@ncukondo/reference-manager 0.13.3 → 0.13.5

package/dist/chunks/{index-C0TB_ha0.js.map → index-4KSTJ3rp.js.map}

@@ -1 +1 @@
-{"version":3,"file":"index-C0TB_ha0.js","sources":["../../src/features/operations/update.ts","../../src/features/format/citation-fallback.ts","../../src/features/format/citation-csl.ts","../../src/features/pagination/sorter.ts","../../src/features/pagination/paginate.ts","../../src/config/csl-styles.ts","../../src/features/operations/remove.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/server/routes/add.ts","../../src/features/operations/cite.ts","../../src/server/routes/cite.ts","../../src/server/routes/health.ts","../../src/features/operations/list.ts","../../src/server/routes/list.ts","../../src/server/routes/references.ts","../../src/features/operations/search.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","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, plugins } 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   * Custom CSL style XML content.\n   * When provided, this XML is registered and used instead of built-in styles.\n   */\n  styleXml?: 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 * Register a custom CSL style with citation-js.\n * Returns the style name to use for formatting.\n * @throws Error if CSL XML is invalid or malformed\n */\nfunction registerCustomStyle(styleName: string, styleXml: string): string {\n  // Basic XML validation\n  if (!styleXml.includes(\"<style\") || !styleXml.includes(\"</style>\")) {\n    throw new Error(\n      \"Invalid CSL file: Missing <style> element. The file may be malformed or not a valid CSL style.\"\n    );\n  }\n\n  // Check for required CSL sections\n  const hasCitation = styleXml.includes(\"<citation\") || styleXml.includes(\"<citation>\");\n  const hasBibliography = styleXml.includes(\"<bibliography\") || styleXml.includes(\"<bibliography>\");\n  if (!hasCitation && !hasBibliography) {\n    throw new Error(\n      \"Invalid CSL file: Missing <citation> or <bibliography> section. \" +\n        \"A valid CSL style must define at least one of these sections.\"\n    );\n  }\n\n  try {\n    const config = plugins.config.get(\"@csl\");\n    config.templates.add(styleName, styleXml);\n    return styleName;\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    throw new Error(`Failed to register CSL style '${styleName}': ${message}`);\n  }\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  let style = options.style || \"apa\";\n  const format = options.format || \"text\";\n  const locale = options.locale || \"en-US\";\n\n  // Register custom style if XML is provided\n  if (options.styleXml) {\n    style = registerCustomStyle(style, options.styleXml);\n  }\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  let style = options.style || \"apa\";\n  const format = options.format || \"text\";\n  const locale = options.locale || \"en-US\";\n\n  // Register custom style if XML is provided\n  if (options.styleXml) {\n    style = registerCustomStyle(style, options.styleXml);\n  }\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","/**\n * Reference sorter\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { SortField, SortOrder } from \"./types.js\";\n\n/**\n * Extract created_at timestamp from item, returns epoch (0) if missing\n */\nfunction getCreatedAt(item: CslItem): number {\n  const createdAt = item.custom?.created_at;\n  if (!createdAt) return 0;\n  return new Date(createdAt).getTime();\n}\n\n/**\n * Extract updated timestamp from item, falls back to created_at\n */\nfunction getUpdatedAt(item: CslItem): number {\n  const timestamp = item.custom?.timestamp;\n  if (timestamp) return new Date(timestamp).getTime();\n  return getCreatedAt(item);\n}\n\n/**\n * Extract published date as comparable number\n * Returns 0 (epoch) if missing\n */\nfunction getPublishedDate(item: CslItem): number {\n  const dateParts = item.issued?.[\"date-parts\"]?.[0];\n  if (!dateParts || dateParts.length === 0) return 0;\n\n  const year = dateParts[0] ?? 0;\n  const month = dateParts[1] ?? 1;\n  const day = dateParts[2] ?? 1;\n\n  return new Date(year, month - 1, day).getTime();\n}\n\n/**\n * Extract first author's sortable name\n * Returns \"Anonymous\" if no author\n */\nfunction getAuthorName(item: CslItem): string {\n  const firstAuthor = item.author?.[0];\n  if (!firstAuthor) return \"Anonymous\";\n\n  return firstAuthor.family ?? firstAuthor.literal ?? \"Anonymous\";\n}\n\n/**\n * Extract title, returns empty string if missing\n */\nfunction getTitle(item: CslItem): string {\n  return item.title ?? \"\";\n}\n\n/**\n * Get sort value for a given field\n */\nfunction getSortValue(item: CslItem, field: SortField): number | string {\n  switch (field) {\n    case \"created\":\n      return getCreatedAt(item);\n    case \"updated\":\n      return getUpdatedAt(item);\n    case \"published\":\n      return getPublishedDate(item);\n    case \"author\":\n      return getAuthorName(item).toLowerCase();\n    case \"title\":\n      return getTitle(item).toLowerCase();\n  }\n}\n\n/**\n * Compare function for sorting\n */\nfunction compareValues(a: number | string, b: number | string, order: SortOrder): number {\n  const multiplier = order === \"desc\" ? -1 : 1;\n\n  if (typeof a === \"number\" && typeof b === \"number\") {\n    return (a - b) * multiplier;\n  }\n\n  const strA = String(a);\n  const strB = String(b);\n  return strA.localeCompare(strB) * multiplier;\n}\n\n/**\n * Sort references by the specified field and order.\n * Uses secondary sort: created (desc), then id (asc) for stability.\n *\n * @param items - References to sort\n * @param sort - Sort field\n * @param order - Sort order\n * @returns Sorted references (new array, does not mutate input)\n */\nexport function sortReferences(items: CslItem[], sort: SortField, order: SortOrder): CslItem[] {\n  return [...items].sort((a, b) => {\n    // Primary sort\n    const aValue = getSortValue(a, sort);\n    const bValue = getSortValue(b, sort);\n    const primaryCompare = compareValues(aValue, bValue, order);\n\n    if (primaryCompare !== 0) return primaryCompare;\n\n    // Secondary sort: created (desc)\n    const aCreated = getCreatedAt(a);\n    const bCreated = getCreatedAt(b);\n    const createdCompare = bCreated - aCreated; // desc\n\n    if (createdCompare !== 0) return createdCompare;\n\n    // Tertiary sort: id (asc) for stability\n    return a.id.localeCompare(b.id);\n  });\n}\n","/**\n * Pagination applier\n */\n\nexport interface PaginateOptions {\n  limit?: number;\n  offset?: number;\n}\n\nexport interface PaginateResult<T> {\n  items: T[];\n  nextOffset: number | null;\n}\n\n/**\n * Apply pagination to an array of items.\n *\n * @param items - Items to paginate\n * @param options - Pagination options (limit=0 or undefined means unlimited)\n * @returns Paginated items with nextOffset (null if no more items)\n */\nexport function paginate<T>(items: T[], options: PaginateOptions): PaginateResult<T> {\n  const offset = options.offset ?? 0;\n  const limit = options.limit ?? 0;\n\n  // Validate inputs\n  if (limit < 0) {\n    throw new Error(\"limit must be non-negative\");\n  }\n  if (offset < 0) {\n    throw new Error(\"offset must be non-negative\");\n  }\n\n  const isUnlimited = limit === 0;\n\n  // Apply offset\n  const afterOffset = items.slice(offset);\n\n  // Apply limit (0 means unlimited)\n  const paginatedItems = isUnlimited ? afterOffset : afterOffset.slice(0, limit);\n\n  // Calculate nextOffset\n  let nextOffset: number | null = null;\n  if (!isUnlimited && paginatedItems.length > 0) {\n    const nextPosition = offset + paginatedItems.length;\n    if (nextPosition < items.length) {\n      nextOffset = nextPosition;\n    }\n  }\n\n  return {\n    items: paginatedItems,\n    nextOffset,\n  };\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","import { unlink } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../core/library-interface.js\";\nimport type { FulltextType } from \"../fulltext/index.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  /** Directory containing fulltext files (required if deleteFulltext is true) */\n  fulltextDirectory?: string;\n  /** Whether to delete associated fulltext files */\n  deleteFulltext?: boolean;\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  /** Fulltext types that were deleted (only when deleteFulltext=true) */\n  deletedFulltextTypes?: FulltextType[];\n}\n\n/**\n * Get fulltext attachment types from a CSL item.\n */\nexport function getFulltextAttachmentTypes(item: CslItem): FulltextType[] {\n  const types: FulltextType[] = [];\n  const fulltext = item.custom?.fulltext;\n\n  if (fulltext?.pdf) {\n    types.push(\"pdf\");\n  }\n  if (fulltext?.markdown) {\n    types.push(\"markdown\");\n  }\n\n  return types;\n}\n\n/**\n * Delete fulltext files associated with an item.\n */\nasync function deleteFulltextFiles(item: CslItem, fulltextDirectory: string): Promise<void> {\n  const fulltext = item.custom?.fulltext;\n  if (!fulltext) {\n    return;\n  }\n\n  const filesToDelete: string[] = [];\n\n  if (fulltext.pdf) {\n    filesToDelete.push(join(fulltextDirectory, fulltext.pdf));\n  }\n  if (fulltext.markdown) {\n    filesToDelete.push(join(fulltextDirectory, fulltext.markdown));\n  }\n\n  for (const filePath of filesToDelete) {\n    try {\n      await unlink(filePath);\n    } catch {\n      // Ignore errors (file might not exist)\n    }\n  }\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\", fulltextDirectory, deleteFulltext = false } = options;\n\n  const result = await library.remove(identifier, { idType });\n\n  if (!result.removed || !result.removedItem) {\n    return { removed: false };\n  }\n\n  // Delete fulltext files if requested\n  let deletedFulltextTypes: FulltextType[] | undefined;\n  if (deleteFulltext && fulltextDirectory) {\n    deletedFulltextTypes = getFulltextAttachmentTypes(result.removedItem);\n    if (deletedFulltextTypes.length > 0) {\n      await deleteFulltextFiles(result.removedItem, fulltextDirectory);\n    }\n  }\n\n  await library.save();\n\n  return {\n    removed: true,\n    removedItem: result.removedItem,\n    ...(deletedFulltextTypes && deletedFulltextTypes.length > 0 && { deletedFulltextTypes }),\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  | \"nbib\"\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  \".nbib\": \"nbib\",\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  // NBIB (PubMed MEDLINE): starts with PMID-\n  if (trimmed.startsWith(\"PMID-\")) {\n    return \"nbib\";\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+$/;\n\n/**\n * PubMed configuration for API requests\n */\nexport interface PubmedConfig {\n  email?: string;\n  apiKey?: string;\n}\n\n/**\n * Categorized failure reasons for JSON output\n */\nexport type FailureReason =\n  | \"not_found\"\n  | \"fetch_error\"\n  | \"parse_error\"\n  | \"validation_error\"\n  | \"unknown\";\n\n/**\n * Result of fetching a single identifier\n */\nexport type FetchResult =\n  | { success: true; item: CslItem }\n  | { success: false; error: string; reason: FailureReason };\n\n/**\n * Result of fetching a PMID (includes pmid for tracking)\n */\nexport type PmidFetchResult =\n  | { pmid: string; success: true; item: CslItem }\n  | { pmid: string; success: false; error: string; reason: FailureReason };\n\n/**\n * Results of fetching multiple PMIDs\n */\nexport type FetchResults = PmidFetchResult[];\n\n/**\n * Build PMC API URL with query parameters\n */\nfunction buildPmcUrl(pmids: string[], config: PubmedConfig): string {\n  const url = new URL(PMC_API_BASE);\n  url.searchParams.set(\"format\", \"csl\");\n\n  // Add each PMID as separate id parameter\n  for (const pmid of pmids) {\n    url.searchParams.append(\"id\", pmid);\n  }\n\n  if (config.email) {\n    url.searchParams.set(\"email\", config.email);\n  }\n  if (config.apiKey) {\n    url.searchParams.set(\"api_key\", config.apiKey);\n  }\n\n  return url.toString();\n}\n\n/**\n * Extract PMID from CSL-JSON item id field\n * PMC API returns id like \"pmid:12345678\"\n */\nfunction extractPmidFromId(id: string | undefined): string | undefined {\n  if (!id) return undefined;\n  const match = id.match(/^pmid:(\\d+)$/);\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      reason: \"validation_error\",\n    };\n  }\n  return {\n    pmid,\n    success: false as const,\n    error: `PMID ${pmid} not found`,\n    reason: \"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        reason: \"fetch_error\",\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      reason: \"fetch_error\",\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      reason: \"validation_error\",\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        reason: \"not_found\",\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}: ${parseResult.error.message}`,\n        reason: \"validation_error\",\n      };\n    }\n\n    return { success: true, item: parseResult.data };\n  } catch (error) {\n    const errorMsg = error instanceof Error ? error.message : String(error);\n    return {\n      success: false,\n      error: errorMsg,\n      reason: \"fetch_error\",\n    };\n  }\n}\n\n/** ISBN-10 pattern: 9 digits + (digit or X) */\nconst ISBN10_PATTERN = /^\\d{9}[\\dX]$/;\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      reason: \"validation_error\",\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        reason: \"not_found\",\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        reason: \"validation_error\",\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      reason: \"fetch_error\",\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 * NBIB to RIS tag mapping\n *\n * Maps PubMed MEDLINE tags to RIS equivalents\n */\nconst NBIB_TO_RIS_TAG_MAP: Record<string, string> = {\n  PMID: \"AN\", // PubMed ID -> Accession Number\n  TI: \"TI\", // Title -> Title\n  FAU: \"AU\", // Full Author -> Author\n  AU: \"AU\", // Author -> Author (short form, use FAU when available)\n  JT: \"JO\", // Journal Title -> Journal Name\n  TA: \"JA\", // Title Abbreviation -> Journal Abbreviation\n  AB: \"AB\", // Abstract -> Abstract\n  VI: \"VL\", // Volume -> Volume\n  IP: \"IS\", // Issue/Part -> Issue Number\n  PG: \"SP\", // Pagination -> Start Page (includes range)\n  DP: \"PY\", // Date of Publication -> Publication Year\n  LA: \"LA\", // Language -> Language\n  MH: \"KW\", // MeSH Headings -> Keywords\n  OT: \"KW\", // Other Terms -> Keywords\n  AD: \"AD\", // Affiliation/Address -> Author Address\n  IS: \"SN\", // ISSN -> Serial Number\n  PT: \"TY\", // Publication Type -> Type of Reference\n};\n\n/**\n * Publication type mapping from NBIB to RIS\n */\nconst NBIB_PUBLICATION_TYPE_MAP: Record<string, string> = {\n  \"Journal Article\": \"JOUR\",\n  Review: \"JOUR\",\n  Book: \"BOOK\",\n  \"Book Chapter\": \"CHAP\",\n  \"Conference Paper\": \"CPAPER\",\n  Thesis: \"THES\",\n  Report: \"RPRT\",\n};\n\n/**\n * Parse a single NBIB entry into tag-value pairs\n */\nfunction parseNbibEntry(entry: string): Array<{ tag: string; value: string }> {\n  const result: Array<{ tag: string; value: string }> = [];\n  const lines = entry.split(\"\\n\");\n\n  let currentTag = \"\";\n  let currentValue = \"\";\n\n  for (const line of lines) {\n    // Check if line starts with a tag (2-4 uppercase letters followed by space(s) and dash)\n    const tagMatch = line.match(/^([A-Z]{2,4})\\s*-\\s*(.*)$/);\n\n    if (tagMatch) {\n      // Save previous tag-value pair\n      if (currentTag) {\n        result.push({ tag: currentTag, value: currentValue.trim() });\n      }\n      currentTag = tagMatch[1] ?? \"\";\n      currentValue = tagMatch[2] ?? \"\";\n    } else if (currentTag && line.match(/^\\s+/)) {\n      // Continuation line (starts with whitespace)\n      currentValue += ` ${line.trim()}`;\n    }\n  }\n\n  // Save the last tag-value pair\n  if (currentTag) {\n    result.push({ tag: currentTag, value: currentValue.trim() });\n  }\n\n  return result;\n}\n\n/**\n * Convert a single NBIB tag-value pair to RIS line\n * @returns RIS line or null if tag should be skipped\n */\nfunction convertNbibTagToRisLine(\n  tag: string,\n  value: string\n): { line: string; isType?: boolean } | null {\n  // Handle DOI specially (AID tag with [doi] suffix)\n  if (tag === \"AID\" && value.includes(\"[doi]\")) {\n    const doi = value.replace(/\\s*\\[doi\\].*$/, \"\").trim();\n    return { line: `DO  - ${doi}` };\n  }\n\n  // Handle PII specially (AID tag with [pii] suffix)\n  if (tag === \"AID\" && value.includes(\"[pii]\")) {\n    const pii = value.replace(/\\s*\\[pii\\].*$/, \"\").trim();\n    return { line: `C1  - ${pii}` }; // C1 = Custom Field 1\n  }\n\n  // Get mapped RIS tag\n  const risTag = NBIB_TO_RIS_TAG_MAP[tag];\n  if (!risTag) {\n    return null; // Skip unmapped tags\n  }\n\n  // Handle publication year (extract year only)\n  if (risTag === \"PY\") {\n    const yearMatch = value.match(/^(\\d{4})/);\n    return yearMatch ? { line: `PY  - ${yearMatch[1]}` } : null;\n  }\n\n  // Handle publication type\n  if (risTag === \"TY\") {\n    const risType = NBIB_PUBLICATION_TYPE_MAP[value] || \"JOUR\";\n    return { line: `TY  - ${risType}`, isType: true };\n  }\n\n  return { line: `${risTag}  - ${value}` };\n}\n\n/**\n * Convert a single NBIB entry to RIS format\n */\nfunction convertSingleNbibEntryToRis(entry: string): string {\n  const parsed = parseNbibEntry(entry);\n\n  if (parsed.length === 0) {\n    return \"\";\n  }\n\n  const risLines: string[] = [];\n  let hasType = false;\n\n  for (const { tag, value } of parsed) {\n    const converted = convertNbibTagToRisLine(tag, value);\n    if (!converted) {\n      continue;\n    }\n\n    if (converted.isType) {\n      risLines.unshift(converted.line); // TY must be first\n      hasType = true;\n    } else {\n      risLines.push(converted.line);\n    }\n  }\n\n  // Add default type if not present\n  if (!hasType) {\n    risLines.unshift(\"TY  - JOUR\");\n  }\n\n  // Add end record tag\n  risLines.push(\"ER  -\");\n\n  return risLines.join(\"\\n\");\n}\n\n/**\n * Convert NBIB (PubMed MEDLINE) format to RIS format\n *\n * @param content - NBIB content string\n * @returns RIS format string\n */\nexport function convertNbibToRis(content: string): string {\n  const trimmed = content.trim();\n\n  if (!trimmed) {\n    return \"\";\n  }\n\n  // Split into entries by blank lines (PMID- starts each entry)\n  const entries = trimmed.split(/\\n\\s*\\n/).filter((e) => e.trim());\n\n  const risEntries = entries.map((entry) => convertSingleNbibEntryToRis(entry)).filter(Boolean);\n\n  return risEntries.join(\"\\n\\n\");\n}\n\n/**\n * Parse NBIB (PubMed MEDLINE) content to CSL-JSON\n *\n * Converts NBIB to RIS format first, then parses with citation-js\n *\n * @param content - NBIB content string\n * @returns Parse result with CSL-JSON items\n */\nexport function parseNbib(content: string): ParseResult {\n  const trimmed = content.trim();\n\n  // Handle empty input\n  if (!trimmed) {\n    return { success: true, items: [] };\n  }\n\n  // Convert NBIB to RIS\n  const risContent = convertNbibToRis(trimmed);\n\n  if (!risContent) {\n    return {\n      success: false,\n      items: [],\n      error: \"Failed to convert NBIB to RIS: No valid entries found\",\n    };\n  }\n\n  // Parse the RIS content\n  return parseRis(risContent);\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 { FailureReason, PubmedConfig } from \"./fetcher.js\";\nimport { normalizeDoi, normalizeIsbn, normalizePmid } from \"./normalizer.js\";\nimport { parseBibtex, parseNbib, parseRis } from \"./parser.js\";\n\n// Re-export FailureReason for external use\nexport type { FailureReason } from \"./fetcher.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; reason: FailureReason };\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    reason: \"validation_error\" as const,\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          reason: fetchResult.reason,\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({\n        success: false,\n        error: fetchResult.error,\n        source: doi,\n        reason: fetchResult.reason,\n      });\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({\n        success: false,\n        error: fetchResult.error,\n        source: isbn,\n        reason: fetchResult.reason,\n      });\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          reason: \"validation_error\",\n        });\n      }\n    }\n    return { results };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    return {\n      results: [\n        {\n          success: false,\n          error: `Failed to parse JSON: ${message}`,\n          source: \"json\",\n          reason: \"parse_error\",\n        },\n      ],\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        {\n          success: false,\n          error: parseResult.error ?? \"Failed to parse BibTeX\",\n          source: \"bibtex\",\n          reason: \"parse_error\",\n        },\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        {\n          success: false,\n          error: parseResult.error ?? \"Failed to parse RIS\",\n          source: \"ris\",\n          reason: \"parse_error\",\n        },\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 * Parse NBIB content and return import result\n */\nfunction parseNbibContent(content: string): ImportResult {\n  const parseResult = parseNbib(content);\n\n  if (!parseResult.success) {\n    return {\n      results: [\n        {\n          success: false,\n          error: parseResult.error ?? \"Failed to parse NBIB\",\n          source: \"nbib\",\n          reason: \"parse_error\",\n        },\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: \"nbib\",\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            reason: \"validation_error\",\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    case \"nbib\":\n      return parseNbibContent(content);\n    default:\n      return {\n        results: [\n          {\n            success: false,\n            error: `Unsupported format for content parsing: ${actualFormat}`,\n            source: \"content\",\n            reason: \"validation_error\",\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: ${message}`,\n        source: filePath,\n        reason: \"fetch_error\",\n      },\n    ];\n  }\n}\n\n/**\n * Process identifier inputs (PMID/DOI)\n */\nasync function processIdentifiers(\n  inputs: string[],\n  options: ImportInputsOptions\n): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n  const validIdentifiers: string[] = [];\n\n  // Separate valid identifiers from invalid inputs\n  for (const input of inputs) {\n    // Check if it's a valid identifier\n    const isValidPmid = isPmid(input);\n    const isValidDoi = isDoi(input);\n    const isValidIsbn = isIsbn(input);\n\n    if (isValidPmid || isValidDoi || isValidIsbn) {\n      validIdentifiers.push(input);\n    } else {\n      // Not a valid identifier\n      const hint = looksLikeFilePath(input)\n        ? \" Hint: If this is a file path, check that the file exists.\"\n        : \"\";\n      results.push({\n        success: false,\n        error: `Cannot interpret '${input}' as identifier (not a valid PMID, DOI, or ISBN).${hint}`,\n        source: input,\n        reason: \"validation_error\",\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\" || format === \"nbib\") {\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\" || format === \"isbn\") {\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 (\n    detectedFormat === \"json\" ||\n    detectedFormat === \"bibtex\" ||\n    detectedFormat === \"ris\" ||\n    detectedFormat === \"nbib\"\n  ) {\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 { generateId } from \"../../core/identifier/generator.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// Re-export FailureReason for external use\nexport type { FailureReason } 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  source: string;\n  id: string;\n  uuid: 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  reason: import(\"../import/importer.js\").FailureReason;\n}\n\n/**\n * Information about a skipped duplicate\n */\nexport interface SkippedItem {\n  source: string;\n  existingId: string;\n  duplicateType: import(\"../duplicate/types.js\").DuplicateType;\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 {\n      type: \"failed\",\n      item: { source: result.source, error: result.error, reason: result.reason },\n    };\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: {\n          source: result.source,\n          existingId: existingMatch.existing.id ?? \"\",\n          duplicateType: existingMatch.type,\n        },\n      };\n    }\n  }\n\n  // Resolve ID collision\n  const allExistingIds = new Set([...existingItems.map((i) => i.id), ...addedIds]);\n  const generatedId = generateId(item);\n  const { id, changed } = resolveIdCollision(generatedId, allExistingIds);\n\n  const finalItem: CslItem = { ...item, id };\n\n  // Add to library\n  const addedToLibrary = await library.add(finalItem);\n  addedIds.add(id);\n\n  // Build result (uuid comes from the library-added item which has ensured UUID)\n  const uuid = addedToLibrary.custom?.uuid ?? \"\";\n  const addedItem: AddedItem = {\n    source: result.source,\n    id,\n    uuid,\n    title: typeof finalItem.title === \"string\" ? finalItem.title : \"\",\n  };\n\n  if (changed) {\n    addedItem.idChanged = true;\n    addedItem.originalId = generatedId;\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 { 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 { isBuiltinStyle, resolveStyle } 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  styleXml?: 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(style: string | undefined, hasCustomXml: boolean): boolean {\n  if (hasCustomXml) {\n    return false;\n  }\n  if (style && !isBuiltinStyle(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.style, !!options.styleXml);\n  const style = options.style ?? \"apa\";\n  const locale = options.locale ?? \"en-US\";\n  const format = options.format ?? \"text\";\n  const styleXml = options.styleXml;\n\n  if (useFallback) {\n    return inText ? formatInText([item]) : formatBibliography([item]);\n  }\n\n  const formatOptions = { style, locale, format, ...(styleXml && { styleXml }) };\n  return inText\n    ? formatInTextCSL([item], formatOptions)\n    : formatBibliographyCSL([item], formatOptions);\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  // Resolve style: load custom CSL file if specified\n  let resolvedStyle = style;\n  let styleXml: string | undefined;\n\n  if (cslFile) {\n    const resolution = resolveStyle({ cslFile });\n    resolvedStyle = resolution.styleName;\n    styleXml = resolution.styleXml;\n  }\n\n  for (const identifier of identifiers) {\n    const result = await generateCitationForIdentifier(library, identifier, idType, inText, {\n      style: resolvedStyle,\n      styleXml,\n      locale,\n      format,\n    });\n    results.push(result);\n  }\n\n  return { results };\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 type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport {\n  type PaginationOptions,\n  type SortField,\n  type SortOptions,\n  type SortOrder,\n  paginate,\n  sortReferences,\n} from \"../pagination/index.js\";\n\n/**\n * Options for listReferences operation\n */\nexport interface ListOptions extends PaginationOptions, SortOptions {}\n\n/**\n * Result of listReferences operation\n */\nexport interface ListResult {\n  /** Raw CslItem array */\n  items: CslItem[];\n  /** Total count before pagination */\n  total: number;\n  /** Applied limit (0 if unlimited) */\n  limit: number;\n  /** Applied offset */\n  offset: number;\n  /** Next page offset, null if no more results */\n  nextOffset: number | null;\n}\n\n/**\n * List all references from the library.\n *\n * @param library - The library to list references from\n * @param options - Pagination and sorting options\n * @returns Raw CslItem[] with pagination metadata\n */\nexport async function listReferences(library: ILibrary, options: ListOptions): Promise<ListResult> {\n  const sort: SortField = options.sort ?? \"updated\";\n  const order: SortOrder = options.order ?? \"desc\";\n  const limit = options.limit ?? 0;\n  const offset = options.offset ?? 0;\n\n  // Get all items\n  const allItems = await library.getAll();\n  const total = allItems.length;\n\n  // Sort\n  const sorted = sortReferences(allItems, sort, order);\n\n  // Paginate\n  const { items: paginatedItems, nextOffset } = paginate(sorted, { limit, offset });\n\n  return {\n    items: paginatedItems,\n    total,\n    limit,\n    offset,\n    nextOffset,\n  };\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\";\nimport { sortFieldSchema, sortOrderSchema } from \"../../features/pagination/index.js\";\nimport { pickDefined } from \"../../utils/object.js\";\n\n/**\n * Request body schema for list endpoint\n */\nconst listRequestBodySchema = z.object({\n  sort: sortFieldSchema.optional(),\n  order: sortOrderSchema.optional(),\n  limit: z.number().int().min(0).optional(),\n  offset: z.number().int().min(0).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      const errorMessage = parseResult.error.issues[0]?.message ?? \"Invalid request body\";\n      return c.json({ error: errorMessage }, 400);\n    }\n\n    const requestBody = parseResult.data;\n\n    // Build options for listReferences\n    const options: ListOptions = pickDefined(requestBody, [\n      \"sort\",\n      \"order\",\n      \"limit\",\n      \"offset\",\n    ] as const);\n\n    // Call listReferences operation - always returns raw CslItem[]\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 type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport {\n  type PaginationOptions,\n  type SearchSortField,\n  type SortField,\n  type SortOrder,\n  paginate,\n  sortReferences,\n} from \"../pagination/index.js\";\nimport { search } from \"../search/matcher.js\";\nimport { sortResults as sortByRelevance } from \"../search/sorter.js\";\nimport { tokenize } from \"../search/tokenizer.js\";\n\n/**\n * Sort options for search (includes relevance)\n */\nexport interface SearchSortOptions {\n  sort?: SearchSortField;\n  order?: SortOrder;\n}\n\n/**\n * Options for searchReferences operation\n */\nexport interface SearchOperationOptions extends PaginationOptions, SearchSortOptions {\n  /** Search query string */\n  query: string;\n}\n\n/**\n * Result of searchReferences operation\n */\nexport interface SearchResult {\n  /** Raw CslItem array */\n  items: CslItem[];\n  /** Total count before pagination */\n  total: number;\n  /** Applied limit (0 if unlimited) */\n  limit: number;\n  /** Applied offset */\n  offset: number;\n  /** Next page offset, null if no more results */\n  nextOffset: number | null;\n}\n\n/**\n * Search references in the library and return raw CslItem[] results.\n *\n * @param library - The library to search in\n * @param options - Search query and pagination options\n * @returns Raw CslItem[] with pagination metadata\n */\nexport async function searchReferences(\n  library: ILibrary,\n  options: SearchOperationOptions\n): Promise<SearchResult> {\n  const query = options.query;\n  const sort: SearchSortField = options.sort ?? \"updated\";\n  const order: SortOrder = options.order ?? \"desc\";\n  const limit = options.limit ?? 0;\n  const offset = options.offset ?? 0;\n\n  // Get all references\n  const allItems = await library.getAll();\n\n  // Search and get matched 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\n    // If sorting by relevance, use the search sorter\n    if (sort === \"relevance\") {\n      const sorted = sortByRelevance(results);\n      matchedItems =\n        order === \"desc\"\n          ? sorted.map((r) => r.reference)\n          : sorted.map((r) => r.reference).reverse();\n    } else {\n      matchedItems = results.map((r) => r.reference);\n    }\n  }\n\n  const total = matchedItems.length;\n\n  // Sort (unless already sorted by relevance)\n  let sorted: CslItem[];\n  if (sort === \"relevance\") {\n    sorted = matchedItems;\n  } else {\n    sorted = sortReferences(matchedItems, sort as SortField, order);\n  }\n\n  // Paginate\n  const { items: paginatedItems, nextOffset } = paginate(sorted, { limit, offset });\n\n  return {\n    items: paginatedItems,\n    total,\n    limit,\n    offset,\n    nextOffset,\n  };\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\";\nimport { searchSortFieldSchema, sortOrderSchema } from \"../../features/pagination/index.js\";\nimport { pickDefined } from \"../../utils/object.js\";\n\n/**\n * Request body schema for search endpoint\n */\nconst searchRequestBodySchema = z.object({\n  query: z.string(),\n  sort: searchSortFieldSchema.optional(),\n  order: sortOrderSchema.optional(),\n  limit: z.number().int().min(0).optional(),\n  offset: z.number().int().min(0).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 createSearchRoute(library: Library) {\n  const route = new Hono();\n\n  // POST / - Search 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 = searchRequestBodySchema.safeParse(body);\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    const requestBody = parseResult.data;\n\n    // Build options for searchReferences\n    const options: SearchOperationOptions = {\n      query: requestBody.query,\n      ...pickDefined(requestBody, [\"sort\", \"order\", \"limit\", \"offset\"] as const),\n    };\n\n    // Call searchReferences operation - always returns raw CslItem[]\n    const result = await searchReferences(library, options);\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import { Hono } from \"hono\";\nimport type { 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    });\n  });\n\n  await fileWatcher.start();\n\n  // Create dispose function\n  const dispose = async (): Promise<void> => {\n    fileWatcher.close();\n  };\n\n  return {\n    app,\n    library,\n    fileWatcher,\n    dispose,\n  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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, plugins } 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   * Custom CSL style XML content.\n   * When provided, this XML is registered and used instead of built-in styles.\n   */\n  styleXml?: 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 * Register a custom CSL style with citation-js.\n * Returns the style name to use for formatting.\n * @throws Error if CSL XML is invalid or malformed\n */\nfunction registerCustomStyle(styleName: string, styleXml: string): string {\n  // Basic XML validation\n  if (!styleXml.includes(\"<style\") || !styleXml.includes(\"</style>\")) {\n    throw new Error(\n      \"Invalid CSL file: Missing <style> element. The file may be malformed or not a valid CSL style.\"\n    );\n  }\n\n  // Check for required CSL sections\n  const hasCitation = styleXml.includes(\"<citation\") || styleXml.includes(\"<citation>\");\n  const hasBibliography = styleXml.includes(\"<bibliography\") || styleXml.includes(\"<bibliography>\");\n  if (!hasCitation && !hasBibliography) {\n    throw new Error(\n      \"Invalid CSL file: Missing <citation> or <bibliography> section. \" +\n        \"A valid CSL style must define at least one of these sections.\"\n    );\n  }\n\n  try {\n    const config = plugins.config.get(\"@csl\");\n    config.templates.add(styleName, styleXml);\n    return styleName;\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    throw new Error(`Failed to register CSL style '${styleName}': ${message}`);\n  }\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  let style = options.style || \"apa\";\n  const format = options.format || \"text\";\n  const locale = options.locale || \"en-US\";\n\n  // Register custom style if XML is provided\n  if (options.styleXml) {\n    style = registerCustomStyle(style, options.styleXml);\n  }\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  let style = options.style || \"apa\";\n  const format = options.format || \"text\";\n  const locale = options.locale || \"en-US\";\n\n  // Register custom style if XML is provided\n  if (options.styleXml) {\n    style = registerCustomStyle(style, options.styleXml);\n  }\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","/**\n * Reference sorter\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { SortField, SortOrder } from \"./types.js\";\n\n/**\n * Extract created_at timestamp from item, returns epoch (0) if missing\n */\nfunction getCreatedAt(item: CslItem): number {\n  const createdAt = item.custom?.created_at;\n  if (!createdAt) return 0;\n  return new Date(createdAt).getTime();\n}\n\n/**\n * Extract updated timestamp from item, falls back to created_at\n */\nfunction getUpdatedAt(item: CslItem): number {\n  const timestamp = item.custom?.timestamp;\n  if (timestamp) return new Date(timestamp).getTime();\n  return getCreatedAt(item);\n}\n\n/**\n * Extract published date as comparable number\n * Returns 0 (epoch) if missing\n */\nfunction getPublishedDate(item: CslItem): number {\n  const dateParts = item.issued?.[\"date-parts\"]?.[0];\n  if (!dateParts || dateParts.length === 0) return 0;\n\n  const year = dateParts[0] ?? 0;\n  const month = dateParts[1] ?? 1;\n  const day = dateParts[2] ?? 1;\n\n  return new Date(year, month - 1, day).getTime();\n}\n\n/**\n * Extract first author's sortable name\n * Returns \"Anonymous\" if no author\n */\nfunction getAuthorName(item: CslItem): string {\n  const firstAuthor = item.author?.[0];\n  if (!firstAuthor) return \"Anonymous\";\n\n  return firstAuthor.family ?? firstAuthor.literal ?? \"Anonymous\";\n}\n\n/**\n * Extract title, returns empty string if missing\n */\nfunction getTitle(item: CslItem): string {\n  return item.title ?? \"\";\n}\n\n/**\n * Get sort value for a given field\n */\nfunction getSortValue(item: CslItem, field: SortField): number | string {\n  switch (field) {\n    case \"created\":\n      return getCreatedAt(item);\n    case \"updated\":\n      return getUpdatedAt(item);\n    case \"published\":\n      return getPublishedDate(item);\n    case \"author\":\n      return getAuthorName(item).toLowerCase();\n    case \"title\":\n      return getTitle(item).toLowerCase();\n  }\n}\n\n/**\n * Compare function for sorting\n */\nfunction compareValues(a: number | string, b: number | string, order: SortOrder): number {\n  const multiplier = order === \"desc\" ? -1 : 1;\n\n  if (typeof a === \"number\" && typeof b === \"number\") {\n    return (a - b) * multiplier;\n  }\n\n  const strA = String(a);\n  const strB = String(b);\n  return strA.localeCompare(strB) * multiplier;\n}\n\n/**\n * Sort references by the specified field and order.\n * Uses secondary sort: created (desc), then id (asc) for stability.\n *\n * @param items - References to sort\n * @param sort - Sort field\n * @param order - Sort order\n * @returns Sorted references (new array, does not mutate input)\n */\nexport function sortReferences(items: CslItem[], sort: SortField, order: SortOrder): CslItem[] {\n  return [...items].sort((a, b) => {\n    // Primary sort\n    const aValue = getSortValue(a, sort);\n    const bValue = getSortValue(b, sort);\n    const primaryCompare = compareValues(aValue, bValue, order);\n\n    if (primaryCompare !== 0) return primaryCompare;\n\n    // Secondary sort: created (desc)\n    const aCreated = getCreatedAt(a);\n    const bCreated = getCreatedAt(b);\n    const createdCompare = bCreated - aCreated; // desc\n\n    if (createdCompare !== 0) return createdCompare;\n\n    // Tertiary sort: id (asc) for stability\n    return a.id.localeCompare(b.id);\n  });\n}\n","/**\n * Pagination applier\n */\n\nexport interface PaginateOptions {\n  limit?: number;\n  offset?: number;\n}\n\nexport interface PaginateResult<T> {\n  items: T[];\n  nextOffset: number | null;\n}\n\n/**\n * Apply pagination to an array of items.\n *\n * @param items - Items to paginate\n * @param options - Pagination options (limit=0 or undefined means unlimited)\n * @returns Paginated items with nextOffset (null if no more items)\n */\nexport function paginate<T>(items: T[], options: PaginateOptions): PaginateResult<T> {\n  const offset = options.offset ?? 0;\n  const limit = options.limit ?? 0;\n\n  // Validate inputs\n  if (limit < 0) {\n    throw new Error(\"limit must be non-negative\");\n  }\n  if (offset < 0) {\n    throw new Error(\"offset must be non-negative\");\n  }\n\n  const isUnlimited = limit === 0;\n\n  // Apply offset\n  const afterOffset = items.slice(offset);\n\n  // Apply limit (0 means unlimited)\n  const paginatedItems = isUnlimited ? afterOffset : afterOffset.slice(0, limit);\n\n  // Calculate nextOffset\n  let nextOffset: number | null = null;\n  if (!isUnlimited && paginatedItems.length > 0) {\n    const nextPosition = offset + paginatedItems.length;\n    if (nextPosition < items.length) {\n      nextOffset = nextPosition;\n    }\n  }\n\n  return {\n    items: paginatedItems,\n    nextOffset,\n  };\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","import { unlink } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../core/library-interface.js\";\nimport type { FulltextType } from \"../fulltext/index.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  /** Directory containing fulltext files (required if deleteFulltext is true) */\n  fulltextDirectory?: string;\n  /** Whether to delete associated fulltext files */\n  deleteFulltext?: boolean;\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  /** Fulltext types that were deleted (only when deleteFulltext=true) */\n  deletedFulltextTypes?: FulltextType[];\n}\n\n/**\n * Get fulltext attachment types from a CSL item.\n */\nexport function getFulltextAttachmentTypes(item: CslItem): FulltextType[] {\n  const types: FulltextType[] = [];\n  const fulltext = item.custom?.fulltext;\n\n  if (fulltext?.pdf) {\n    types.push(\"pdf\");\n  }\n  if (fulltext?.markdown) {\n    types.push(\"markdown\");\n  }\n\n  return types;\n}\n\n/**\n * Delete fulltext files associated with an item.\n */\nasync function deleteFulltextFiles(item: CslItem, fulltextDirectory: string): Promise<void> {\n  const fulltext = item.custom?.fulltext;\n  if (!fulltext) {\n    return;\n  }\n\n  const filesToDelete: string[] = [];\n\n  if (fulltext.pdf) {\n    filesToDelete.push(join(fulltextDirectory, fulltext.pdf));\n  }\n  if (fulltext.markdown) {\n    filesToDelete.push(join(fulltextDirectory, fulltext.markdown));\n  }\n\n  for (const filePath of filesToDelete) {\n    try {\n      await unlink(filePath);\n    } catch {\n      // Ignore errors (file might not exist)\n    }\n  }\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\", fulltextDirectory, deleteFulltext = false } = options;\n\n  const result = await library.remove(identifier, { idType });\n\n  if (!result.removed || !result.removedItem) {\n    return { removed: false };\n  }\n\n  // Delete fulltext files if requested\n  let deletedFulltextTypes: FulltextType[] | undefined;\n  if (deleteFulltext && fulltextDirectory) {\n    deletedFulltextTypes = getFulltextAttachmentTypes(result.removedItem);\n    if (deletedFulltextTypes.length > 0) {\n      await deleteFulltextFiles(result.removedItem, fulltextDirectory);\n    }\n  }\n\n  await library.save();\n\n  return {\n    removed: true,\n    removedItem: result.removedItem,\n    ...(deletedFulltextTypes && deletedFulltextTypes.length > 0 && { deletedFulltextTypes }),\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  | \"nbib\"\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  \".nbib\": \"nbib\",\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  // NBIB (PubMed MEDLINE): starts with PMID-\n  if (trimmed.startsWith(\"PMID-\")) {\n    return \"nbib\";\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+$/;\n\n/**\n * PubMed configuration for API requests\n */\nexport interface PubmedConfig {\n  email?: string;\n  apiKey?: string;\n}\n\n/**\n * Categorized failure reasons for JSON output\n */\nexport type FailureReason =\n  | \"not_found\"\n  | \"fetch_error\"\n  | \"parse_error\"\n  | \"validation_error\"\n  | \"unknown\";\n\n/**\n * Result of fetching a single identifier\n */\nexport type FetchResult =\n  | { success: true; item: CslItem }\n  | { success: false; error: string; reason: FailureReason };\n\n/**\n * Result of fetching a PMID (includes pmid for tracking)\n */\nexport type PmidFetchResult =\n  | { pmid: string; success: true; item: CslItem }\n  | { pmid: string; success: false; error: string; reason: FailureReason };\n\n/**\n * Results of fetching multiple PMIDs\n */\nexport type FetchResults = PmidFetchResult[];\n\n/**\n * Build PMC API URL with query parameters\n */\nfunction buildPmcUrl(pmids: string[], config: PubmedConfig): string {\n  const url = new URL(PMC_API_BASE);\n  url.searchParams.set(\"format\", \"csl\");\n\n  // Add each PMID as separate id parameter\n  for (const pmid of pmids) {\n    url.searchParams.append(\"id\", pmid);\n  }\n\n  if (config.email) {\n    url.searchParams.set(\"email\", config.email);\n  }\n  if (config.apiKey) {\n    url.searchParams.set(\"api_key\", config.apiKey);\n  }\n\n  return url.toString();\n}\n\n/**\n * Extract PMID from CSL-JSON item id field\n * PMC API returns id like \"pmid:12345678\"\n */\nfunction extractPmidFromId(id: string | undefined): string | undefined {\n  if (!id) return undefined;\n  const match = id.match(/^pmid:(\\d+)$/);\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      reason: \"validation_error\",\n    };\n  }\n  return {\n    pmid,\n    success: false as const,\n    error: `PMID ${pmid} not found`,\n    reason: \"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        reason: \"fetch_error\",\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      reason: \"fetch_error\",\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      reason: \"validation_error\",\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        reason: \"not_found\",\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}: ${parseResult.error.message}`,\n        reason: \"validation_error\",\n      };\n    }\n\n    return { success: true, item: parseResult.data };\n  } catch (error) {\n    const errorMsg = error instanceof Error ? error.message : String(error);\n    return {\n      success: false,\n      error: errorMsg,\n      reason: \"fetch_error\",\n    };\n  }\n}\n\n/** ISBN-10 pattern: 9 digits + (digit or X) */\nconst ISBN10_PATTERN = /^\\d{9}[\\dX]$/;\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      reason: \"validation_error\",\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        reason: \"not_found\",\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        reason: \"validation_error\",\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      reason: \"fetch_error\",\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 * NBIB to RIS tag mapping\n *\n * Maps PubMed MEDLINE tags to RIS equivalents\n */\nconst NBIB_TO_RIS_TAG_MAP: Record<string, string> = {\n  PMID: \"AN\", // PubMed ID -> Accession Number\n  TI: \"TI\", // Title -> Title\n  FAU: \"AU\", // Full Author -> Author\n  AU: \"AU\", // Author -> Author (short form, use FAU when available)\n  JT: \"JO\", // Journal Title -> Journal Name\n  TA: \"JA\", // Title Abbreviation -> Journal Abbreviation\n  AB: \"AB\", // Abstract -> Abstract\n  VI: \"VL\", // Volume -> Volume\n  IP: \"IS\", // Issue/Part -> Issue Number\n  PG: \"SP\", // Pagination -> Start Page (includes range)\n  DP: \"PY\", // Date of Publication -> Publication Year\n  LA: \"LA\", // Language -> Language\n  MH: \"KW\", // MeSH Headings -> Keywords\n  OT: \"KW\", // Other Terms -> Keywords\n  AD: \"AD\", // Affiliation/Address -> Author Address\n  IS: \"SN\", // ISSN -> Serial Number\n  PT: \"TY\", // Publication Type -> Type of Reference\n};\n\n/**\n * Publication type mapping from NBIB to RIS\n */\nconst NBIB_PUBLICATION_TYPE_MAP: Record<string, string> = {\n  \"Journal Article\": \"JOUR\",\n  Review: \"JOUR\",\n  Book: \"BOOK\",\n  \"Book Chapter\": \"CHAP\",\n  \"Conference Paper\": \"CPAPER\",\n  Thesis: \"THES\",\n  Report: \"RPRT\",\n};\n\n/**\n * Parse a single NBIB entry into tag-value pairs\n */\nfunction parseNbibEntry(entry: string): Array<{ tag: string; value: string }> {\n  const result: Array<{ tag: string; value: string }> = [];\n  const lines = entry.split(\"\\n\");\n\n  let currentTag = \"\";\n  let currentValue = \"\";\n\n  for (const line of lines) {\n    // Check if line starts with a tag (2-4 uppercase letters followed by space(s) and dash)\n    const tagMatch = line.match(/^([A-Z]{2,4})\\s*-\\s*(.*)$/);\n\n    if (tagMatch) {\n      // Save previous tag-value pair\n      if (currentTag) {\n        result.push({ tag: currentTag, value: currentValue.trim() });\n      }\n      currentTag = tagMatch[1] ?? \"\";\n      currentValue = tagMatch[2] ?? \"\";\n    } else if (currentTag && line.match(/^\\s+/)) {\n      // Continuation line (starts with whitespace)\n      currentValue += ` ${line.trim()}`;\n    }\n  }\n\n  // Save the last tag-value pair\n  if (currentTag) {\n    result.push({ tag: currentTag, value: currentValue.trim() });\n  }\n\n  return result;\n}\n\n/**\n * Convert a single NBIB tag-value pair to RIS line\n * @returns RIS line or null if tag should be skipped\n */\nfunction convertNbibTagToRisLine(\n  tag: string,\n  value: string\n): { line: string; isType?: boolean } | null {\n  // Handle DOI specially (AID tag with [doi] suffix)\n  if (tag === \"AID\" && value.includes(\"[doi]\")) {\n    const doi = value.replace(/\\s*\\[doi\\].*$/, \"\").trim();\n    return { line: `DO  - ${doi}` };\n  }\n\n  // Handle PII specially (AID tag with [pii] suffix)\n  if (tag === \"AID\" && value.includes(\"[pii]\")) {\n    const pii = value.replace(/\\s*\\[pii\\].*$/, \"\").trim();\n    return { line: `C1  - ${pii}` }; // C1 = Custom Field 1\n  }\n\n  // Get mapped RIS tag\n  const risTag = NBIB_TO_RIS_TAG_MAP[tag];\n  if (!risTag) {\n    return null; // Skip unmapped tags\n  }\n\n  // Handle publication year (extract year only)\n  if (risTag === \"PY\") {\n    const yearMatch = value.match(/^(\\d{4})/);\n    return yearMatch ? { line: `PY  - ${yearMatch[1]}` } : null;\n  }\n\n  // Handle publication type\n  if (risTag === \"TY\") {\n    const risType = NBIB_PUBLICATION_TYPE_MAP[value] || \"JOUR\";\n    return { line: `TY  - ${risType}`, isType: true };\n  }\n\n  return { line: `${risTag}  - ${value}` };\n}\n\n/**\n * Convert a single NBIB entry to RIS format\n */\nfunction convertSingleNbibEntryToRis(entry: string): string {\n  const parsed = parseNbibEntry(entry);\n\n  if (parsed.length === 0) {\n    return \"\";\n  }\n\n  const risLines: string[] = [];\n  let hasType = false;\n\n  for (const { tag, value } of parsed) {\n    const converted = convertNbibTagToRisLine(tag, value);\n    if (!converted) {\n      continue;\n    }\n\n    if (converted.isType) {\n      risLines.unshift(converted.line); // TY must be first\n      hasType = true;\n    } else {\n      risLines.push(converted.line);\n    }\n  }\n\n  // Add default type if not present\n  if (!hasType) {\n    risLines.unshift(\"TY  - JOUR\");\n  }\n\n  // Add end record tag\n  risLines.push(\"ER  -\");\n\n  return risLines.join(\"\\n\");\n}\n\n/**\n * Convert NBIB (PubMed MEDLINE) format to RIS format\n *\n * @param content - NBIB content string\n * @returns RIS format string\n */\nexport function convertNbibToRis(content: string): string {\n  const trimmed = content.trim();\n\n  if (!trimmed) {\n    return \"\";\n  }\n\n  // Split into entries by blank lines (PMID- starts each entry)\n  const entries = trimmed.split(/\\n\\s*\\n/).filter((e) => e.trim());\n\n  const risEntries = entries.map((entry) => convertSingleNbibEntryToRis(entry)).filter(Boolean);\n\n  return risEntries.join(\"\\n\\n\");\n}\n\n/**\n * Parse NBIB (PubMed MEDLINE) content to CSL-JSON\n *\n * Converts NBIB to RIS format first, then parses with citation-js\n *\n * @param content - NBIB content string\n * @returns Parse result with CSL-JSON items\n */\nexport function parseNbib(content: string): ParseResult {\n  const trimmed = content.trim();\n\n  // Handle empty input\n  if (!trimmed) {\n    return { success: true, items: [] };\n  }\n\n  // Convert NBIB to RIS\n  const risContent = convertNbibToRis(trimmed);\n\n  if (!risContent) {\n    return {\n      success: false,\n      items: [],\n      error: \"Failed to convert NBIB to RIS: No valid entries found\",\n    };\n  }\n\n  // Parse the RIS content\n  return parseRis(risContent);\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 { FailureReason, PubmedConfig } from \"./fetcher.js\";\nimport { normalizeDoi, normalizeIsbn, normalizePmid } from \"./normalizer.js\";\nimport { parseBibtex, parseNbib, parseRis } from \"./parser.js\";\n\n// Re-export FailureReason for external use\nexport type { FailureReason } from \"./fetcher.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; reason: FailureReason };\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    reason: \"validation_error\" as const,\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          reason: fetchResult.reason,\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({\n        success: false,\n        error: fetchResult.error,\n        source: doi,\n        reason: fetchResult.reason,\n      });\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({\n        success: false,\n        error: fetchResult.error,\n        source: isbn,\n        reason: fetchResult.reason,\n      });\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          reason: \"validation_error\",\n        });\n      }\n    }\n    return { results };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    return {\n      results: [\n        {\n          success: false,\n          error: `Failed to parse JSON: ${message}`,\n          source: \"json\",\n          reason: \"parse_error\",\n        },\n      ],\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        {\n          success: false,\n          error: parseResult.error ?? \"Failed to parse BibTeX\",\n          source: \"bibtex\",\n          reason: \"parse_error\",\n        },\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        {\n          success: false,\n          error: parseResult.error ?? \"Failed to parse RIS\",\n          source: \"ris\",\n          reason: \"parse_error\",\n        },\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 * Parse NBIB content and return import result\n */\nfunction parseNbibContent(content: string): ImportResult {\n  const parseResult = parseNbib(content);\n\n  if (!parseResult.success) {\n    return {\n      results: [\n        {\n          success: false,\n          error: parseResult.error ?? \"Failed to parse NBIB\",\n          source: \"nbib\",\n          reason: \"parse_error\",\n        },\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: \"nbib\",\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            reason: \"validation_error\",\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    case \"nbib\":\n      return parseNbibContent(content);\n    default:\n      return {\n        results: [\n          {\n            success: false,\n            error: `Unsupported format for content parsing: ${actualFormat}`,\n            source: \"content\",\n            reason: \"validation_error\",\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: ${message}`,\n        source: filePath,\n        reason: \"fetch_error\",\n      },\n    ];\n  }\n}\n\n/**\n * Process identifier inputs (PMID/DOI)\n */\nasync function processIdentifiers(\n  inputs: string[],\n  options: ImportInputsOptions\n): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n  const validIdentifiers: string[] = [];\n\n  // Separate valid identifiers from invalid inputs\n  for (const input of inputs) {\n    // Check if it's a valid identifier\n    const isValidPmid = isPmid(input);\n    const isValidDoi = isDoi(input);\n    const isValidIsbn = isIsbn(input);\n\n    if (isValidPmid || isValidDoi || isValidIsbn) {\n      validIdentifiers.push(input);\n    } else {\n      // Not a valid identifier\n      const hint = looksLikeFilePath(input)\n        ? \" Hint: If this is a file path, check that the file exists.\"\n        : \"\";\n      results.push({\n        success: false,\n        error: `Cannot interpret '${input}' as identifier (not a valid PMID, DOI, or ISBN).${hint}`,\n        source: input,\n        reason: \"validation_error\",\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\" || format === \"nbib\") {\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\" || format === \"isbn\") {\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 (\n    detectedFormat === \"json\" ||\n    detectedFormat === \"bibtex\" ||\n    detectedFormat === \"ris\" ||\n    detectedFormat === \"nbib\"\n  ) {\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 { generateId } from \"../../core/identifier/generator.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// Re-export FailureReason for external use\nexport type { FailureReason } 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  source: string;\n  id: string;\n  uuid: string;\n  title: string;\n  /** True if the original ID from source file was changed due to collision */\n  idChanged?: boolean;\n  /** Original ID from source file 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  reason: import(\"../import/importer.js\").FailureReason;\n}\n\n/**\n * Information about a skipped duplicate\n */\nexport interface SkippedItem {\n  source: string;\n  existingId: string;\n  duplicateType: import(\"../duplicate/types.js\").DuplicateType;\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 {\n      type: \"failed\",\n      item: { source: result.source, error: result.error, reason: result.reason },\n    };\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: {\n          source: result.source,\n          existingId: existingMatch.existing.id ?? \"\",\n          duplicateType: existingMatch.type,\n        },\n      };\n    }\n  }\n\n  // Resolve ID collision\n  // Prioritize original ID from source file; generate ID only if not present\n  const allExistingIds = new Set([...existingItems.map((i) => i.id), ...addedIds]);\n  const originalId = item.id?.trim() || \"\";\n  const hasOriginalId = originalId.length > 0;\n  const baseId = hasOriginalId ? originalId : generateId(item);\n  const { id, changed } = resolveIdCollision(baseId, allExistingIds);\n\n  const finalItem: CslItem = { ...item, id };\n\n  // Add to library\n  const addedToLibrary = await library.add(finalItem);\n  addedIds.add(id);\n\n  // Build result (uuid comes from the library-added item which has ensured UUID)\n  const uuid = addedToLibrary.custom?.uuid ?? \"\";\n  const addedItem: AddedItem = {\n    source: result.source,\n    id,\n    uuid,\n    title: typeof finalItem.title === \"string\" ? finalItem.title : \"\",\n  };\n\n  // Report idChanged only when original ID from source was changed due to collision\n  // Generated ID collisions are internal and not reported\n  if (hasOriginalId && changed) {\n    addedItem.idChanged = true;\n    addedItem.originalId = originalId;\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 { 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 { isBuiltinStyle, resolveStyle } 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  /** Default style from config (used when style is not specified) */\n  defaultStyle?: string;\n  /** Directory or directories to search for custom CSL files */\n  cslDirectory?: string | 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  styleXml?: 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(style: string | undefined, hasCustomXml: boolean): boolean {\n  if (hasCustomXml) {\n    return false;\n  }\n  if (style && !isBuiltinStyle(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.style, !!options.styleXml);\n  const style = options.style ?? \"apa\";\n  const locale = options.locale ?? \"en-US\";\n  const format = options.format ?? \"text\";\n  const styleXml = options.styleXml;\n\n  if (useFallback) {\n    return inText ? formatInText([item]) : formatBibliography([item]);\n  }\n\n  const formatOptions = { style, locale, format, ...(styleXml && { styleXml }) };\n  return inText\n    ? formatInTextCSL([item], formatOptions)\n    : formatBibliographyCSL([item], formatOptions);\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 {\n    identifiers,\n    idType = \"id\",\n    inText = false,\n    style,\n    cslFile,\n    defaultStyle,\n    cslDirectory,\n    locale,\n    format,\n  } = options;\n  const results: CiteItemResult[] = [];\n\n  // Resolve style using the full resolution chain:\n  // 1. cslFile (exact path)\n  // 2. style (if built-in)\n  // 3. Search in cslDirectory\n  // 4. defaultStyle (if built-in or found in cslDirectory)\n  // 5. Fallback to 'apa'\n  const resolution = resolveStyle({\n    ...(cslFile !== undefined && { cslFile }),\n    ...(style !== undefined && { style }),\n    ...(defaultStyle !== undefined && { defaultStyle }),\n    ...(cslDirectory !== undefined && { cslDirectory }),\n  });\n\n  for (const identifier of identifiers) {\n    const result = await generateCitationForIdentifier(library, identifier, idType, inText, {\n      style: resolution.styleName,\n      styleXml: resolution.styleXml,\n      locale,\n      format,\n    });\n    results.push(result);\n  }\n\n  return { results };\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 type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport {\n  type PaginationOptions,\n  type SortField,\n  type SortOptions,\n  type SortOrder,\n  paginate,\n  sortReferences,\n} from \"../pagination/index.js\";\n\n/**\n * Options for listReferences operation\n */\nexport interface ListOptions extends PaginationOptions, SortOptions {}\n\n/**\n * Result of listReferences operation\n */\nexport interface ListResult {\n  /** Raw CslItem array */\n  items: CslItem[];\n  /** Total count before pagination */\n  total: number;\n  /** Applied limit (0 if unlimited) */\n  limit: number;\n  /** Applied offset */\n  offset: number;\n  /** Next page offset, null if no more results */\n  nextOffset: number | null;\n}\n\n/**\n * List all references from the library.\n *\n * @param library - The library to list references from\n * @param options - Pagination and sorting options\n * @returns Raw CslItem[] with pagination metadata\n */\nexport async function listReferences(library: ILibrary, options: ListOptions): Promise<ListResult> {\n  const sort: SortField = options.sort ?? \"updated\";\n  const order: SortOrder = options.order ?? \"desc\";\n  const limit = options.limit ?? 0;\n  const offset = options.offset ?? 0;\n\n  // Get all items\n  const allItems = await library.getAll();\n  const total = allItems.length;\n\n  // Sort\n  const sorted = sortReferences(allItems, sort, order);\n\n  // Paginate\n  const { items: paginatedItems, nextOffset } = paginate(sorted, { limit, offset });\n\n  return {\n    items: paginatedItems,\n    total,\n    limit,\n    offset,\n    nextOffset,\n  };\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\";\nimport { sortFieldSchema, sortOrderSchema } from \"../../features/pagination/index.js\";\nimport { pickDefined } from \"../../utils/object.js\";\n\n/**\n * Request body schema for list endpoint\n */\nconst listRequestBodySchema = z.object({\n  sort: sortFieldSchema.optional(),\n  order: sortOrderSchema.optional(),\n  limit: z.number().int().min(0).optional(),\n  offset: z.number().int().min(0).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      const errorMessage = parseResult.error.issues[0]?.message ?? \"Invalid request body\";\n      return c.json({ error: errorMessage }, 400);\n    }\n\n    const requestBody = parseResult.data;\n\n    // Build options for listReferences\n    const options: ListOptions = pickDefined(requestBody, [\n      \"sort\",\n      \"order\",\n      \"limit\",\n      \"offset\",\n    ] as const);\n\n    // Call listReferences operation - always returns raw CslItem[]\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 type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport {\n  type PaginationOptions,\n  type SearchSortField,\n  type SortField,\n  type SortOrder,\n  paginate,\n  sortReferences,\n} from \"../pagination/index.js\";\nimport { search } from \"../search/matcher.js\";\nimport { sortResults as sortByRelevance } from \"../search/sorter.js\";\nimport { tokenize } from \"../search/tokenizer.js\";\n\n/**\n * Sort options for search (includes relevance)\n */\nexport interface SearchSortOptions {\n  sort?: SearchSortField;\n  order?: SortOrder;\n}\n\n/**\n * Options for searchReferences operation\n */\nexport interface SearchOperationOptions extends PaginationOptions, SearchSortOptions {\n  /** Search query string */\n  query: string;\n}\n\n/**\n * Result of searchReferences operation\n */\nexport interface SearchResult {\n  /** Raw CslItem array */\n  items: CslItem[];\n  /** Total count before pagination */\n  total: number;\n  /** Applied limit (0 if unlimited) */\n  limit: number;\n  /** Applied offset */\n  offset: number;\n  /** Next page offset, null if no more results */\n  nextOffset: number | null;\n}\n\n/**\n * Search references in the library and return raw CslItem[] results.\n *\n * @param library - The library to search in\n * @param options - Search query and pagination options\n * @returns Raw CslItem[] with pagination metadata\n */\nexport async function searchReferences(\n  library: ILibrary,\n  options: SearchOperationOptions\n): Promise<SearchResult> {\n  const query = options.query;\n  const sort: SearchSortField = options.sort ?? \"updated\";\n  const order: SortOrder = options.order ?? \"desc\";\n  const limit = options.limit ?? 0;\n  const offset = options.offset ?? 0;\n\n  // Get all references\n  const allItems = await library.getAll();\n\n  // Search and get matched 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\n    // If sorting by relevance, use the search sorter\n    if (sort === \"relevance\") {\n      const sorted = sortByRelevance(results);\n      matchedItems =\n        order === \"desc\"\n          ? sorted.map((r) => r.reference)\n          : sorted.map((r) => r.reference).reverse();\n    } else {\n      matchedItems = results.map((r) => r.reference);\n    }\n  }\n\n  const total = matchedItems.length;\n\n  // Sort (unless already sorted by relevance)\n  let sorted: CslItem[];\n  if (sort === \"relevance\") {\n    sorted = matchedItems;\n  } else {\n    sorted = sortReferences(matchedItems, sort as SortField, order);\n  }\n\n  // Paginate\n  const { items: paginatedItems, nextOffset } = paginate(sorted, { limit, offset });\n\n  return {\n    items: paginatedItems,\n    total,\n    limit,\n    offset,\n    nextOffset,\n  };\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\";\nimport { searchSortFieldSchema, sortOrderSchema } from \"../../features/pagination/index.js\";\nimport { pickDefined } from \"../../utils/object.js\";\n\n/**\n * Request body schema for search endpoint\n */\nconst searchRequestBodySchema = z.object({\n  query: z.string(),\n  sort: searchSortFieldSchema.optional(),\n  order: sortOrderSchema.optional(),\n  limit: z.number().int().min(0).optional(),\n  offset: z.number().int().min(0).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 createSearchRoute(library: Library) {\n  const route = new Hono();\n\n  // POST / - Search 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 = searchRequestBodySchema.safeParse(body);\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    const requestBody = parseResult.data;\n\n    // Build options for searchReferences\n    const options: SearchOperationOptions = {\n      query: requestBody.query,\n      ...pickDefined(requestBody, [\"sort\", \"order\", \"limit\", \"offset\"] as const),\n    };\n\n    // Call searchReferences operation - always returns raw CslItem[]\n    const result = await searchReferences(library, options);\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import { Hono } from \"hono\";\nimport type { 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 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