success: false as const,\n        error: errorMsg,\n      }));\n    }\n\n    const data = await response.json();\n\n    // Normalize response to array\n    const rawItems: unknown[] = Array.isArray(data) ? data : [data];\n\n    // Parse raw items and build results\n    const { foundItems, validationErrors } = parseRawItems(rawItems);\n\n    // Build results for each requested PMID\n    return pmids.map((pmid) => buildPmidResult(pmid, foundItems, validationErrors));\n  } catch (error) {\n    const errorMsg = error instanceof Error ? error.message : String(error);\n    return pmids.map((pmid) => ({\n      pmid,\n      success: false as const,\n      error: errorMsg,\n    }));\n  }\n}\n\n/**\n * Fetch metadata for a DOI using citation-js\n *\n * Uses @citation-js/plugin-doi for content negotiation\n */\nexport async function fetchDoi(doi: string): Promise<FetchResult> {\n  // Validate DOI format\n  if (!DOI_PATTERN.test(doi)) {\n    return {\n      success: false,\n      error: `Invalid DOI format: ${doi}`,\n    };\n  }\n\n  // Apply rate limiting (crossref)\n  const rateLimiter = getRateLimiter(\"crossref\", {});\n  await rateLimiter.acquire();\n\n  try {\n    // Use citation-js Cite.async for DOI resolution\n    const cite = await Cite.async(doi);\n    const rawItems = cite.get({ format: \"real\", type: \"json\" });\n\n    if (!rawItems || !Array.isArray(rawItems) || rawItems.length === 0) {\n      return {\n        success: false,\n        error: `No data returned for DOI ${doi}`,\n      };\n    }\n\n    // Validate using zod schema\n    const parseResult = CslItemSchema.safeParse(rawItems[0]);\n    if (!parseResult.success) {\n      return {\n        success: false,\n        error: `Invalid CSL-JSON data for DOI ${doi}: ${parseResult.error.message}`,\n      };\n    }\n\n    return { success: true, item: parseResult.data };\n  } catch (error) {\n    const errorMsg = error instanceof Error ? error.message : String(error);\n    return {\n      success: false,\n      error: errorMsg,\n    };\n  }\n}\n\n/** ISBN-10 pattern: 9 digits + (digit or X) */\nconst ISBN10_PATTERN = /^\\d{9}[\\dX]$/;\n\n/** ISBN-13 pattern: 13 digits */\nconst ISBN13_PATTERN = /^\\d{13}$/;\n\n/**\n * Fetch metadata for an ISBN using Google Books API via citation-js\n *\n * @param isbn - Normalized ISBN (10 or 13 digits, no hyphens)\n * @returns FetchResult with CSL-JSON item or error\n */\nexport async function fetchIsbn(isbn: string): Promise<FetchResult> {\n  // Validate ISBN format\n  if (!ISBN10_PATTERN.test(isbn) && !ISBN13_PATTERN.test(isbn)) {\n    return {\n      success: false,\n      error: `Invalid ISBN format: ${isbn}`,\n    };\n  }\n\n  // Apply rate limiting (google books - daily limit so we use a generic limiter)\n  const rateLimiter = getRateLimiter(\"isbn\", {});\n  await rateLimiter.acquire();\n\n  try {\n    // Use citation-js Cite.async for ISBN resolution\n    const cite = await Cite.async(isbn);\n    const rawItems = cite.get({ format: \"real\", type: \"json\" });\n\n    if (!rawItems || !Array.isArray(rawItems) || rawItems.length === 0) {\n      return {\n        success: false,\n        error: `No data returned for ISBN ${isbn}`,\n      };\n    }\n\n    // Validate using zod schema\n    const parseResult = CslItemSchema.safeParse(rawItems[0]);\n    if (!parseResult.success) {\n      return {\n        success: false,\n        error: `Invalid CSL-JSON data for ISBN ${isbn}: ${parseResult.error.message}`,\n      };\n    }\n\n    return { success: true, item: parseResult.data };\n  } catch (error) {\n    const errorMsg = error instanceof Error ? error.message : String(error);\n    return {\n      success: false,\n      error: errorMsg,\n    };\n  }\n}\n","/**\n * Parser module for BibTeX and RIS formats\n *\n * Uses citation-js plugins for parsing:\n * - @citation-js/plugin-bibtex for BibTeX\n * - @citation-js/plugin-ris for RIS\n */\n\nimport { Cite } from \"@citation-js/core\";\nimport \"@citation-js/plugin-bibtex\";\nimport \"@citation-js/plugin-ris\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\n\n/**\n * Result of a parse operation\n */\nexport type ParseResult = {\n  success: boolean;\n  items: CslItem[];\n  error?: string;\n};\n\n/**\n * Parse BibTeX content to CSL-JSON\n *\n * @param content - BibTeX content string\n * @returns Parse result with CSL-JSON items\n */\nexport function parseBibtex(content: string): ParseResult {\n  return parseWithCitationJs(content, \"bibtex\");\n}\n\n/**\n * Parse RIS content to CSL-JSON\n *\n * @param content - RIS content string\n * @returns Parse result with CSL-JSON items\n */\nexport function parseRis(content: string): ParseResult {\n  return parseWithCitationJs(content, \"ris\");\n}\n\n/**\n * Parse content using citation-js\n */\nfunction parseWithCitationJs(content: string, format: string): ParseResult {\n  const trimmed = content.trim();\n\n  // Handle empty input\n  if (!trimmed) {\n    return { success: true, items: [] };\n  }\n\n  try {\n    // Parse with citation-js (auto-detection works well for bibtex/ris)\n    const cite = new Cite(trimmed);\n\n    // Get CSL-JSON output\n    const items = cite.get({ format: \"real\", type: \"json\" }) as CslItem[];\n\n    // Handle case where parsing produces no results\n    if (!items || items.length === 0) {\n      // Check if input looks like valid format but has no entries\n      if (isEmptyFormat(trimmed, format)) {\n        return { success: true, items: [] };\n      }\n\n      return {\n        success: false,\n        items: [],\n        error: `No valid ${format.toUpperCase()} entries found`,\n      };\n    }\n\n    return { success: true, items };\n  } catch (error) {\n    const errorMessage = error instanceof Error ? error.message : String(error);\n\n    // Check if this is truly empty content (comments only for bibtex)\n    if (isEmptyFormat(trimmed, format)) {\n      return { success: true, items: [] };\n    }\n\n    return {\n      success: false,\n      items: [],\n      error: `Failed to parse ${format.toUpperCase()}: ${errorMessage}`,\n    };\n  }\n}\n\n/**\n * Check if content is \"empty\" for the given format\n * (e.g., only comments for BibTeX)\n */\nfunction isEmptyFormat(content: string, format: string): boolean {\n  if (format === \"bibtex\") {\n    // BibTeX comments start with %\n    const lines = content.split(\"\\n\");\n    return lines.every((line) => {\n      const trimmed = line.trim();\n      return trimmed === \"\" || trimmed.startsWith(\"%\");\n    });\n  }\n\n  return false;\n}\n","/**\n * Importer orchestration module\n *\n * Coordinates format detection, parsing, and fetching to import references\n * from various input formats.\n */\n\nimport { existsSync, readFileSync } from \"node:fs\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { CslItemSchema } from \"../../core/csl-json/types.js\";\nimport {\n  cacheDoiResult,\n  cacheIsbnResult,\n  cachePmidResult,\n  getDoiFromCache,\n  getIsbnFromCache,\n  getPmidFromCache,\n} from \"./cache.js\";\nimport { detectByContent, detectByExtension, isDoi, isIsbn, isPmid } from \"./detector.js\";\nimport type { InputFormat } from \"./detector.js\";\nimport { fetchDoi, fetchIsbn, fetchPmids } from \"./fetcher.js\";\nimport type { PubmedConfig } from \"./fetcher.js\";\nimport { normalizeDoi, normalizeIsbn, normalizePmid } from \"./normalizer.js\";\nimport { parseBibtex, parseRis } from \"./parser.js\";\n\n/**\n * Result of importing a single item\n */\nexport type ImportItemResult =\n  | { success: true; item: CslItem; source: string }\n  | { success: false; error: string; source: string };\n\n/**\n * Result of an import operation\n */\nexport interface ImportResult {\n  results: ImportItemResult[];\n}\n\n/**\n * Options for import operations\n */\nexport interface ImportOptions {\n  pubmedConfig?: PubmedConfig;\n}\n\n/**\n * Classified identifiers\n */\ninterface ClassifiedIdentifiers {\n  pmids: string[];\n  dois: string[];\n  isbns: string[];\n  unknowns: string[];\n}\n\n/**\n * Classify identifiers into PMIDs, DOIs, and unknowns\n */\nfunction classifyIdentifiers(identifiers: string[]): ClassifiedIdentifiers {\n  const pmids: string[] = [];\n  const dois: string[] = [];\n  const isbns: string[] = [];\n  const unknowns: string[] = [];\n\n  for (const id of identifiers) {\n    if (isPmid(id)) {\n      pmids.push(normalizePmid(id));\n    } else if (isDoi(id)) {\n      dois.push(normalizeDoi(id));\n    } else if (isIsbn(id)) {\n      isbns.push(normalizeIsbn(id));\n    } else {\n      unknowns.push(id);\n    }\n  }\n\n  return { pmids, dois, isbns, unknowns };\n}\n\n/**\n * Build error results for unknown identifiers\n */\nfunction buildUnknownResults(unknowns: string[]): ImportItemResult[] {\n  return unknowns.map((unknown) => ({\n    success: false as const,\n    error: `Cannot interpret '${unknown}' as identifier (not a valid PMID or DOI)`,\n    source: unknown,\n  }));\n}\n\n/**\n * Fetch PMIDs with cache support\n */\nasync function fetchPmidsWithCache(\n  pmids: string[],\n  pubmedConfig: PubmedConfig\n): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n  const pmidsToFetch: string[] = [];\n\n  // Check cache first\n  for (const pmid of pmids) {\n    const cached = getPmidFromCache(pmid);\n    if (cached) {\n      results.push({ success: true, item: cached, source: pmid });\n    } else {\n      pmidsToFetch.push(pmid);\n    }\n  }\n\n  // Fetch uncached PMIDs\n  if (pmidsToFetch.length > 0) {\n    const fetchResults = await fetchPmids(pmidsToFetch, pubmedConfig);\n    for (const fetchResult of fetchResults) {\n      if (fetchResult.success) {\n        cachePmidResult(fetchResult.pmid, fetchResult.item);\n        results.push({\n          success: true,\n          item: fetchResult.item,\n          source: fetchResult.pmid,\n        });\n      } else {\n        results.push({\n          success: false,\n          error: fetchResult.error,\n          source: fetchResult.pmid,\n        });\n      }\n    }\n  }\n\n  return results;\n}\n\n/**\n * Fetch DOIs with cache support\n */\nasync function fetchDoisWithCache(dois: string[]): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n\n  for (const doi of dois) {\n    const cached = getDoiFromCache(doi);\n    if (cached) {\n      results.push({ success: true, item: cached, source: doi });\n      continue;\n    }\n\n    const fetchResult = await fetchDoi(doi);\n    if (fetchResult.success) {\n      cacheDoiResult(doi, fetchResult.item);\n      results.push({ success: true, item: fetchResult.item, source: doi });\n    } else {\n      results.push({ success: false, error: fetchResult.error, source: doi });\n    }\n  }\n\n  return results;\n}\n\n/**\n * Fetch ISBNs with caching\n */\nasync function fetchIsbnsWithCache(isbns: string[]): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n\n  for (const isbn of isbns) {\n    const cached = getIsbnFromCache(isbn);\n    if (cached) {\n      results.push({ success: true, item: cached, source: isbn });\n      continue;\n    }\n\n    const fetchResult = await fetchIsbn(isbn);\n    if (fetchResult.success) {\n      cacheIsbnResult(isbn, fetchResult.item);\n      results.push({ success: true, item: fetchResult.item, source: isbn });\n    } else {\n      results.push({ success: false, error: fetchResult.error, source: isbn });\n    }\n  }\n\n  return results;\n}\n\n/**\n * Parse JSON content and return import result\n */\nfunction parseJsonContent(content: string): ImportResult {\n  try {\n    const parsed = JSON.parse(content);\n    const items: unknown[] = Array.isArray(parsed) ? parsed : [parsed];\n\n    if (items.length === 0) {\n      return { results: [] };\n    }\n\n    const results: ImportItemResult[] = [];\n    for (const item of items) {\n      const parseResult = CslItemSchema.safeParse(item);\n      if (parseResult.success) {\n        results.push({ success: true, item: parseResult.data, source: \"json\" });\n      } else {\n        results.push({\n          success: false,\n          error: `Invalid CSL-JSON: ${parseResult.error.message}`,\n          source: \"json\",\n        });\n      }\n    }\n    return { results };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    return {\n      results: [{ success: false, error: `Failed to parse JSON: ${message}`, source: \"json\" }],\n    };\n  }\n}\n\n/**\n * Parse BibTeX content and return import result\n */\nfunction parseBibtexContent(content: string): ImportResult {\n  const parseResult = parseBibtex(content);\n\n  if (!parseResult.success) {\n    return {\n      results: [\n        { success: false, error: parseResult.error ?? \"Failed to parse BibTeX\", source: \"bibtex\" },\n      ],\n    };\n  }\n\n  if (parseResult.items.length === 0) {\n    return { results: [] };\n  }\n\n  return {\n    results: parseResult.items.map((item) => ({\n      success: true as const,\n      item,\n      source: \"bibtex\",\n    })),\n  };\n}\n\n/**\n * Parse RIS content and return import result\n */\nfunction parseRisContent(content: string): ImportResult {\n  const parseResult = parseRis(content);\n\n  if (!parseResult.success) {\n    return {\n      results: [\n        { success: false, error: parseResult.error ?? \"Failed to parse RIS\", source: \"ris\" },\n      ],\n    };\n  }\n\n  if (parseResult.items.length === 0) {\n    return { results: [] };\n  }\n\n  return {\n    results: parseResult.items.map((item) => ({\n      success: true as const,\n      item,\n      source: \"ris\",\n    })),\n  };\n}\n\n/**\n * Import references from content string\n *\n * @param content - The content to parse\n * @param format - The format of the content (or \"auto\" for detection)\n * @param options - Import options\n * @returns Import result with parsed items\n */\nexport async function importFromContent(\n  content: string,\n  format: InputFormat | \"auto\",\n  _options: ImportOptions\n): Promise<ImportResult> {\n  // Determine the actual format\n  let actualFormat: InputFormat;\n  if (format === \"auto\") {\n    actualFormat = detectByContent(content);\n    if (actualFormat === \"unknown\") {\n      return {\n        results: [\n          {\n            success: false,\n            error: \"Cannot detect input format. Use --format to specify explicitly.\",\n            source: \"content\",\n          },\n        ],\n      };\n    }\n  } else {\n    actualFormat = format;\n  }\n\n  // Parse based on format\n  switch (actualFormat) {\n    case \"json\":\n      return parseJsonContent(content);\n    case \"bibtex\":\n      return parseBibtexContent(content);\n    case \"ris\":\n      return parseRisContent(content);\n    default:\n      return {\n        results: [\n          {\n            success: false,\n            error: `Unsupported format for content parsing: ${actualFormat}`,\n            source: \"content\",\n          },\n        ],\n      };\n  }\n}\n\n/**\n * Import references from identifier strings (PMID or DOI)\n *\n * @param identifiers - Array of identifier strings\n * @param options - Import options (requires pubmedConfig for PMID fetching)\n * @returns Import result with fetched items\n */\nexport async function importFromIdentifiers(\n  identifiers: string[],\n  options: ImportOptions\n): Promise<ImportResult> {\n  if (identifiers.length === 0) {\n    return { results: [] };\n  }\n\n  // Classify identifiers\n  const { pmids, dois, isbns, unknowns } = classifyIdentifiers(identifiers);\n\n  // Collect results\n  const results: ImportItemResult[] = [];\n\n  // Add errors for unknown identifiers\n  results.push(...buildUnknownResults(unknowns));\n\n  // Fetch PMIDs with cache\n  const pmidResults = await fetchPmidsWithCache(pmids, options.pubmedConfig ?? {});\n  results.push(...pmidResults);\n\n  // Fetch DOIs with cache\n  const doiResults = await fetchDoisWithCache(dois);\n  results.push(...doiResults);\n\n  // Fetch ISBNs with cache\n  const isbnResults = await fetchIsbnsWithCache(isbns);\n  results.push(...isbnResults);\n\n  return { results };\n}\n\n/**\n * Options for importFromInputs\n */\nexport interface ImportInputsOptions extends ImportOptions {\n  /** Explicit format specification (default: auto) */\n  format?: InputFormat | \"auto\";\n  /** Content from stdin (if provided, processed before file/identifier inputs) */\n  stdinContent?: string;\n}\n\n/**\n * Unified entry point for importing references from file paths or identifiers\n *\n * Classifies inputs as files or identifiers:\n * - If path exists as file → read and parse\n * - If path does not exist → interpret as identifier (PMID/DOI)\n *\n * @param inputs - Array of file paths or identifier strings\n * @param options - Import options including format specification\n * @returns Import result with all parsed/fetched items\n */\n\n/**\n * Check if input looks like a file path (has file-like extension)\n */\nfunction looksLikeFilePath(input: string): boolean {\n  const fileExtensions = [\".json\", \".bib\", \".ris\", \".txt\", \".xml\", \".yaml\", \".yml\"];\n  const lowerInput = input.toLowerCase();\n  return fileExtensions.some((ext) => lowerInput.endsWith(ext));\n}\n\n/**\n * Process a single file input\n */\nasync function processFile(\n  filePath: string,\n  options: ImportInputsOptions\n): Promise<ImportItemResult[]> {\n  try {\n    const content = readFileSync(filePath, \"utf-8\");\n\n    // Determine format\n    let format: InputFormat | \"auto\";\n    if (options.format && options.format !== \"auto\") {\n      format = options.format;\n    } else {\n      // Try extension first\n      const extFormat = detectByExtension(filePath);\n      format = extFormat !== \"unknown\" ? extFormat : \"auto\";\n    }\n\n    const result = await importFromContent(content, format, options);\n\n    // Update source to be the file path\n    return result.results.map((r) => ({\n      ...r,\n      source: filePath,\n    }));\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    return [\n      {\n        success: false,\n        error: `Failed to read file: ${message}`,\n        source: filePath,\n      },\n    ];\n  }\n}\n\n/**\n * Process identifier inputs (PMID/DOI)\n */\nasync function processIdentifiers(\n  inputs: string[],\n  options: ImportInputsOptions\n): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n  const validIdentifiers: string[] = [];\n\n  // Separate valid identifiers from invalid inputs\n  for (const input of inputs) {\n    // Check if it's a valid identifier\n    const isValidPmid = isPmid(input);\n    const isValidDoi = isDoi(input);\n\n    if (isValidPmid || isValidDoi) {\n      validIdentifiers.push(input);\n    } else {\n      // Not a valid identifier\n      const hint = looksLikeFilePath(input)\n        ? \" Hint: If this is a file path, check that the file exists.\"\n        : \"\";\n      results.push({\n        success: false,\n        error: `Cannot interpret '${input}' as identifier (not a valid PMID or DOI).${hint}`,\n        source: input,\n      });\n    }\n  }\n\n  // Fetch valid identifiers\n  if (validIdentifiers.length > 0) {\n    const fetchResult = await importFromIdentifiers(validIdentifiers, options);\n    results.push(...fetchResult.results);\n  }\n\n  return results;\n}\n\nexport async function importFromInputs(\n  inputs: string[],\n  options: ImportInputsOptions\n): Promise<ImportResult> {\n  const allResults: ImportItemResult[] = [];\n\n  // Process stdinContent if provided\n  if (options.stdinContent?.trim()) {\n    const stdinResults = await processStdinContent(options.stdinContent, options);\n    allResults.push(...stdinResults);\n  }\n\n  // Process file/identifier inputs\n  if (inputs.length > 0) {\n    const identifiersToFetch: string[] = [];\n\n    // Process each input\n    for (const input of inputs) {\n      if (existsSync(input)) {\n        // Input is an existing file\n        const fileResults = await processFile(input, options);\n        allResults.push(...fileResults);\n      } else {\n        // Input does not exist as file - treat as potential identifier\n        identifiersToFetch.push(input);\n      }\n    }\n\n    // Process identifiers\n    if (identifiersToFetch.length > 0) {\n      const identifierResults = await processIdentifiers(identifiersToFetch, options);\n      allResults.push(...identifierResults);\n    }\n  }\n\n  return { results: allResults };\n}\n\n/**\n * Process stdin content based on format detection\n * - For file formats (json/bibtex/ris): parse directly\n * - For identifier formats (pmid/doi) or auto with identifiers: split and process\n */\nasync function processStdinContent(\n  content: string,\n  options: ImportInputsOptions\n): Promise<ImportItemResult[]> {\n  const format = options.format || \"auto\";\n\n  // If explicit file format specified, parse as content\n  if (format === \"json\" || format === \"bibtex\" || format === \"ris\") {\n    const result = await importFromContent(content, format, options);\n    return result.results.map((r) => ({\n      ...r,\n      source: r.source === \"content\" ? \"stdin\" : r.source,\n    }));\n  }\n\n  // If explicit identifier format, split and process\n  if (format === \"pmid\" || format === \"doi\") {\n    const identifiers = content.split(/\\s+/).filter((s) => s.length > 0);\n    return processIdentifiers(identifiers, options);\n  }\n\n  // Auto-detect format from content\n  const detectedFormat = detectByContent(content);\n\n  if (detectedFormat === \"json\" || detectedFormat === \"bibtex\" || detectedFormat === \"ris\") {\n    // File format detected - parse as content\n    const result = await importFromContent(content, detectedFormat, options);\n    return result.results.map((r) => ({\n      ...r,\n      source: r.source === \"content\" ? \"stdin\" : r.source,\n    }));\n  }\n\n  // Not a file format - treat as whitespace-separated identifiers\n  const identifiers = content.split(/\\s+/).filter((s) => s.length > 0);\n  if (identifiers.length === 0) {\n    return [];\n  }\n\n  return processIdentifiers(identifiers, options);\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { detectDuplicate } from \"../duplicate/detector.js\";\nimport type { InputFormat } from \"../import/detector.js\";\nimport type { PubmedConfig } from \"../import/fetcher.js\";\nimport {\n  type ImportInputsOptions,\n  type ImportItemResult,\n  importFromInputs,\n} from \"../import/importer.js\";\n\n/**\n * Options for adding references\n */\nexport interface AddReferencesOptions {\n  /** Skip duplicate detection */\n  force?: boolean;\n  /** Explicit input format (default: auto) */\n  format?: InputFormat | \"auto\";\n  /** PubMed API configuration */\n  pubmedConfig?: PubmedConfig;\n  /** Content from stdin (if provided, processed before file/identifier inputs) */\n  stdinContent?: string;\n}\n\n/**\n * Information about a successfully added reference\n */\nexport interface AddedItem {\n  id: string;\n  title: string;\n  /** True if the ID was changed due to collision */\n  idChanged?: boolean;\n  /** Original ID before collision resolution */\n  originalId?: string;\n}\n\n/**\n * Information about a failed import\n */\nexport interface FailedItem {\n  source: string;\n  error: string;\n}\n\n/**\n * Information about a skipped duplicate\n */\nexport interface SkippedItem {\n  source: string;\n  existingId: string;\n}\n\n/**\n * Result of addReferences operation\n */\nexport interface AddReferencesResult {\n  added: AddedItem[];\n  failed: FailedItem[];\n  skipped: SkippedItem[];\n}\n\n/**\n * Add references to a library from various input sources.\n *\n * This function orchestrates:\n * 1. Import from inputs (files or identifiers)\n * 2. Duplicate detection (unless force=true)\n * 3. ID collision resolution\n * 4. Library save\n *\n * @param inputs - File paths or identifiers (PMID, DOI)\n * @param library - Target library\n * @param options - Add options\n * @returns Result with added, failed, and skipped items\n */\nexport async function addReferences(\n  inputs: string[],\n  library: ILibrary,\n  options: AddReferencesOptions\n): Promise<AddReferencesResult> {\n  const added: AddedItem[] = [];\n  const failed: FailedItem[] = [];\n  const skipped: SkippedItem[] = [];\n\n  // 1. Import from inputs\n  const importOptions = buildImportOptions(options);\n  const importResult = await importFromInputs(inputs, importOptions);\n\n  // Get existing items for duplicate/collision checks (getAll now returns CslItem[] directly)\n  const existingItems = await library.getAll();\n\n  // Track IDs we've added in this batch (for collision detection within batch)\n  const addedIds = new Set<string>();\n\n  // 2. Process each import result\n  for (const result of importResult.results) {\n    const processed = await processImportResult(\n      result,\n      existingItems,\n      addedIds,\n      options.force ?? false,\n      library\n    );\n\n    if (processed.type === \"failed\") {\n      failed.push(processed.item);\n    } else if (processed.type === \"skipped\") {\n      skipped.push(processed.item);\n    } else {\n      added.push(processed.item);\n    }\n  }\n\n  // 3. Save library if any items were added\n  if (added.length > 0) {\n    await library.save();\n  }\n\n  return { added, failed, skipped };\n}\n\n/**\n * Build import options from add options\n */\nfunction buildImportOptions(options: AddReferencesOptions): ImportInputsOptions {\n  const importOptions: ImportInputsOptions = {};\n  if (options.format !== undefined) {\n    importOptions.format = options.format;\n  }\n  if (options.pubmedConfig !== undefined) {\n    importOptions.pubmedConfig = options.pubmedConfig;\n  }\n  if (options.stdinContent !== undefined) {\n    importOptions.stdinContent = options.stdinContent;\n  }\n  return importOptions;\n}\n\ntype ProcessResult =\n  | { type: \"added\"; item: AddedItem }\n  | { type: \"failed\"; item: FailedItem }\n  | { type: \"skipped\"; item: SkippedItem };\n\n/**\n * Process a single import result\n */\nasync function processImportResult(\n  result: ImportItemResult,\n  existingItems: CslItem[],\n  addedIds: Set<string>,\n  force: boolean,\n  library: ILibrary\n): Promise<ProcessResult> {\n  if (!result.success) {\n    return { type: \"failed\", item: { source: result.source, error: result.error } };\n  }\n\n  const item = result.item;\n\n  // Check for duplicates (unless force=true)\n  if (!force) {\n    const duplicateResult = detectDuplicate(item, existingItems);\n    const existingMatch = duplicateResult.matches[0];\n    if (existingMatch) {\n      return {\n        type: \"skipped\",\n        item: { source: result.source, existingId: existingMatch.existing.id ?? \"\" },\n      };\n    }\n  }\n\n  // Resolve ID collision\n  const allExistingIds = new Set([...existingItems.map((i) => i.id), ...addedIds]);\n  const { id, changed } = resolveIdCollision(item.id, allExistingIds);\n\n  const finalItem: CslItem = { ...item, id };\n\n  // Add to library\n  await library.add(finalItem);\n  addedIds.add(id);\n\n  // Build result\n  const addedItem: AddedItem = {\n    id,\n    title: typeof finalItem.title === \"string\" ? finalItem.title : \"\",\n  };\n\n  if (changed) {\n    addedItem.idChanged = true;\n    addedItem.originalId = item.id;\n  }\n\n  return { type: \"added\", item: addedItem };\n}\n\n/**\n * Generate an alphabetic suffix for ID collision resolution.\n * 0 -> 'a', 1 -> 'b', ..., 25 -> 'z', 26 -> 'aa', etc.\n */\nfunction generateSuffix(index: number): string {\n  const alphabet = \"abcdefghijklmnopqrstuvwxyz\";\n  let suffix = \"\";\n  let n = index;\n\n  do {\n    suffix = alphabet[n % 26] + suffix;\n    n = Math.floor(n / 26) - 1;\n  } while (n >= 0);\n\n  return suffix;\n}\n\n/**\n * Resolve ID collision by appending alphabetic suffix.\n */\nfunction resolveIdCollision(\n  baseId: string,\n  existingIds: Set<string>\n): { id: string; changed: boolean } {\n  if (!existingIds.has(baseId)) {\n    return { id: baseId, changed: false };\n  }\n\n  // Find next available suffix\n  let index = 0;\n  let newId: string;\n\n  do {\n    const suffix = generateSuffix(index);\n    newId = `${baseId}${suffix}`;\n    index++;\n  } while (existingIds.has(newId));\n\n  return { id: newId, changed: true };\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\n\n/**\n * Format a single author as \"Family, Given-Initial.\"\n */\nfunction formatAuthor(author: {\n  family?: string | undefined;\n  given?: string | undefined;\n}): string {\n  const family = author.family || \"\";\n  const givenInitial = author.given ? `${author.given.charAt(0)}.` : \"\";\n  return givenInitial ? `${family}, ${givenInitial}` : family;\n}\n\n/**\n * Format authors array as \"Family1, G.; Family2, G.\"\n */\nfunction formatAuthors(\n  authors: Array<{\n    family?: string | undefined;\n    given?: string | undefined;\n    literal?: string | undefined;\n    \"dropping-particle\"?: string | undefined;\n    \"non-dropping-particle\"?: string | undefined;\n    suffix?: string | undefined;\n  }>\n): string {\n  return authors.map(formatAuthor).join(\"; \");\n}\n\n/**\n * Format a single reference in pretty format\n */\nfunction formatSingleReference(item: CslItem): string {\n  const lines: string[] = [];\n\n  // Header line: [id] title\n  const header = item.title ? `[${item.id}] ${item.title}` : `[${item.id}]`;\n  lines.push(header);\n\n  // Authors (if present)\n  if (item.author && item.author.length > 0) {\n    lines.push(`  Authors: ${formatAuthors(item.author)}`);\n  }\n\n  // Year\n  const year = item.issued?.[\"date-parts\"]?.[0]?.[0];\n  lines.push(`  Year: ${year || \"(no year)\"}`);\n\n  // Type\n  lines.push(`  Type: ${item.type}`);\n\n  // DOI (if present)\n  if (item.DOI) {\n    lines.push(`  DOI: ${item.DOI}`);\n  }\n\n  // PMID (if present)\n  if (item.PMID) {\n    lines.push(`  PMID: ${item.PMID}`);\n  }\n\n  // PMCID (if present)\n  if (item.PMCID) {\n    lines.push(`  PMCID: ${item.PMCID}`);\n  }\n\n  // URL (if present)\n  if (item.URL) {\n    lines.push(`  URL: ${item.URL}`);\n  }\n\n  // UUID (always)\n  const uuid = item.custom?.uuid || \"(no uuid)\";\n  lines.push(`  UUID: ${uuid}`);\n\n  return lines.join(\"\\n\");\n}\n\n/**\n * Format references in pretty-printed format\n */\nexport function formatPretty(items: CslItem[]): string {\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  return items.map(formatSingleReference).join(\"\\n\\n\");\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\n\n/**\n * Map CSL-JSON type to BibTeX entry type\n */\nfunction mapEntryType(cslType: string): string {\n  const typeMap: Record<string, string> = {\n    article: \"article\",\n    \"article-journal\": \"article\",\n    \"article-magazine\": \"article\",\n    \"article-newspaper\": \"article\",\n    book: \"book\",\n    chapter: \"inbook\",\n    \"paper-conference\": \"inproceedings\",\n    thesis: \"phdthesis\",\n    report: \"techreport\",\n    webpage: \"misc\",\n  };\n\n  return typeMap[cslType] || \"misc\";\n}\n\n/**\n * Format a single author as \"Family, Given\"\n */\nfunction formatBibtexAuthor(author: {\n  family?: string | undefined;\n  given?: string | undefined;\n  literal?: string | undefined;\n}): string {\n  if (author.literal) {\n    return author.literal;\n  }\n  const family = author.family || \"\";\n  const given = author.given || \"\";\n  return given ? `${family}, ${given}` : family;\n}\n\n/**\n * Format authors for BibTeX as \"Family1, Given1 and Family2, Given2\"\n */\nfunction formatBibtexAuthors(\n  authors: Array<{\n    family?: string | undefined;\n    given?: string | undefined;\n    literal?: string | undefined;\n    \"dropping-particle\"?: string | undefined;\n    \"non-dropping-particle\"?: string | undefined;\n    suffix?: string | undefined;\n  }>\n): string {\n  return authors.map(formatBibtexAuthor).join(\" and \");\n}\n\n/**\n * Format a BibTeX field\n */\nfunction formatField(name: string, value: string): string {\n  return `  ${name} = {${value}},`;\n}\n\n/**\n * Add basic bibliographic fields to BibTeX entry\n */\nfunction addBasicFields(lines: string[], item: CslItem): void {\n  // Title\n  if (item.title) {\n    lines.push(formatField(\"title\", item.title));\n  }\n\n  // Authors\n  if (item.author && item.author.length > 0) {\n    lines.push(formatField(\"author\", formatBibtexAuthors(item.author)));\n  }\n\n  // Year\n  const year = item.issued?.[\"date-parts\"]?.[0]?.[0];\n  if (year) {\n    lines.push(formatField(\"year\", String(year)));\n  }\n}\n\n/**\n * Add publication details to BibTeX entry\n */\nfunction addPublicationDetails(lines: string[], item: CslItem, entryType: string): void {\n  // Container-title (journal or booktitle depending on type)\n  if (item[\"container-title\"]) {\n    if (entryType === \"article\") {\n      lines.push(formatField(\"journal\", item[\"container-title\"]));\n    } else if (entryType === \"inbook\" || entryType === \"inproceedings\") {\n      lines.push(formatField(\"booktitle\", item[\"container-title\"]));\n    }\n  }\n\n  // Volume\n  if (item.volume) {\n    lines.push(formatField(\"volume\", item.volume));\n  }\n\n  // Issue -> number\n  if (item.issue) {\n    lines.push(formatField(\"number\", item.issue));\n  }\n\n  // Pages\n  if (item.page) {\n    lines.push(formatField(\"pages\", item.page));\n  }\n\n  // Publisher\n  if (item.publisher) {\n    lines.push(formatField(\"publisher\", item.publisher));\n  }\n}\n\n/**\n * Add identifier fields to BibTeX entry\n */\nfunction addIdentifierFields(lines: string[], item: CslItem): void {\n  // DOI\n  if (item.DOI) {\n    lines.push(formatField(\"doi\", item.DOI));\n  }\n\n  // URL\n  if (item.URL) {\n    lines.push(formatField(\"url\", item.URL));\n  }\n\n  // PMID or PMCID in note field\n  if (item.PMID) {\n    lines.push(formatField(\"note\", `PMID: ${item.PMID}`));\n  } else if (item.PMCID) {\n    lines.push(formatField(\"note\", `PMCID: ${item.PMCID}`));\n  }\n}\n\n/**\n * Format a single reference as BibTeX entry\n */\nfunction formatSingleBibtexEntry(item: CslItem): string {\n  const entryType = mapEntryType(item.type);\n  const lines: string[] = [];\n\n  // Opening line: @type{citation-key,\n  lines.push(`@${entryType}{${item.id},`);\n\n  // Add fields in sections\n  addBasicFields(lines, item);\n  addPublicationDetails(lines, item, entryType);\n  addIdentifierFields(lines, item);\n\n  // Closing brace\n  lines.push(\"}\");\n\n  return lines.join(\"\\n\");\n}\n\n/**\n * Format references as BibTeX\n */\nexport function formatBibtex(items: CslItem[]): string {\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  return items.map(formatSingleBibtexEntry).join(\"\\n\\n\");\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\n\n/**\n * Extract first author name with initial\n * Returns \"Family G\" or \"Family\" if no given name\n */\nfunction formatFirstAuthor(item: CslItem): string {\n  if (!item.author || item.author.length === 0) {\n    return \"Unknown\";\n  }\n\n  const firstAuthor = item.author[0];\n  if (!firstAuthor) {\n    return \"Unknown\";\n  }\n\n  const family = firstAuthor.family || \"Unknown\";\n  const givenInitial = firstAuthor.given ? firstAuthor.given[0] : \"\";\n\n  if (givenInitial) {\n    return `${family} ${givenInitial}`;\n  }\n  return family;\n}\n\n/**\n * Check if item has multiple authors\n */\nfunction hasMultipleAuthors(item: CslItem): boolean {\n  return (item.author?.length || 0) > 1;\n}\n\n/**\n * Extract year from CSL-JSON issued field\n */\nfunction extractYear(item: CslItem): string {\n  if (item.issued?.[\"date-parts\"]?.[0]?.[0]) {\n    return String(item.issued[\"date-parts\"][0][0]);\n  }\n  return \"n.d.\";\n}\n\n/**\n * Get journal abbreviation (prefer short title)\n */\nfunction getJournalAbbrev(item: CslItem): string {\n  const containerTitleShort = (item as Record<string, unknown>)[\"container-title-short\"];\n  if (typeof containerTitleShort === \"string\") {\n    return containerTitleShort;\n  }\n  return item[\"container-title\"] || \"\";\n}\n\n/**\n * Format volume/issue/pages section\n * Returns formats like: \"10(2):123-145\", \"10:123-145\", \"10(2)\", \"10\", or \"\"\n */\nfunction formatVolumeIssuePage(item: CslItem): string {\n  const volume = item.volume;\n  const issue = item.issue;\n  const page = item.page;\n\n  if (!volume && !issue && !page) {\n    return \"\";\n  }\n\n  let result = \"\";\n\n  if (volume) {\n    result += volume;\n    if (issue) {\n      result += `(${issue})`;\n    }\n    if (page) {\n      result += `:${page}`;\n    }\n  } else if (page) {\n    result += page;\n  }\n\n  return result;\n}\n\n/**\n * Get identifier (PMID > DOI > URL priority)\n */\nfunction getIdentifier(item: CslItem): string {\n  if (item.PMID) {\n    return `PMID:${item.PMID}`;\n  }\n  if (item.DOI) {\n    return `DOI:${item.DOI}`;\n  }\n  if (item.URL) {\n    return item.URL;\n  }\n  return \"\";\n}\n\n/**\n * Format a single bibliography entry\n */\nfunction formatBibliographyEntry(item: CslItem): string {\n  const parts: string[] = [];\n\n  // Author\n  const author = formatFirstAuthor(item);\n  const etAl = hasMultipleAuthors(item) ? \" et al\" : \"\";\n  parts.push(`${author}${etAl}.`);\n\n  // Journal\n  const journal = getJournalAbbrev(item);\n  if (journal) {\n    parts.push(`${journal}.`);\n  }\n\n  // Year and volume/issue/pages\n  const year = extractYear(item);\n  const volumeIssuePage = formatVolumeIssuePage(item);\n\n  if (volumeIssuePage) {\n    parts.push(`${year};${volumeIssuePage}.`);\n  } else {\n    parts.push(`${year}.`);\n  }\n\n  // Identifier\n  const identifier = getIdentifier(item);\n  if (identifier) {\n    parts.push(`${identifier}.`);\n  }\n\n  // Title\n  if (item.title) {\n    parts.push(`${item.title}.`);\n  }\n\n  return parts.join(\" \");\n}\n\n/**\n * Get first author family name only (for in-text citations)\n */\nfunction getFirstAuthorFamilyName(item: CslItem): string {\n  if (!item.author || item.author.length === 0) {\n    return \"Unknown\";\n  }\n\n  const firstAuthor = item.author[0];\n  if (!firstAuthor) {\n    return \"Unknown\";\n  }\n\n  return firstAuthor.family || \"Unknown\";\n}\n\n/**\n * Format a single in-text citation (without parentheses)\n * Returns \"Family et al, YYYY\" or \"Family, YYYY\"\n */\nfunction formatInTextEntry(item: CslItem): string {\n  const author = getFirstAuthorFamilyName(item);\n  const etAl = hasMultipleAuthors(item) ? \" et al\" : \"\";\n  const year = extractYear(item);\n\n  return `${author}${etAl}, ${year}`;\n}\n\n/**\n * Format CSL-JSON items as simplified AMA-like bibliography entries.\n *\n * Format: FirstAuthor [et al]. JournalAbbrev. YYYY;volume(issue):pages. PMID:xxxxx [or DOI:xxxxx]. Title.\n *\n * Multiple items are separated by double newlines.\n *\n * @param items - Array of CSL-JSON items\n * @returns Formatted bibliography entries separated by double newlines\n */\nexport function formatBibliography(items: CslItem[]): string {\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  return items.map(formatBibliographyEntry).join(\"\\n\\n\");\n}\n\n/**\n * Format CSL-JSON items as simplified in-text citations.\n *\n * Format: (FirstAuthor et al, YYYY)\n *\n * Multiple items are separated by semicolons and enclosed in parentheses.\n *\n * @param items - Array of CSL-JSON items\n * @returns Formatted in-text citation(s) enclosed in parentheses\n */\nexport function formatInText(items: CslItem[]): string {\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  const citations = items.map(formatInTextEntry).join(\"; \");\n  return `(${citations})`;\n}\n","import { Cite } from \"@citation-js/core\";\nimport \"@citation-js/plugin-csl\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { formatBibliography, formatInText } from \"./citation-fallback.js\";\n\n/**\n * Options for CSL citation formatting\n */\nexport type CitationFormatOptions = {\n  /**\n   * CSL style name (e.g., 'apa', 'vancouver', 'chicago')\n   * @default 'apa'\n   */\n  style?: string;\n\n  /**\n   * Output format: text, html, or rtf\n   * @default 'text'\n   */\n  format?: \"text\" | \"html\" | \"rtf\";\n\n  /**\n   * Locale code (e.g., 'en-US', 'en-GB')\n   * @default 'en-US'\n   */\n  locale?: string;\n};\n\n/**\n * Format CSL-JSON items as bibliography using CSL processor.\n * Falls back to simplified format if CSL processing fails.\n *\n * @param items - Array of CSL-JSON items\n * @param options - Formatting options\n * @returns Formatted bibliography entries\n */\nexport function formatBibliographyCSL(items: CslItem[], options: CitationFormatOptions): string {\n  // Handle empty array\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  // Set defaults\n  const style = options.style || \"apa\";\n  const format = options.format || \"text\";\n  const locale = options.locale || \"en-US\";\n\n  try {\n    // Create Cite instance with CSL-JSON data\n    const cite = new Cite(items);\n\n    // Format as bibliography\n    const result = cite.format(\"bibliography\", {\n      format,\n      template: style,\n      lang: locale,\n    });\n\n    return result;\n  } catch (error) {\n    // Fall back to simplified format on any error\n    const errorMessage = error instanceof Error ? error.message : String(error);\n    process.stderr.write(\n      `Warning: CSL processing failed (style: ${style}), falling back to simplified format: ${errorMessage}\\n`\n    );\n    return formatBibliography(items);\n  }\n}\n\n/**\n * Format CSL-JSON items as in-text citations using CSL processor.\n * Falls back to simplified format if CSL processing fails.\n *\n * @param items - Array of CSL-JSON items\n * @param options - Formatting options\n * @returns Formatted in-text citation(s)\n */\nexport function formatInTextCSL(items: CslItem[], options: CitationFormatOptions): string {\n  // Handle empty array\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  // Set defaults\n  const style = options.style || \"apa\";\n  const format = options.format || \"text\";\n  const locale = options.locale || \"en-US\";\n\n  try {\n    // Create Cite instance with CSL-JSON data\n    const cite = new Cite(items);\n\n    // Format as in-text citation\n    const result = cite.format(\"citation\", {\n      format,\n      template: style,\n      lang: locale,\n    });\n\n    return result;\n  } catch (error) {\n    // Fall back to simplified format on any error\n    const errorMessage = error instanceof Error ? error.message : String(error);\n    process.stderr.write(\n      `Warning: CSL processing failed (style: ${style}), falling back to simplified format: ${errorMessage}\\n`\n    );\n    return formatInText(items);\n  }\n}\n","import { isBuiltinStyle } from \"../../config/csl-styles.js\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../core/library-interface.js\";\nimport {\n  formatBibliography,\n  formatBibliographyCSL,\n  formatInText,\n  formatInTextCSL,\n} from \"../format/index.js\";\n\n/**\n * Options for citeReferences operation\n */\nexport interface CiteOperationOptions {\n  /** Reference IDs or UUIDs to cite */\n  identifiers: string[];\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType;\n  /** CSL style name or path to CSL file */\n  style?: string;\n  /** Path to custom CSL file */\n  cslFile?: string;\n  /** Locale for citation formatting (default: \"en-US\") */\n  locale?: string;\n  /** Output format (default: \"text\") */\n  format?: \"text\" | \"html\" | \"rtf\";\n  /** If true, generate in-text citation instead of bibliography */\n  inText?: boolean;\n}\n\n/**\n * Result for a single citation\n */\nexport type CiteItemResult =\n  | { success: true; identifier: string; citation: string }\n  | { success: false; identifier: string; error: string };\n\n/**\n * Result of citeReferences operation\n */\nexport interface CiteResult {\n  /** Results for each identifier */\n  results: CiteItemResult[];\n}\n\ninterface FormatOptions {\n  style?: string | undefined;\n  cslFile?: string | undefined;\n  locale?: string | undefined;\n  format?: \"text\" | \"html\" | \"rtf\" | undefined;\n}\n\n/**\n * Check if fallback formatter should be used.\n */\nfunction shouldUseFallback(options: FormatOptions): boolean {\n  if (options.cslFile) {\n    return false;\n  }\n  if (options.style && !isBuiltinStyle(options.style)) {\n    return true;\n  }\n  return false;\n}\n\n/**\n * Format a single item as citation.\n */\nfunction formatCitation(item: CslItem, inText: boolean, options: FormatOptions): string {\n  const useFallback = shouldUseFallback(options);\n  const style = options.cslFile ?? options.style ?? \"apa\";\n  const locale = options.locale ?? \"en-US\";\n  const format = options.format ?? \"text\";\n\n  if (useFallback) {\n    return inText ? formatInText([item]) : formatBibliography([item]);\n  }\n\n  return inText\n    ? formatInTextCSL([item], { style, locale, format })\n    : formatBibliographyCSL([item], { style, locale, format });\n}\n\n/**\n * Generate citation for a single identifier.\n */\nasync function generateCitationForIdentifier(\n  library: ILibrary,\n  identifier: string,\n  idType: IdentifierType,\n  inText: boolean,\n  options: FormatOptions\n): Promise<CiteItemResult> {\n  const item = await library.find(identifier, { idType });\n\n  if (!item) {\n    const lookupType = idType === \"uuid\" ? \"UUID\" : idType.toUpperCase();\n    return {\n      success: false,\n      identifier,\n      error: `Reference with ${lookupType} '${identifier}' not found`,\n    };\n  }\n\n  const citation = formatCitation(item, inText, options);\n\n  return {\n    success: true,\n    identifier,\n    citation,\n  };\n}\n\n/**\n * Generate citations for references.\n *\n * @param library - The library to cite from\n * @param options - Citation options including identifiers and style settings\n * @returns Results array with citation or error for each identifier\n */\nexport async function citeReferences(\n  library: ILibrary,\n  options: CiteOperationOptions\n): Promise<CiteResult> {\n  const { identifiers, idType = \"id\", inText = false, style, cslFile, locale, format } = options;\n  const results: CiteItemResult[] = [];\n\n  for (const identifier of identifiers) {\n    const result = await generateCitationForIdentifier(library, identifier, idType, inText, {\n      style,\n      cslFile,\n      locale,\n      format,\n    });\n    results.push(result);\n  }\n\n  return { results };\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { formatBibtex, formatPretty } from \"../format/index.js\";\n\n/**\n * Output format options for list operation\n */\nexport type ListFormat = \"pretty\" | \"json\" | \"bibtex\" | \"ids-only\" | \"uuid\";\n\n/**\n * Options for listReferences operation\n */\nexport interface ListOptions {\n  /** Output format (default: \"pretty\") */\n  format?: ListFormat;\n}\n\n/**\n * Result of listReferences operation\n */\nexport interface ListResult {\n  /** Formatted strings for each reference */\n  items: string[];\n}\n\n/**\n * List all references from the library with specified format.\n *\n * @param library - The library to list references from\n * @param options - Formatting options\n * @returns Formatted strings for each reference\n */\nexport async function listReferences(library: ILibrary, options: ListOptions): Promise<ListResult> {\n  const format = options.format ?? \"pretty\";\n  const items = await library.getAll();\n\n  switch (format) {\n    case \"json\":\n      return { items: items.map((item) => JSON.stringify(item)) };\n\n    case \"bibtex\":\n      // Format each item individually using existing formatter\n      return { items: items.map((item) => formatBibtex([item])) };\n\n    case \"ids-only\":\n      return { items: items.map((item) => item.id) };\n\n    case \"uuid\":\n      return {\n        items: items\n          .filter((item): item is CslItem & { custom: { uuid: string } } =>\n            Boolean(item.custom?.uuid)\n          )\n          .map((item) => item.custom.uuid),\n      };\n\n    default:\n      // Format each item individually using existing formatter (pretty)\n      return { items: items.map((item) => formatPretty([item])) };\n  }\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../core/library-interface.js\";\n\n/**\n * Options for removeReference operation\n */\nexport interface RemoveOperationOptions {\n  /** Reference ID or UUID */\n  identifier: string;\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType;\n}\n\n/**\n * Result of removeReference operation\n */\nexport interface RemoveResult {\n  /** Whether the reference was removed */\n  removed: boolean;\n  /** The removed item (if found and removal succeeded) */\n  removedItem?: CslItem;\n}\n\n/**\n * Remove a reference from the library.\n *\n * @param library - The library to remove from\n * @param options - Remove options including identifier and lookup method\n * @returns Result indicating success and the removed item\n */\nexport async function removeReference(\n  library: ILibrary,\n  options: RemoveOperationOptions\n): Promise<RemoveResult> {\n  const { identifier, idType = \"id\" } = options;\n\n  const result = await library.remove(identifier, { idType });\n\n  if (result.removed) {\n    await library.save();\n  }\n\n  return result;\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { formatBibtex, formatPretty } from \"../format/index.js\";\nimport { search } from \"../search/matcher.js\";\nimport { sortResults } from \"../search/sorter.js\";\nimport { tokenize } from \"../search/tokenizer.js\";\n\n/**\n * Output format options for search operation\n */\nexport type SearchFormat = \"pretty\" | \"json\" | \"bibtex\" | \"ids-only\" | \"uuid\";\n\n/**\n * Options for searchReferences operation\n */\nexport interface SearchOperationOptions {\n  /** Search query string */\n  query: string;\n  /** Output format (default: \"pretty\") */\n  format?: SearchFormat;\n}\n\n/**\n * Result of searchReferences operation\n */\nexport interface SearchResult {\n  /** Formatted strings for each matching reference */\n  items: string[];\n}\n\n/**\n * Search references in the library and return formatted results.\n *\n * @param library - The library to search in\n * @param options - Search query and formatting options\n * @returns Formatted strings for each matching reference\n */\nexport async function searchReferences(\n  library: ILibrary,\n  options: SearchOperationOptions\n): Promise<SearchResult> {\n  const format = options.format ?? \"pretty\";\n  const query = options.query;\n\n  // Get all references\n  const allItems = await library.getAll();\n\n  // If query is empty, return all items\n  let matchedItems: CslItem[];\n  if (!query.trim()) {\n    matchedItems = allItems;\n  } else {\n    // Tokenize and search\n    const tokens = tokenize(query).tokens;\n    const results = search(allItems, tokens);\n    const sorted = sortResults(results);\n    matchedItems = sorted.map((result) => result.reference);\n  }\n\n  // Format results based on format option\n  switch (format) {\n    case \"json\":\n      return { items: matchedItems.map((item) => JSON.stringify(item)) };\n\n    case \"bibtex\":\n      return { items: matchedItems.map((item) => formatBibtex([item])) };\n\n    case \"ids-only\":\n      return { items: matchedItems.map((item) => item.id) };\n\n    case \"uuid\":\n      return {\n        items: matchedItems\n          .filter((item): item is CslItem & { custom: { uuid: string } } =>\n            Boolean(item.custom?.uuid)\n          )\n          .map((item) => item.custom.uuid),\n      };\n\n    default:\n      return { items: matchedItems.map((item) => formatPretty([item])) };\n  }\n}\n","import { Hono } from \"hono\";\nimport type { Config } from \"../../config/schema.js\";\nimport type { Library } from \"../../core/library.js\";\nimport type { InputFormat } from \"../../features/import/detector.js\";\nimport type { PubmedConfig } from \"../../features/import/fetcher.js\";\nimport { type AddReferencesOptions, addReferences } from \"../../features/operations/add.js\";\n\n/**\n * Build PubmedConfig from config, filtering out undefined values\n * to satisfy exactOptionalPropertyTypes requirements.\n */\nfunction buildPubmedConfig(config: Config): PubmedConfig {\n  const pubmedConfig: PubmedConfig = {};\n  if (config.pubmed.email !== undefined) {\n    pubmedConfig.email = config.pubmed.email;\n  }\n  if (config.pubmed.apiKey !== undefined) {\n    pubmedConfig.apiKey = config.pubmed.apiKey;\n  }\n  return pubmedConfig;\n}\n\n/**\n * Create add route for importing references.\n * @param library - Library instance to use for operations\n * @param config - Configuration with PubMed settings\n * @returns Hono app with add route\n */\nexport function createAddRoute(library: Library, config: Config) {\n  const route = new Hono();\n\n  // POST / - Add references from inputs\n  route.post(\"/\", async (c) => {\n    // Parse request body\n    let body: unknown;\n    try {\n      body = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    // Validate inputs\n    if (!body || typeof body !== \"object\") {\n      return c.json({ error: \"Request body must be an object\" }, 400);\n    }\n\n    const { inputs, options } = body as {\n      inputs?: unknown;\n      options?: { force?: boolean; format?: string };\n    };\n\n    if (!inputs || !Array.isArray(inputs) || inputs.length === 0) {\n      return c.json({ error: \"inputs must be a non-empty array of strings\" }, 400);\n    }\n\n    // Ensure all inputs are strings\n    if (!inputs.every((input) => typeof input === \"string\")) {\n      return c.json({ error: \"All inputs must be strings\" }, 400);\n    }\n\n    // Build options\n    const addOptions: AddReferencesOptions = {\n      force: options?.force ?? false,\n      pubmedConfig: buildPubmedConfig(config),\n    };\n\n    if (options?.format) {\n      addOptions.format = options.format as InputFormat | \"auto\";\n    }\n\n    // Call addReferences\n    const result = await addReferences(inputs as string[], library, addOptions);\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import { Hono } from \"hono\";\nimport { z } from \"zod\";\nimport type { Library } from \"../../core/library.js\";\nimport {\n  type CiteOperationOptions,\n  type CiteResult,\n  citeReferences,\n} from \"../../features/operations/cite.js\";\n\n/**\n * Zod schema for cite request body\n */\nconst CiteRequestSchema = z.object({\n  identifiers: z.array(z.string()).min(1, \"identifiers must be a non-empty array\"),\n  idType: z.enum([\"id\", \"uuid\", \"doi\", \"pmid\", \"isbn\"]).optional(),\n  inText: z.boolean().optional(),\n  style: z.string().optional(),\n  cslFile: z.string().optional(),\n  locale: z.string().optional(),\n  format: z.enum([\"text\", \"html\"]).optional(),\n});\n\ntype CiteRequestBody = z.infer<typeof CiteRequestSchema>;\n\n/**\n * Build cite operation options from validated request body.\n */\nfunction buildCiteOptions(body: CiteRequestBody): CiteOperationOptions {\n  return {\n    identifiers: body.identifiers,\n    ...(body.idType !== undefined && { idType: body.idType }),\n    ...(body.inText !== undefined && { inText: body.inText }),\n    ...(body.style !== undefined && { style: body.style }),\n    ...(body.cslFile !== undefined && { cslFile: body.cslFile }),\n    ...(body.locale !== undefined && { locale: body.locale }),\n    ...(body.format !== undefined && { format: body.format }),\n  };\n}\n\n/**\n * Create cite route for generating citations.\n * @param library - Library instance to use for operations\n * @returns Hono app with cite route\n */\nexport function createCiteRoute(library: Library) {\n  const route = new Hono();\n\n  // POST / - Generate citations for identifiers\n  route.post(\"/\", async (c) => {\n    // Parse request body\n    let rawBody: unknown;\n    try {\n      rawBody = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    // Validate with zod schema\n    const parseResult = CiteRequestSchema.safeParse(rawBody);\n    if (!parseResult.success) {\n      const errorMessage = parseResult.error.issues[0]?.message ?? \"Invalid request body\";\n      return c.json({ error: errorMessage }, 400);\n    }\n\n    // Call citeReferences operation\n    const result: CiteResult = await citeReferences(library, buildCiteOptions(parseResult.data));\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import { Hono } from \"hono\";\n\n/**\n * Health check route.\n * Returns a simple status to verify the server is running.\n */\nexport const healthRoute = new Hono();\n\nhealthRoute.get(\"/\", (c) => {\n  return c.json({ status: \"ok\" });\n});\n","import { Hono } from \"hono\";\nimport { z } from \"zod\";\nimport type { Library } from \"../../core/library.js\";\nimport { type ListOptions, listReferences } from \"../../features/operations/list.js\";\n\n/**\n * Request body schema for list endpoint\n */\nconst listRequestBodySchema = z.object({\n  format: z.enum([\"pretty\", \"json\", \"bibtex\", \"ids-only\", \"uuid\"]).optional(),\n});\n\n/**\n * Request body type for list endpoint\n */\nexport type ListRequestBody = z.infer<typeof listRequestBodySchema>;\n\n/**\n * Creates list route for HTTP server\n */\nexport function createListRoute(library: Library) {\n  const route = new Hono();\n\n  // POST / - List all references\n  route.post(\"/\", async (c) => {\n    // Parse request body\n    let body: unknown;\n    try {\n      body = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    // Validate body with zod\n    const parseResult = listRequestBodySchema.safeParse(body);\n    if (!parseResult.success) {\n      return c.json({ error: \"Request body must be an object\" }, 400);\n    }\n\n    const requestBody = parseResult.data;\n\n    // Build options for listReferences\n    const options: ListOptions = {};\n    if (requestBody.format !== undefined) {\n      options.format = requestBody.format;\n    }\n\n    // Call listReferences operation\n    const result = await listReferences(library, options);\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import { Hono } from \"hono\";\nimport type { Library } from \"../../core/library.js\";\nimport { removeReference } from \"../../features/operations/remove.js\";\nimport { updateReference } from \"../../features/operations/update.js\";\n\n/**\n * Create references CRUD route with the given library.\n * @param library - Library instance to use for operations\n * @returns Hono app with references routes\n */\nexport function createReferencesRoute(library: Library) {\n  const route = new Hono();\n\n  // GET / - Get all references (getAll now returns Promise<CslItem[]>)\n  route.get(\"/\", async (c) => {\n    const items = await library.getAll();\n    return c.json(items);\n  });\n\n  // GET /uuid/:uuid - Get reference by UUID\n  route.get(\"/uuid/:uuid\", async (c) => {\n    const uuid = c.req.param(\"uuid\");\n    const item = await library.find(uuid, { idType: \"uuid\" });\n\n    if (!item) {\n      return c.json({ error: \"Reference not found\" }, 404);\n    }\n\n    return c.json(item);\n  });\n\n  // GET /id/:id - Get reference by citation ID\n  route.get(\"/id/:id\", async (c) => {\n    const id = c.req.param(\"id\");\n    const item = await library.find(id);\n\n    if (!item) {\n      return c.json({ error: \"Reference not found\" }, 404);\n    }\n\n    return c.json(item);\n  });\n\n  // POST / - Create new reference\n  route.post(\"/\", async (c) => {\n    try {\n      const body = await c.req.json();\n\n      // Create and add reference (library.add handles validation and returns the added item)\n      const addedItem = await library.add(body);\n\n      return c.json(addedItem, 201);\n    } catch (error) {\n      return c.json(\n        {\n          error: \"Invalid request body\",\n          details: error instanceof Error ? error.message : String(error),\n        },\n        400\n      );\n    }\n  });\n\n  // PUT /uuid/:uuid - Update reference by UUID\n  // Request body: { updates: Partial<CslItem>, onIdCollision?: \"fail\" | \"suffix\" }\n  route.put(\"/uuid/:uuid\", async (c) => {\n    const uuid = c.req.param(\"uuid\");\n\n    let body: unknown;\n    try {\n      body = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    if (!body || typeof body !== \"object\") {\n      return c.json({ error: \"Request body must be an object\" }, 400);\n    }\n\n    const { updates, onIdCollision } = body as {\n      updates?: Partial<import(\"../../core/csl-json/types.js\").CslItem>;\n      onIdCollision?: \"fail\" | \"suffix\";\n    };\n\n    if (!updates || typeof updates !== \"object\") {\n      return c.json({ error: \"Request body must contain 'updates' object\" }, 400);\n    }\n\n    // Use updateReference operation\n    const result = await updateReference(library, {\n      identifier: uuid,\n      idType: \"uuid\",\n      updates,\n      onIdCollision: onIdCollision ?? \"suffix\",\n    });\n\n    // Return operation result with appropriate status code\n    if (!result.updated) {\n      const status = result.idCollision ? 409 : 404;\n      return c.json(result, status);\n    }\n\n    return c.json(result);\n  });\n\n  // PUT /id/:id - Update reference by citation ID\n  // Request body: { updates: Partial<CslItem>, onIdCollision?: \"fail\" | \"suffix\" }\n  route.put(\"/id/:id\", async (c) => {\n    const id = c.req.param(\"id\");\n\n    let body: unknown;\n    try {\n      body = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    if (!body || typeof body !== \"object\") {\n      return c.json({ error: \"Request body must be an object\" }, 400);\n    }\n\n    const { updates, onIdCollision } = body as {\n      updates?: Partial<import(\"../../core/csl-json/types.js\").CslItem>;\n      onIdCollision?: \"fail\" | \"suffix\";\n    };\n\n    if (!updates || typeof updates !== \"object\") {\n      return c.json({ error: \"Request body must contain 'updates' object\" }, 400);\n    }\n\n    // Use updateReference operation with idType: 'id'\n    const result = await updateReference(library, {\n      identifier: id,\n      updates,\n      onIdCollision: onIdCollision ?? \"suffix\",\n    });\n\n    // Return operation result with appropriate status code\n    if (!result.updated) {\n      const status = result.idCollision ? 409 : 404;\n      return c.json(result, status);\n    }\n\n    return c.json(result);\n  });\n\n  // DELETE /uuid/:uuid - Delete reference by UUID\n  route.delete(\"/uuid/:uuid\", async (c) => {\n    const uuid = c.req.param(\"uuid\");\n\n    // Use removeReference operation\n    const result = await removeReference(library, {\n      identifier: uuid,\n      idType: \"uuid\",\n    });\n\n    // Return operation result with appropriate status code\n    if (!result.removed) {\n      return c.json(result, 404);\n    }\n\n    return c.json(result);\n  });\n\n  // DELETE /id/:id - Delete reference by citation ID\n  route.delete(\"/id/:id\", async (c) => {\n    const id = c.req.param(\"id\");\n\n    // Use removeReference operation\n    const result = await removeReference(library, {\n      identifier: id,\n    });\n\n    // Return operation result with appropriate status code\n    if (!result.removed) {\n      return c.json(result, 404);\n    }\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import { Hono } from \"hono\";\nimport { z } from \"zod\";\nimport type { Library } from \"../../core/library.js\";\nimport { type SearchOperationOptions, searchReferences } from \"../../features/operations/search.js\";\n\n/**\n * Request body schema for search endpoint\n */\nconst searchRequestBodySchema = z.object({\n  query: z.string(),\n  format: z.enum([\"pretty\", \"json\", \"bibtex\", \"ids-only\", \"uuid\"]).optional(),\n});\n\n/**\n * Request body type for search endpoint\n */\nexport type SearchRequestBody = z.infer<typeof searchRequestBodySchema>;\n\n/**\n * Creates search route for HTTP server\n */\nexport function 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{ Config } from \"../config/schema.js\";\nimport { Library } from \"../core/library.js\";\nimport { FileWatcher } from \"../features/file-watcher/file-watcher.js\";\nimport { createAddRoute } from \"./routes/add.js\";\nimport { createCiteRoute } from \"./routes/cite.js\";\nimport { healthRoute } from \"./routes/health.js\";\nimport { createListRoute } from \"./routes/list.js\";\nimport { createReferencesRoute } from \"./routes/references.js\";\nimport { createSearchRoute } from \"./routes/search.js\";\n\n/**\n * Result of starting a server with file watcher.\n */\nexport interface ServerWithFileWatcherResult {\n  /** The Hono application */\n  app: Hono;\n  /** The library instance */\n  library: Library;\n  /** The file watcher instance */\n  fileWatcher: FileWatcher;\n  /** Dispose function to clean up resources */\n  dispose: () => Promise<void>;\n}\n\n/**\n * Create the main Hono server application.\n * @param library - Library instance for the references API\n * @param config - Configuration for the server\n * @returns Hono application\n */\nexport function createServer(library: Library, config: Config) {\n  const app = new Hono();\n\n  // Health check route\n  app.route(\"/health\", healthRoute);\n\n  // References API routes\n  const referencesRoute = createReferencesRoute(library);\n  app.route(\"/api/references\", referencesRoute);\n\n  // Add references route\n  const addRoute = createAddRoute(library, config);\n  app.route(\"/api/add\", addRoute);\n\n  // Cite route\n  const citeRoute = createCiteRoute(library);\n  app.route(\"/api/cite\", citeRoute);\n\n  // List route\n  const listRoute = createListRoute(library);\n  app.route(\"/api/list\", listRoute);\n\n  // Search route\n  const searchRoute = createSearchRoute(library);\n  app.route(\"/api/search\", searchRoute);\n\n  return app;\n}\n\n/**\n * Start a server with file watcher for automatic library reload.\n * Uses the same pattern as MCP server file monitoring.\n * @param libraryPath - Path to the library file\n * @param config - Configuration for the server\n * @returns Server with file watcher result\n */\nexport async function startServerWithFileWatcher(\n  libraryPath: string,\n  config: Config\n): Promise<ServerWithFileWatcherResult> {\n  // Load library\n  const library = await Library.load(libraryPath);\n\n  // Create the Hono app\n  const app = createServer(library, config);\n\n  // Create and start file watcher\n  const fileWatcher = new FileWatcher(libraryPath, {\n    debounceMs: config.watch.debounceMs,\n    maxRetries: config.watch.maxRetries,\n    retryDelayMs: config.watch.retryIntervalMs,\n    pollIntervalMs: config.watch.pollIntervalMs,\n  });\n\n  // Listen for file changes\n  // Library.reload() handles self-write detection via hash comparison\n  fileWatcher.on(\"change\", () => {\n    library.reload().catch((error) => {\n      // Log error but don't crash - library continues with previous state\n      console.error(\"Failed to reload library:\", error);\n    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package/dist/cli/commands/fulltext.d.ts

@@ -3,6 +3,7 @@
  *
  * Uses ILibrary interface for unified operations across local and server modes.
  */
+import type { IdentifierType } from "../../core/library-interface.js";
 import type { FulltextType } from "../../features/fulltext/index.js";
 import { type FulltextAttachResult, type FulltextDetachResult, type FulltextGetResult } from "../../features/operations/fulltext/index.js";
 import type { ExecutionContext } from "../execution-context.js";
@@ -15,7 +16,7 @@ export interface FulltextAttachOptions {
     type?: FulltextType;
     move?: boolean;
     force?: boolean;
-    byUuid?: boolean;
+    idType?: IdentifierType;
     fulltextDirectory: string;
     stdinContent?: Buffer;
 }
@@ -26,7 +27,7 @@ export interface FulltextGetOptions {
     identifier: string;
     type?: FulltextType;
     stdout?: boolean;
-    byUuid?: boolean;
+    idType?: IdentifierType;
     fulltextDirectory: string;
 }
 /**
@@ -37,7 +38,7 @@ export interface FulltextDetachOptions {
     type?: FulltextType;
     delete?: boolean;
     force?: boolean;
-    byUuid?: boolean;
+    idType?: IdentifierType;
     fulltextDirectory: string;
 }
 export type { FulltextAttachResult, FulltextGetResult, FulltextDetachResult };

package/dist/cli/commands/fulltext.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"fulltext.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/fulltext.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kCAAkC,CAAC;AACrE,OAAO,EACL,KAAK,oBAAoB,EACzB,KAAK,oBAAoB,EACzB,KAAK,iBAAiB,EAOvB,MAAM,6CAA6C,CAAC;AACrD,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,qBAAqB;IACpC,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,YAAY,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED;;GAEG;AACH,MAAM,WAAW,kBAAkB;IACjC,UAAU,EAAE,MAAM,CAAC;IACnB,IAAI,CAAC,EAAE,YAAY,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,iBAAiB,EAAE,MAAM,CAAC;CAC3B;AAED;;GAEG;AACH,MAAM,WAAW,qBAAqB;IACpC,UAAU,EAAE,MAAM,CAAC;IACnB,IAAI,CAAC,EAAE,YAAY,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,iBAAiB,EAAE,MAAM,CAAC;CAC3B;AAGD,YAAY,EAAE,oBAAoB,EAAE,iBAAiB,EAAE,oBAAoB,EAAE,CAAC;AAE9E;;GAEG;AACH,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,qBAAqB,EAC9B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,oBAAoB,CAAC,CAa/B;AAED;;GAEG;AACH,wBAAsB,kBAAkB,CACtC,OAAO,EAAE,kBAAkB,EAC3B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,iBAAiB,CAAC,CAU5B;AAED;;GAEG;AACH,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,qBAAqB,EAC9B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,oBAAoB,CAAC,CAU/B;AAMD;;GAEG;AACH,wBAAgB,0BAA0B,CAAC,MAAM,EAAE,oBAAoB,GAAG,MAAM,CAiB/E;AAED;;GAEG;AACH,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,iBAAiB,GAAG,MAAM,CAkBzE;AAED;;GAEG;AACH,wBAAgB,0BAA0B,CAAC,MAAM,EAAE,oBAAoB,GAAG,MAAM,CAe/E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,oBAAoB,GAAG,iBAAiB,GAAG,oBAAoB,GACtE,MAAM,CAER"}
+{"version":3,"file":"fulltext.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/fulltext.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACtE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kCAAkC,CAAC;AACrE,OAAO,EACL,KAAK,oBAAoB,EACzB,KAAK,oBAAoB,EACzB,KAAK,iBAAiB,EAOvB,MAAM,6CAA6C,CAAC;AACrD,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,qBAAqB;IACpC,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,YAAY,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,cAAc,CAAC;IACxB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED;;GAEG;AACH,MAAM,WAAW,kBAAkB;IACjC,UAAU,EAAE,MAAM,CAAC;IACnB,IAAI,CAAC,EAAE,YAAY,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,MAAM,CAAC,EAAE,cAAc,CAAC;IACxB,iBAAiB,EAAE,MAAM,CAAC;CAC3B;AAED;;GAEG;AACH,MAAM,WAAW,qBAAqB;IACpC,UAAU,EAAE,MAAM,CAAC;IACnB,IAAI,CAAC,EAAE,YAAY,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,cAAc,CAAC;IACxB,iBAAiB,EAAE,MAAM,CAAC;CAC3B;AAGD,YAAY,EAAE,oBAAoB,EAAE,iBAAiB,EAAE,oBAAoB,EAAE,CAAC;AAE9E;;GAEG;AACH,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,qBAAqB,EAC9B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,oBAAoB,CAAC,CAa/B;AAED;;GAEG;AACH,wBAAsB,kBAAkB,CACtC,OAAO,EAAE,kBAAkB,EAC3B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,iBAAiB,CAAC,CAU5B;AAED;;GAEG;AACH,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,qBAAqB,EAC9B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,oBAAoB,CAAC,CAU/B;AAMD;;GAEG;AACH,wBAAgB,0BAA0B,CAAC,MAAM,EAAE,oBAAoB,GAAG,MAAM,CAiB/E;AAED;;GAEG;AACH,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,iBAAiB,GAAG,MAAM,CAkBzE;AAED;;GAEG;AACH,wBAAgB,0BAA0B,CAAC,MAAM,EAAE,oBAAoB,GAAG,MAAM,CAe/E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,oBAAoB,GAAG,iBAAiB,GAAG,oBAAoB,GACtE,MAAM,CAER"}

package/dist/cli/commands/remove.d.ts

@@ -1,4 +1,5 @@
 import type { CslItem } from "../../core/csl-json/types.js";
+import type { IdentifierType } from "../../core/library-interface.js";
 import type { FulltextType } from "../../features/fulltext/index.js";
 import type { RemoveResult } from "../../features/operations/remove.js";
 import type { ExecutionContext } from "../execution-context.js";
@@ -7,7 +8,7 @@ import type { ExecutionContext } from "../execution-context.js";
  */
 export interface RemoveCommandOptions {
     identifier: string;
-    byUuid?: boolean;
+    idType?: IdentifierType;
 }
 /**
  * Result from remove command execution.

package/dist/cli/commands/remove.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"remove.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/remove.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kCAAkC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,qCAAqC,CAAC;AACxE,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED;;GAEG;AACH,MAAM,MAAM,mBAAmB,GAAG,YAAY,CAAC;AAE/C;;;;;;;GAOG;AACH,wBAAsB,aAAa,CACjC,OAAO,EAAE,oBAAoB,EAC7B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,mBAAmB,CAAC,CAI9B;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,mBAAmB,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,CAW1F;AAED;;;;;GAKG;AACH,wBAAgB,0BAA0B,CAAC,IAAI,EAAE,OAAO,GAAG,YAAY,EAAE,CAYxE;AAED;;;;;GAKG;AACH,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,YAAY,EAAE,GAAG,MAAM,CAInE;AAED;;;;;GAKG;AACH,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,OAAO,EAAE,iBAAiB,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAsBjG"}
+{"version":3,"file":"remove.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/remove.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACtE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kCAAkC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,qCAAqC,CAAC;AACxE,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,cAAc,CAAC;CACzB;AAED;;GAEG;AACH,MAAM,MAAM,mBAAmB,GAAG,YAAY,CAAC;AAE/C;;;;;;;GAOG;AACH,wBAAsB,aAAa,CACjC,OAAO,EAAE,oBAAoB,EAC7B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,mBAAmB,CAAC,CAI9B;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,mBAAmB,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,CAW1F;AAED;;;;;GAKG;AACH,wBAAgB,0BAA0B,CAAC,IAAI,EAAE,OAAO,GAAG,YAAY,EAAE,CAYxE;AAED;;;;;GAKG;AACH,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,YAAY,EAAE,GAAG,MAAM,CAInE;AAED;;;;;GAKG;AACH,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,OAAO,EAAE,iBAAiB,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAsBjG"}

package/dist/cli/commands/update.d.ts

@@ -1,4 +1,5 @@
 import type { CslItem } from "../../core/csl-json/types.js";
+import type { IdentifierType } from "../../core/library-interface.js";
 import type { UpdateOperationResult } from "../../features/operations/update.js";
 import type { ExecutionContext } from "../execution-context.js";
 /**
@@ -7,7 +8,7 @@ import type { ExecutionContext } from "../execution-context.js";
 export interface UpdateCommandOptions {
     identifier: string;
     updates: Partial<CslItem>;
-    byUuid?: boolean;
+    idType?: IdentifierType;
 }
 /**
  * Result from update command execution.

package/dist/cli/commands/update.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/update.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAC;AACjF,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,OAAO,CAAC,OAAO,CAAC,CAAC;IAC1B,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED;;GAEG;AACH,MAAM,MAAM,mBAAmB,GAAG,qBAAqB,CAAC;AAExD;;;;;;;GAOG;AACH,wBAAsB,aAAa,CACjC,OAAO,EAAE,oBAAoB,EAC7B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,mBAAmB,CAAC,CAI9B;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,mBAAmB,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,CAsB1F"}
+{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/update.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACtE,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAC;AACjF,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,OAAO,CAAC,OAAO,CAAC,CAAC;IAC1B,MAAM,CAAC,EAAE,cAAc,CAAC;CACzB;AAED;;GAEG;AACH,MAAM,MAAM,mBAAmB,GAAG,qBAAqB,CAAC;AAExD;;;;;;;GAOG;AACH,wBAAsB,aAAa,CACjC,OAAO,EAAE,oBAAoB,EAC7B,OAAO,EAAE,gBAAgB,GACxB,OAAO,CAAC,mBAAmB,CAAC,CAI9B;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,mBAAmB,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,CAsB1F"}

package/dist/cli/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAoDpC;;GAEG;AACH,wBAAgB,aAAa,IAAI,OAAO,CA8BvC;AAmwBD;;GAEG;AACH,wBAAsB,IAAI,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAaxD"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAoDpC;;GAEG;AACH,wBAAgB,aAAa,IAAI,OAAO,CA8BvC;AAuwBD;;GAEG;AACH,wBAAsB,IAAI,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAaxD"}

package/dist/cli/server-client.d.ts

@@ -1,12 +1,13 @@
 import type { CslItem } from "../core/csl-json/types.js";
 import type { FindOptions, RemoveResult as ILibraryRemoveResult, RemoveOptions, UpdateOptions, UpdateResult } from "../core/library-interface.js";
 import type { AddReferencesResult, CiteResult, ILibraryOperations, ImportOptions, ListOptions, ListResult, SearchOperationOptions, SearchResult } from "../features/operations/index.js";
+import type { IdentifierType } from "../core/library-interface.js";
 /**
  * Options for cite method.
  */
 export interface CiteOptions {
     identifiers: string[];
-    byUuid?: boolean;
+    idType?: IdentifierType;
     inText?: boolean;
     style?: string;
     cslFile?: string;
@@ -27,7 +28,7 @@ export declare class ServerClient implements ILibraryOperations {
     /**
      * Find reference by citation ID or UUID.
      * @param identifier - Citation ID or UUID
-     * @param options - Find options (byUuid to use UUID lookup)
+     * @param options - Find options (idType to specify identifier type)
      * @returns CSL item or undefined if not found
      */
     find(identifier: string, options?: FindOptions): Promise<CslItem | undefined>;
@@ -41,14 +42,14 @@ export declare class ServerClient implements ILibraryOperations {
      * Update reference by citation ID or UUID.
      * @param identifier - Citation ID or UUID
      * @param updates - Partial CSL item with fields to update
-     * @param options - Update options (byUuid to use UUID lookup, onIdCollision for collision handling)
+     * @param options - Update options (idType to specify identifier type, onIdCollision for collision handling)
      * @returns Update result with updated item, success status, and any ID changes
      */
     update(identifier: string, updates: Partial<CslItem>, options?: UpdateOptions): Promise<UpdateResult>;
     /**
      * Remove a reference by citation ID or UUID.
      * @param identifier - The citation ID or UUID of the reference to remove
-     * @param options - Remove options (byUuid to use UUID lookup)
+     * @param options - Remove options (idType to specify identifier type)
      * @returns Remove result with removed status and removedItem
      */
     remove(identifier: string, options?: RemoveOptions): Promise<ILibraryRemoveResult>;

package/dist/cli/server-client.d.ts.map

@@ -1 +1 @@
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