@ncukondo/reference-manager 0.3.0 → 0.4.0

package/dist/chunks/loader-mQ25o6cV.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"loader-mQ25o6cV.js","sources":["../../src/core/identifier/normalize.ts","../../src/core/identifier/generator.ts","../../src/core/identifier/uuid.ts","../../src/core/reference.ts","../../src/utils/hash.ts","../../src/core/csl-json/parser.ts","../../src/core/csl-json/serializer.ts","../../src/core/library.ts","../../src/config/schema.ts","../../src/config/defaults.ts","../../src/config/loader.ts"],"sourcesContent":["/**\n * Normalize text for identifier generation\n * Converts to lowercase, converts spaces to underscores, keeps only alphanumeric and underscores\n * @param text - Text to normalize\n * @returns Normalized text (ASCII alphanumeric and underscores only)\n */\nexport function normalizeText(text: string): string {\n  return text\n    .toLowerCase()\n    .replace(/\\s+/g, \"_\") // Convert spaces to underscores\n    .replace(/[^a-z0-9_]/g, \"\") // Keep only alphanumeric and underscores\n    .replace(/_+/g, \"_\") // Collapse multiple underscores\n    .replace(/^_|_$/g, \"\"); // Remove leading/trailing underscores\n}\n\n/**\n * Normalize author name for identifier\n * @param name - Author name to normalize\n * @returns Normalized name (max 32 chars)\n */\nexport function normalizeAuthorName(name: string): string {\n  const normalized = normalizeText(name);\n  return normalized.slice(0, 32);\n}\n\n/**\n * Create a title slug for identifier\n * @param title - Title to create slug from\n * @returns Title slug (max 32 chars)\n */\nexport function normalizeTitleSlug(title: string): string {\n  const normalized = normalizeText(title);\n  return normalized.slice(0, 32);\n}\n","import type { CslItem } from \"../csl-json/types\";\nimport { normalizeAuthorName, normalizeTitleSlug } from \"./normalize\";\n\n/**\n * Extract author name from CSL-JSON item\n * Returns family name, literal name, or empty string\n */\nfunction extractAuthorName(item: CslItem): string {\n  if (!item.author || item.author.length === 0) {\n    return \"\";\n  }\n\n  const firstAuthor = item.author[0];\n  if (!firstAuthor) {\n    return \"\";\n  }\n\n  // Try family name first\n  if (firstAuthor.family) {\n    return normalizeAuthorName(firstAuthor.family);\n  }\n\n  // Try literal name (e.g., institutional authors)\n  if (firstAuthor.literal) {\n    return normalizeAuthorName(firstAuthor.literal);\n  }\n\n  return \"\";\n}\n\n/**\n * Extract year from CSL-JSON item\n * Returns year string or empty string\n */\nfunction extractYear(item: CslItem): string {\n  if (!item.issued || !item.issued[\"date-parts\"] || item.issued[\"date-parts\"].length === 0) {\n    return \"\";\n  }\n\n  const dateParts = item.issued[\"date-parts\"][0];\n  if (!dateParts || dateParts.length === 0) {\n    return \"\";\n  }\n\n  const year = dateParts[0];\n  return year ? year.toString() : \"\";\n}\n\n/**\n * Determine the title part of the ID based on author, year, and title availability\n * @param hasAuthor - Whether author is available\n * @param hasYear - Whether year is available\n * @param title - Title slug\n * @returns Title part of the ID\n */\nfunction determineTitlePart(hasAuthor: boolean, hasYear: boolean, title: string): string {\n  // No title part needed if both author and year are present\n  if (hasAuthor && hasYear) {\n    return \"\";\n  }\n\n  // Add title if available\n  if (title) {\n    return `-${title}`;\n  }\n\n  // Add \"untitled\" only if both author and year are missing\n  if (!hasAuthor && !hasYear) {\n    return \"-untitled\";\n  }\n\n  return \"\";\n}\n\n/**\n * Generate a BibTeX-style ID for a CSL-JSON item\n * Format: <FirstAuthorFamily>-<Year>[<TitleSlug>][a-z suffix]\n * @param item - CSL-JSON item\n * @returns Generated ID\n */\nexport function generateId(item: CslItem): string {\n  const author = extractAuthorName(item);\n  const year = extractYear(item);\n  const title = item.title ? normalizeTitleSlug(item.title) : \"\";\n\n  // Build base ID with fallbacks\n  const authorPart = author || \"anon\";\n  const yearPart = year || \"nd\"; // no date\n  const titlePart = determineTitlePart(Boolean(author), Boolean(year), title);\n\n  return `${authorPart}-${yearPart}${titlePart}`;\n}\n\n/**\n * Generate suffix for collision handling\n * a, b, c, ..., z, aa, ab, ...\n * @param index - Collision index (0 = no suffix, 1 = 'a', 2 = 'b', ...)\n * @returns Suffix string\n */\nfunction generateSuffix(index: number): string {\n  if (index === 0) {\n    return \"\";\n  }\n\n  let suffix = \"\";\n  let num = index;\n\n  while (num > 0) {\n    num--; // Adjust for 0-based indexing\n    suffix = String.fromCharCode(97 + (num % 26)) + suffix;\n    num = Math.floor(num / 26);\n  }\n\n  return suffix;\n}\n\n/**\n * Generate ID with collision check\n * Appends a, b, c, ... suffix if the base ID already exists\n * @param item - CSL-JSON item\n * @param existingIds - Array of existing IDs\n * @returns Generated ID with collision handling\n */\nexport function generateIdWithCollisionCheck(item: CslItem, existingIds: string[]): string {\n  const baseId = generateId(item);\n\n  // Normalize existing IDs to lowercase for case-insensitive comparison\n  const normalizedExistingIds = existingIds.map((id) => id.toLowerCase());\n\n  // Check for collisions\n  let candidate = baseId;\n  let suffixIndex = 0;\n\n  while (normalizedExistingIds.includes(candidate.toLowerCase())) {\n    suffixIndex++;\n    const suffix = generateSuffix(suffixIndex);\n    candidate = `${baseId}${suffix}`;\n  }\n\n  return candidate;\n}\n","import { randomUUID } from \"node:crypto\";\nimport type { CslCustom } from \"../csl-json/types\";\n\nconst UUID_REGEX = /^[0-9a-f]{8}-[0-9a-f]{4}-4[0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}$/i;\n\n/**\n * Validate if a string is a valid UUID v4\n */\nexport function isValidUuid(uuid: string): boolean {\n  return UUID_REGEX.test(uuid);\n}\n\n/**\n * Generate a new UUID v4\n */\nexport function generateUuid(): string {\n  return randomUUID();\n}\n\n/**\n * Generate a new ISO 8601 timestamp\n */\nexport function generateTimestamp(): string {\n  return new Date().toISOString();\n}\n\n/**\n * Extract UUID from custom field\n */\nexport function extractUuidFromCustom(custom: CslCustom | undefined): string | null {\n  if (!custom || !custom.uuid) {\n    return null;\n  }\n\n  return isValidUuid(custom.uuid) ? custom.uuid : null;\n}\n\n/**\n * Ensure custom metadata has a valid UUID\n * Generates a new UUID if missing or invalid\n */\nfunction ensureUuid(custom: CslCustom | undefined): Partial<CslCustom> & { uuid: string } {\n  const existingUuid = extractUuidFromCustom(custom);\n\n  if (existingUuid && custom) {\n    return custom as Partial<CslCustom> & { uuid: string };\n  }\n\n  const newUuid = generateUuid();\n  return {\n    ...custom,\n    uuid: newUuid,\n  };\n}\n\n/**\n * Ensure custom metadata has a valid created_at timestamp\n * Migrates from legacy timestamp field if needed\n * Generates a new timestamp if missing\n */\nfunction ensureCreatedAt(\n  custom: Partial<CslCustom> & { uuid: string }\n): Partial<CslCustom> & { uuid: string; created_at: string } {\n  // Already has created_at\n  if (custom.created_at) {\n    return custom as Partial<CslCustom> & { uuid: string; created_at: string };\n  }\n\n  // Legacy migration: move timestamp to created_at if timestamp exists but created_at doesn't\n  if (custom.timestamp) {\n    return {\n      ...custom,\n      created_at: custom.timestamp,\n    };\n  }\n\n  // Generate new created_at\n  const newTimestamp = generateTimestamp();\n  return {\n    ...custom,\n    created_at: newTimestamp,\n  };\n}\n\n/**\n * Ensure custom metadata has a valid timestamp (last modification time)\n * Defaults to created_at if missing\n */\nfunction ensureTimestamp(\n  custom: Partial<CslCustom> & { uuid: string; created_at: string }\n): CslCustom {\n  // Already has timestamp\n  if (custom.timestamp) {\n    return custom as CslCustom;\n  }\n\n  // Default to created_at (new item, not yet modified)\n  return {\n    ...custom,\n    timestamp: custom.created_at,\n  };\n}\n\n/**\n * Ensure custom metadata has valid UUID, created_at, and timestamp\n * Handles legacy migration from old timestamp-only format\n * Generates new values if missing or invalid\n */\nexport function ensureCustomMetadata(custom: CslCustom | undefined): CslCustom {\n  const withUuid = ensureUuid(custom);\n  const withCreatedAt = ensureCreatedAt(withUuid);\n  const withTimestamp = ensureTimestamp(withCreatedAt);\n  return withTimestamp;\n}\n","import type { CslItem } from \"./csl-json/types\";\nimport { generateIdWithCollisionCheck } from \"./identifier/generator\";\nimport { ensureCustomMetadata, extractUuidFromCustom } from \"./identifier/uuid\";\n\n/**\n * Options for creating a Reference\n */\nexport interface ReferenceCreateOptions {\n  /** Existing IDs to check for collision */\n  existingIds?: Set<string>;\n}\n\n/**\n * Reference entity wrapping a CSL-JSON item\n */\nexport class Reference {\n  private item: CslItem;\n  private uuid: string;\n\n  constructor(item: CslItem) {\n    // Ensure UUID and timestamp are present and valid in custom field\n    const customMetadata = ensureCustomMetadata(item.custom);\n    this.item = { ...item, custom: customMetadata };\n\n    // Extract UUID from the custom field\n    const extractedUuid = extractUuidFromCustom(customMetadata);\n    if (!extractedUuid) {\n      throw new Error(\"Failed to extract UUID after ensureCustomMetadata\");\n    }\n    this.uuid = extractedUuid;\n  }\n\n  /**\n   * Factory method to create a Reference with UUID and ID generation\n   */\n  static create(item: CslItem, options?: ReferenceCreateOptions): Reference {\n    const existingIds = options?.existingIds || new Set<string>();\n\n    // Generate ID if not provided or empty\n    let updatedItem = item;\n    if (!item.id || item.id.trim() === \"\") {\n      const generatedId = generateIdWithCollisionCheck(item, Array.from(existingIds));\n      updatedItem = { ...item, id: generatedId };\n    }\n\n    return new Reference(updatedItem);\n  }\n\n  /**\n   * Get the underlying CSL-JSON item\n   */\n  getItem(): CslItem {\n    return this.item;\n  }\n\n  /**\n   * Get the UUID (internal stable identifier)\n   */\n  getUuid(): string {\n    return this.uuid;\n  }\n\n  /**\n   * Get the ID (Pandoc citation key / BibTeX-key)\n   */\n  getId(): string {\n    return this.item.id;\n  }\n\n  /**\n   * Get the title\n   */\n  getTitle(): string | undefined {\n    return this.item.title;\n  }\n\n  /**\n   * Get the authors\n   */\n  getAuthors(): CslItem[\"author\"] {\n    return this.item.author;\n  }\n\n  /**\n   * Get the year from issued date\n   */\n  getYear(): number | undefined {\n    const issued = this.item.issued;\n    if (!issued || !issued[\"date-parts\"] || issued[\"date-parts\"].length === 0) {\n      return undefined;\n    }\n    const firstDate = issued[\"date-parts\"][0];\n    return firstDate && firstDate.length > 0 ? firstDate[0] : undefined;\n  }\n\n  /**\n   * Get the DOI\n   */\n  getDoi(): string | undefined {\n    return this.item.DOI;\n  }\n\n  /**\n   * Get the PMID\n   */\n  getPmid(): string | undefined {\n    return this.item.PMID;\n  }\n\n  /**\n   * Get the PMCID\n   */\n  getPmcid(): string | undefined {\n    return this.item.PMCID;\n  }\n\n  /**\n   * Get the URL\n   */\n  getUrl(): string | undefined {\n    return this.item.URL;\n  }\n\n  /**\n   * Get the keyword\n   */\n  getKeyword(): string[] | undefined {\n    return this.item.keyword;\n  }\n\n  /**\n   * Get additional URLs from custom metadata\n   */\n  getAdditionalUrls(): string[] | undefined {\n    return this.item.custom?.additional_urls;\n  }\n\n  /**\n   * Get the creation timestamp from custom metadata (immutable)\n   */\n  getCreatedAt(): string {\n    if (!this.item.custom?.created_at) {\n      throw new Error(\"created_at is missing from custom metadata\");\n    }\n    return this.item.custom.created_at;\n  }\n\n  /**\n   * Get the last modification timestamp from custom metadata\n   */\n  getTimestamp(): string {\n    if (!this.item.custom?.timestamp) {\n      throw new Error(\"timestamp is missing from custom metadata\");\n    }\n    return this.item.custom.timestamp;\n  }\n\n  /**\n   * Update the timestamp to current time\n   * Call this whenever the reference is modified\n   */\n  touch(): void {\n    if (!this.item.custom) {\n      throw new Error(\"custom metadata is missing\");\n    }\n    this.item.custom.timestamp = new Date().toISOString();\n  }\n\n  /**\n   * Get the type\n   */\n  getType(): string {\n    return this.item.type;\n  }\n}\n","import { createHash } from \"node:crypto\";\nimport { createReadStream } from \"node:fs\";\n\n/**\n * Compute SHA-256 hash of a string\n */\nexport function computeHash(input: string): string {\n  return createHash(\"sha256\").update(input, \"utf-8\").digest(\"hex\");\n}\n\n/**\n * Compute SHA-256 hash of a file\n */\nexport async function computeFileHash(filePath: string): Promise<string> {\n  return new Promise((resolve, reject) => {\n    const hash = createHash(\"sha256\");\n    const stream = createReadStream(filePath);\n\n    stream.on(\"data\", (chunk) => hash.update(chunk));\n    stream.on(\"end\", () => resolve(hash.digest(\"hex\")));\n    stream.on(\"error\", (error) => reject(error));\n  });\n}\n","import { readFile } from \"node:fs/promises\";\nimport { ensureCustomMetadata } from \"../identifier/uuid\";\nimport { type CslLibrary, CslLibrarySchema } from \"./types\";\n\n/**\n * Convert keyword field from semicolon-separated string to array\n * @param keyword - Semicolon-separated string or undefined\n * @returns Array of keywords or undefined\n */\nfunction parseKeyword(keyword: unknown): string[] | undefined {\n  if (typeof keyword !== \"string\") {\n    return undefined;\n  }\n\n  if (keyword.trim() === \"\") {\n    return undefined;\n  }\n\n  const keywords = keyword\n    .split(\";\")\n    .map((k) => k.trim())\n    .filter((k) => k !== \"\");\n\n  return keywords.length > 0 ? keywords : undefined;\n}\n\n/**\n * Parse a CSL-JSON file and ensure all entries have valid UUIDs and timestamps\n * @param filePath - Path to the CSL-JSON file\n * @returns Array of CSL-JSON items with guaranteed UUIDs and timestamps\n * @throws Error if file cannot be read or JSON is invalid\n */\nexport async function parseCslJson(filePath: string): Promise<CslLibrary> {\n  // Read file\n  const content = await readFile(filePath, \"utf-8\");\n\n  // Parse JSON\n  let rawData: unknown;\n  try {\n    rawData = JSON.parse(content);\n  } catch (error) {\n    throw new Error(\n      `Failed to parse JSON: ${error instanceof Error ? error.message : String(error)}`\n    );\n  }\n\n  // Convert keyword fields from string to array before validation\n  if (Array.isArray(rawData)) {\n    rawData = rawData.map((item: unknown) => {\n      if (item && typeof item === \"object\" && \"keyword\" in item) {\n        const itemWithKeyword = item as Record<string, unknown>;\n        return {\n          ...itemWithKeyword,\n          keyword: parseKeyword(itemWithKeyword.keyword),\n        };\n      }\n      return item;\n    });\n  }\n\n  // Validate with zod\n  const parseResult = CslLibrarySchema.safeParse(rawData);\n\n  if (!parseResult.success) {\n    throw new Error(`Invalid CSL-JSON structure: ${parseResult.error.message}`);\n  }\n\n  const library = parseResult.data;\n\n  // Ensure all entries have valid UUIDs and timestamps\n  const processedLibrary: CslLibrary = library.map((item) => {\n    const updatedCustom = ensureCustomMetadata(item.custom);\n\n    return {\n      ...item,\n      custom: updatedCustom,\n    };\n  });\n\n  return processedLibrary;\n}\n","import { mkdir, writeFile } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\nimport type { CslLibrary } from \"./types\";\n\n/**\n * Convert keyword array to semicolon-separated string\n * @param keywords - Array of keywords or undefined\n * @returns Semicolon-separated string or undefined\n */\nfunction serializeKeyword(keywords: string[] | undefined): string | undefined {\n  if (!keywords || keywords.length === 0) {\n    return undefined;\n  }\n\n  return keywords.join(\"; \");\n}\n\n/**\n * Serialize a CSL-JSON library to a formatted JSON string\n * @param library - CSL-JSON library (array of items)\n * @returns Formatted JSON string with 2-space indentation\n */\nexport function serializeCslJson(library: CslLibrary): string {\n  // Convert keyword arrays to semicolon-separated strings\n  const libraryForJson = library.map((item) => {\n    const { keyword, ...rest } = item;\n    const serializedKeyword = serializeKeyword(keyword);\n\n    if (serializedKeyword === undefined) {\n      return rest;\n    }\n\n    return {\n      ...rest,\n      keyword: serializedKeyword,\n    };\n  });\n\n  return JSON.stringify(libraryForJson, null, 2);\n}\n\n/**\n * Write a CSL-JSON library to a file\n * @param filePath - Path to write the CSL-JSON file\n * @param library - CSL-JSON library to write\n * @throws Error if file cannot be written\n */\nexport async function writeCslJson(filePath: string, library: CslLibrary): Promise<void> {\n  // Ensure parent directory exists\n  const dir = dirname(filePath);\n  await mkdir(dir, { recursive: true });\n\n  // Serialize and write\n  const content = serializeCslJson(library);\n  await writeFile(filePath, content, \"utf-8\");\n}\n","import { computeFileHash } from \"../utils/hash\";\nimport { parseCslJson } from \"./csl-json/parser\";\nimport { writeCslJson } from \"./csl-json/serializer\";\nimport type { CslItem } from \"./csl-json/types\";\nimport { Reference } from \"./reference\";\n\n/**\n * Options for update operations\n */\nexport interface UpdateOptions {\n  /** How to handle ID collision: 'fail' (default) or 'suffix' */\n  onIdCollision?: \"fail\" | \"suffix\";\n}\n\n/**\n * Result of an update operation\n */\nexport interface UpdateResult {\n  /** Whether the update was successful */\n  updated: boolean;\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 * Library manager for CSL-JSON references\n */\nexport class Library {\n  private filePath: string;\n  private references: Reference[] = [];\n  private currentHash: string | null = null;\n\n  // Indices for fast lookup\n  private uuidIndex: Map<string, Reference> = new Map();\n  private idIndex: Map<string, Reference> = new Map();\n  private doiIndex: Map<string, Reference> = new Map();\n  private pmidIndex: Map<string, Reference> = new Map();\n\n  private constructor(filePath: string, items: CslItem[]) {\n    this.filePath = filePath;\n\n    // Create references and build indices\n    for (const item of items) {\n      const ref = new Reference(item);\n      this.references.push(ref);\n      this.addToIndices(ref);\n    }\n  }\n\n  /**\n   * Load library from file\n   */\n  static async load(filePath: string): Promise<Library> {\n    const items = await parseCslJson(filePath);\n    const library = new Library(filePath, items);\n    // Compute and store file hash after loading\n    library.currentHash = await computeFileHash(filePath);\n    return library;\n  }\n\n  /**\n   * Save library to file\n   */\n  async save(): Promise<void> {\n    const items = this.references.map((ref) => ref.getItem());\n    await writeCslJson(this.filePath, items);\n    // Update file hash after saving\n    this.currentHash = await computeFileHash(this.filePath);\n  }\n\n  /**\n   * Add a reference to the library\n   */\n  add(item: CslItem): void {\n    // Collect existing IDs for collision check\n    const existingIds = new Set(this.references.map((ref) => ref.getId()));\n\n    // Create reference with collision check\n    const ref = Reference.create(item, { existingIds });\n\n    // Add to library\n    this.references.push(ref);\n    this.addToIndices(ref);\n  }\n\n  /**\n   * Remove a reference by UUID\n   */\n  removeByUuid(uuid: string): boolean {\n    const ref = this.uuidIndex.get(uuid);\n    if (!ref) {\n      return false;\n    }\n\n    return this.removeReference(ref);\n  }\n\n  /**\n   * Remove a reference by ID\n   */\n  removeById(id: string): boolean {\n    const ref = this.idIndex.get(id);\n    if (!ref) {\n      return false;\n    }\n\n    return this.removeReference(ref);\n  }\n\n  /**\n   * Update a reference by UUID.\n   * @param uuid - The UUID of the reference to update\n   * @param updates - Partial updates to apply to the reference\n   * @returns true if the reference was found and updated, false otherwise\n   */\n  updateByUuid(uuid: string, updates: Partial<CslItem>, options: UpdateOptions = {}): UpdateResult {\n    const ref = this.uuidIndex.get(uuid);\n    if (!ref) {\n      return { updated: false };\n    }\n\n    return this.updateReference(ref, updates, options);\n  }\n\n  /**\n   * Update a reference by ID.\n   * @param id - The ID of the reference to update\n   * @param updates - Partial updates to apply to the reference\n   * @returns true if the reference was found and updated, false otherwise\n   */\n  updateById(id: string, updates: Partial<CslItem>, options: UpdateOptions = {}): UpdateResult {\n    const ref = this.idIndex.get(id);\n    if (!ref) {\n      return { updated: false };\n    }\n\n    return this.updateReference(ref, updates, options);\n  }\n\n  /**\n   * Find a reference by UUID\n   */\n  findByUuid(uuid: string): Reference | undefined {\n    return this.uuidIndex.get(uuid);\n  }\n\n  /**\n   * Find a reference by ID\n   */\n  findById(id: string): Reference | undefined {\n    return this.idIndex.get(id);\n  }\n\n  /**\n   * Find a reference by DOI\n   */\n  findByDoi(doi: string): Reference | undefined {\n    return this.doiIndex.get(doi);\n  }\n\n  /**\n   * Find a reference by PMID\n   */\n  findByPmid(pmid: string): Reference | undefined {\n    return this.pmidIndex.get(pmid);\n  }\n\n  /**\n   * Get all references\n   */\n  getAll(): Reference[] {\n    return [...this.references];\n  }\n\n  /**\n   * Get the file path\n   */\n  getFilePath(): string {\n    return this.filePath;\n  }\n\n  /**\n   * Get the current file hash\n   * Returns null if the library has not been loaded or saved yet\n   */\n  getCurrentHash(): string | null {\n    return this.currentHash;\n  }\n\n  /**\n   * Add reference to all indices\n   */\n  private addToIndices(ref: Reference): void {\n    // UUID index\n    this.uuidIndex.set(ref.getUuid(), ref);\n\n    // ID index\n    this.idIndex.set(ref.getId(), ref);\n\n    // DOI index\n    const doi = ref.getDoi();\n    if (doi) {\n      this.doiIndex.set(doi, ref);\n    }\n\n    // PMID index\n    const pmid = ref.getPmid();\n    if (pmid) {\n      this.pmidIndex.set(pmid, ref);\n    }\n  }\n\n  /**\n   * Remove reference from all indices and array\n   */\n  private removeReference(ref: Reference): boolean {\n    const index = this.references.indexOf(ref);\n    if (index === -1) {\n      return false;\n    }\n    this.references.splice(index, 1);\n    this.removeFromIndices(ref);\n    return true;\n  }\n\n  /**\n   * Update a reference with partial updates.\n   * Preserves uuid and created_at, updates timestamp.\n   */\n  private updateReference(\n    ref: Reference,\n    updates: Partial<CslItem>,\n    options: UpdateOptions = {}\n  ): UpdateResult {\n    const index = this.references.indexOf(ref);\n    if (index === -1) {\n      return { updated: false };\n    }\n\n    const existingItem = ref.getItem();\n    const currentId = ref.getId();\n    const { newId, idChanged, collision } = this.resolveNewId(\n      updates.id ?? existingItem.id,\n      currentId,\n      options\n    );\n\n    if (collision) {\n      return { updated: false, idCollision: true };\n    }\n\n    const updatedItem = this.buildUpdatedItem(existingItem, updates, newId);\n\n    // Remove old reference from indices\n    this.removeFromIndices(ref);\n\n    // Create new reference and replace in array\n    const newRef = new Reference(updatedItem);\n    this.references[index] = newRef;\n    this.addToIndices(newRef);\n\n    const result: UpdateResult = { updated: true };\n    if (idChanged) {\n      result.idChanged = true;\n      result.newId = newId;\n    }\n    return result;\n  }\n\n  /**\n   * Resolve the new ID, handling collisions based on options.\n   */\n  private resolveNewId(\n    requestedId: string,\n    currentId: string,\n    options: UpdateOptions\n  ): { newId: string; idChanged: boolean; collision: boolean } {\n    if (requestedId === currentId) {\n      return { newId: requestedId, idChanged: false, collision: false };\n    }\n\n    const conflictingRef = this.idIndex.get(requestedId);\n    if (!conflictingRef) {\n      return { newId: requestedId, idChanged: false, collision: false };\n    }\n\n    const onIdCollision = options.onIdCollision ?? \"fail\";\n    if (onIdCollision === \"fail\") {\n      return { newId: requestedId, idChanged: false, collision: true };\n    }\n\n    // onIdCollision === \"suffix\": resolve by adding suffix\n    const existingIds = new Set(this.references.map((r) => r.getId()));\n    existingIds.delete(currentId);\n    const resolvedId = this.resolveIdCollision(requestedId, existingIds);\n    return { newId: resolvedId, idChanged: true, collision: false };\n  }\n\n  /**\n   * Build the updated CslItem, preserving uuid and created_at.\n   */\n  private buildUpdatedItem(\n    existingItem: CslItem,\n    updates: Partial<CslItem>,\n    newId: string\n  ): CslItem {\n    return {\n      ...existingItem,\n      ...updates,\n      id: newId,\n      type: updates.type ?? existingItem.type,\n      custom: {\n        ...(existingItem.custom || {}),\n        ...(updates.custom || {}),\n        uuid: existingItem.custom?.uuid || \"\",\n        created_at: existingItem.custom?.created_at || new Date().toISOString(),\n        timestamp: new Date().toISOString(),\n      },\n    };\n  }\n\n  /**\n   * Remove a reference from all indices.\n   */\n  private removeFromIndices(ref: Reference): void {\n    this.uuidIndex.delete(ref.getUuid());\n    this.idIndex.delete(ref.getId());\n\n    const doi = ref.getDoi();\n    if (doi) {\n      this.doiIndex.delete(doi);\n    }\n\n    const pmid = ref.getPmid();\n    if (pmid) {\n      this.pmidIndex.delete(pmid);\n    }\n  }\n\n  /**\n   * Generate an alphabetic suffix for ID collision resolution.\n   * 0 -> 'a', 1 -> 'b', ..., 25 -> 'z', 26 -> 'aa', etc.\n   */\n  private 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   */\n  private resolveIdCollision(baseId: string, existingIds: Set<string>): string {\n    if (!existingIds.has(baseId)) {\n      return baseId;\n    }\n\n    let index = 0;\n    let newId: string;\n\n    do {\n      const suffix = this.generateSuffix(index);\n      newId = `${baseId}${suffix}`;\n      index++;\n    } while (existingIds.has(newId));\n\n    return newId;\n  }\n}\n","/**\n * Configuration schema using Zod\n */\n\nimport { z } from \"zod\";\n\n/**\n * Log level schema\n */\nexport const logLevelSchema = z.enum([\"silent\", \"info\", \"debug\"]);\n\n/**\n * Backup configuration schema\n */\nexport const backupConfigSchema = z.object({\n  maxGenerations: z.number().int().positive(),\n  maxAgeDays: z.number().int().positive(),\n  directory: z.string().min(1),\n});\n\n/**\n * File watching configuration schema\n */\nexport const watchConfigSchema = z.object({\n  enabled: z.boolean(),\n  debounceMs: z.number().int().nonnegative(),\n  pollIntervalMs: z.number().int().positive(),\n  retryIntervalMs: z.number().int().positive(),\n  maxRetries: z.number().int().nonnegative(),\n});\n\n/**\n * Server configuration schema\n */\nexport const serverConfigSchema = z.object({\n  autoStart: z.boolean(),\n  autoStopMinutes: z.number().int().nonnegative(),\n});\n\n/**\n * Citation format schema\n */\nexport const citationFormatSchema = z.enum([\"text\", \"html\", \"rtf\"]);\n\n/**\n * Citation configuration schema\n */\nexport const citationConfigSchema = z.object({\n  defaultStyle: z.string(),\n  cslDirectory: z.array(z.string()),\n  defaultLocale: z.string(),\n  defaultFormat: citationFormatSchema,\n});\n\n/**\n * PubMed API configuration schema\n */\nexport const pubmedConfigSchema = z.object({\n  email: z.string().optional(),\n  apiKey: z.string().optional(),\n});\n\n/**\n * Fulltext storage configuration schema\n */\nexport const fulltextConfigSchema = z.object({\n  directory: z.string().min(1),\n});\n\n/**\n * Complete configuration schema\n */\nexport const configSchema = z.object({\n  library: z.string().min(1),\n  logLevel: logLevelSchema,\n  backup: backupConfigSchema,\n  watch: watchConfigSchema,\n  server: serverConfigSchema,\n  citation: citationConfigSchema,\n  pubmed: pubmedConfigSchema,\n  fulltext: fulltextConfigSchema,\n});\n\n/**\n * Partial configuration schema (for TOML files)\n * Supports both camelCase and snake_case field names\n */\nexport const partialConfigSchema = z\n  .object({\n    library: z.string().min(1).optional(),\n    logLevel: logLevelSchema.optional(),\n    log_level: logLevelSchema.optional(), // snake_case support\n    backup: z\n      .object({\n        maxGenerations: z.number().int().positive().optional(),\n        max_generations: z.number().int().positive().optional(),\n        maxAgeDays: z.number().int().positive().optional(),\n        max_age_days: z.number().int().positive().optional(),\n        directory: z.string().min(1).optional(),\n      })\n      .optional(),\n    watch: z\n      .object({\n        enabled: z.boolean().optional(),\n        debounceMs: z.number().int().nonnegative().optional(),\n        debounce_ms: z.number().int().nonnegative().optional(),\n        pollIntervalMs: z.number().int().positive().optional(),\n        poll_interval_ms: z.number().int().positive().optional(),\n        retryIntervalMs: z.number().int().positive().optional(),\n        retry_interval_ms: z.number().int().positive().optional(),\n        maxRetries: z.number().int().nonnegative().optional(),\n        max_retries: z.number().int().nonnegative().optional(),\n      })\n      .optional(),\n    server: z\n      .object({\n        autoStart: z.boolean().optional(),\n        auto_start: z.boolean().optional(),\n        autoStopMinutes: z.number().int().nonnegative().optional(),\n        auto_stop_minutes: z.number().int().nonnegative().optional(),\n      })\n      .optional(),\n    citation: z\n      .object({\n        defaultStyle: z.string().optional(),\n        default_style: z.string().optional(),\n        cslDirectory: z.union([z.string(), z.array(z.string())]).optional(),\n        csl_directory: z.union([z.string(), z.array(z.string())]).optional(),\n        defaultLocale: z.string().optional(),\n        default_locale: z.string().optional(),\n        defaultFormat: citationFormatSchema.optional(),\n        default_format: citationFormatSchema.optional(),\n      })\n      .optional(),\n    pubmed: z\n      .object({\n        email: z.string().optional(),\n        apiKey: z.string().optional(),\n        api_key: z.string().optional(),\n      })\n      .optional(),\n    fulltext: z\n      .object({\n        directory: z.string().min(1).optional(),\n      })\n      .optional(),\n  })\n  .passthrough(); // Allow unknown fields in TOML files\n\n/**\n * Inferred types from schemas\n */\nexport type LogLevel = z.infer<typeof logLevelSchema>;\nexport type BackupConfig = z.infer<typeof backupConfigSchema>;\nexport type WatchConfig = z.infer<typeof watchConfigSchema>;\nexport type ServerConfig = z.infer<typeof serverConfigSchema>;\nexport type CitationFormat = z.infer<typeof citationFormatSchema>;\nexport type CitationConfig = z.infer<typeof citationConfigSchema>;\nexport type PubmedConfig = z.infer<typeof pubmedConfigSchema>;\nexport type FulltextConfig = z.infer<typeof fulltextConfigSchema>;\nexport type Config = z.infer<typeof configSchema>;\nexport type PartialConfig = z.infer<typeof partialConfigSchema>;\n\n/**\n * Deep partial type for Config\n */\nexport type DeepPartialConfig = {\n  library?: string;\n  logLevel?: LogLevel;\n  backup?: Partial<BackupConfig>;\n  watch?: Partial<WatchConfig>;\n  server?: Partial<ServerConfig>;\n  citation?: Partial<CitationConfig>;\n  pubmed?: Partial<PubmedConfig>;\n  fulltext?: Partial<FulltextConfig>;\n};\n\n/**\n * Normalize backup configuration from snake_case to camelCase\n */\nfunction normalizeBackupConfig(\n  backup: Partial<{\n    maxGenerations?: number;\n    max_generations?: number;\n    maxAgeDays?: number;\n    max_age_days?: number;\n    directory?: string;\n  }>\n): Partial<BackupConfig> | undefined {\n  const normalized: Partial<BackupConfig> = {};\n\n  const maxGenerations = backup.maxGenerations ?? backup.max_generations;\n  if (maxGenerations !== undefined) {\n    normalized.maxGenerations = maxGenerations;\n  }\n\n  const maxAgeDays = backup.maxAgeDays ?? backup.max_age_days;\n  if (maxAgeDays !== undefined) {\n    normalized.maxAgeDays = maxAgeDays;\n  }\n\n  if (backup.directory !== undefined) {\n    normalized.directory = backup.directory;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize watch configuration from snake_case to camelCase\n */\nfunction normalizeWatchConfig(\n  watch: Partial<{\n    enabled?: boolean;\n    debounceMs?: number;\n    debounce_ms?: number;\n    pollIntervalMs?: number;\n    poll_interval_ms?: number;\n    retryIntervalMs?: number;\n    retry_interval_ms?: number;\n    maxRetries?: number;\n    max_retries?: number;\n  }>\n): Partial<WatchConfig> | undefined {\n  const normalized: Partial<WatchConfig> = {};\n\n  if (watch.enabled !== undefined) {\n    normalized.enabled = watch.enabled;\n  }\n\n  const debounceMs = watch.debounceMs ?? watch.debounce_ms;\n  if (debounceMs !== undefined) {\n    normalized.debounceMs = debounceMs;\n  }\n\n  const pollIntervalMs = watch.pollIntervalMs ?? watch.poll_interval_ms;\n  if (pollIntervalMs !== undefined) {\n    normalized.pollIntervalMs = pollIntervalMs;\n  }\n\n  const retryIntervalMs = watch.retryIntervalMs ?? watch.retry_interval_ms;\n  if (retryIntervalMs !== undefined) {\n    normalized.retryIntervalMs = retryIntervalMs;\n  }\n\n  const maxRetries = watch.maxRetries ?? watch.max_retries;\n  if (maxRetries !== undefined) {\n    normalized.maxRetries = maxRetries;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize server configuration from snake_case to camelCase\n */\nfunction normalizeServerConfig(\n  server: Partial<{\n    autoStart?: boolean;\n    auto_start?: boolean;\n    autoStopMinutes?: number;\n    auto_stop_minutes?: number;\n  }>\n): Partial<ServerConfig> | undefined {\n  const normalized: Partial<ServerConfig> = {};\n\n  const autoStart = server.autoStart ?? server.auto_start;\n  if (autoStart !== undefined) {\n    normalized.autoStart = autoStart;\n  }\n\n  const autoStopMinutes = server.autoStopMinutes ?? server.auto_stop_minutes;\n  if (autoStopMinutes !== undefined) {\n    normalized.autoStopMinutes = autoStopMinutes;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize citation configuration from snake_case to camelCase\n */\nfunction normalizeCitationConfig(\n  citation: Partial<{\n    defaultStyle?: string;\n    default_style?: string;\n    cslDirectory?: string | string[];\n    csl_directory?: string | string[];\n    defaultLocale?: string;\n    default_locale?: string;\n    defaultFormat?: CitationFormat;\n    default_format?: CitationFormat;\n  }>\n): Partial<CitationConfig> | undefined {\n  const normalized: Partial<CitationConfig> = {};\n\n  const defaultStyle = citation.defaultStyle ?? citation.default_style;\n  if (defaultStyle !== undefined) {\n    normalized.defaultStyle = defaultStyle;\n  }\n\n  const cslDirectory = citation.cslDirectory ?? citation.csl_directory;\n  if (cslDirectory !== undefined) {\n    // Normalize to array: string -> [string]\n    normalized.cslDirectory = Array.isArray(cslDirectory) ? cslDirectory : [cslDirectory];\n  }\n\n  const defaultLocale = citation.defaultLocale ?? citation.default_locale;\n  if (defaultLocale !== undefined) {\n    normalized.defaultLocale = defaultLocale;\n  }\n\n  const defaultFormat = citation.defaultFormat ?? citation.default_format;\n  if (defaultFormat !== undefined) {\n    normalized.defaultFormat = defaultFormat;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize pubmed configuration from snake_case to camelCase\n */\nfunction normalizePubmedConfig(\n  pubmed: Partial<{\n    email?: string;\n    apiKey?: string;\n    api_key?: string;\n  }>\n): Partial<PubmedConfig> | undefined {\n  const normalized: Partial<PubmedConfig> = {};\n\n  if (pubmed.email !== undefined) {\n    normalized.email = pubmed.email;\n  }\n\n  const apiKey = pubmed.apiKey ?? pubmed.api_key;\n  if (apiKey !== undefined) {\n    normalized.apiKey = apiKey;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize snake_case fields to camelCase\n */\nexport function normalizePartialConfig(partial: PartialConfig): DeepPartialConfig {\n  const normalized: DeepPartialConfig = {};\n\n  // Library\n  if (partial.library !== undefined) {\n    normalized.library = partial.library;\n  }\n\n  // Log level (prefer camelCase, fallback to snake_case)\n  const logLevel = partial.logLevel ?? partial.log_level;\n  if (logLevel !== undefined) {\n    normalized.logLevel = logLevel;\n  }\n\n  // Backup\n  const backup =\n    partial.backup !== undefined\n      ? normalizeBackupConfig(partial.backup as Parameters<typeof normalizeBackupConfig>[0])\n      : undefined;\n  if (backup) {\n    normalized.backup = backup;\n  }\n\n  // Watch\n  const watch =\n    partial.watch !== undefined\n      ? normalizeWatchConfig(partial.watch as Parameters<typeof normalizeWatchConfig>[0])\n      : undefined;\n  if (watch) {\n    normalized.watch = watch;\n  }\n\n  // Server\n  const server =\n    partial.server !== undefined\n      ? normalizeServerConfig(partial.server as Parameters<typeof normalizeServerConfig>[0])\n      : undefined;\n  if (server) {\n    normalized.server = server;\n  }\n\n  // Citation\n  const citation =\n    partial.citation !== undefined\n      ? normalizeCitationConfig(partial.citation as Parameters<typeof normalizeCitationConfig>[0])\n      : undefined;\n  if (citation) {\n    normalized.citation = citation;\n  }\n\n  // PubMed\n  const pubmed =\n    partial.pubmed !== undefined\n      ? normalizePubmedConfig(partial.pubmed as Parameters<typeof normalizePubmedConfig>[0])\n      : undefined;\n  if (pubmed) {\n    normalized.pubmed = pubmed;\n  }\n\n  // Fulltext\n  const fulltext =\n    partial.fulltext !== undefined ? normalizeFulltextConfig(partial.fulltext) : undefined;\n  if (fulltext) {\n    normalized.fulltext = fulltext;\n  }\n\n  return normalized;\n}\n\n/**\n * Normalize fulltext configuration\n */\nfunction normalizeFulltextConfig(fulltext: {\n  directory?: string | undefined;\n}): Partial<FulltextConfig> | undefined {\n  const normalized: Partial<FulltextConfig> = {};\n\n  if (fulltext.directory !== undefined) {\n    normalized.directory = fulltext.directory;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n","/**\n * Default configuration values\n */\n\nimport { tmpdir } from \"node:os\";\nimport { homedir } from \"node:os\";\nimport { join } from \"node:path\";\nimport type { Config } from \"./schema.js\";\n\n/**\n * Get the default backup directory\n * Uses $TMPDIR/reference-manager/backups/\n */\nexport function getDefaultBackupDirectory(): string {\n  return join(tmpdir(), \"reference-manager\", \"backups\");\n}\n\n/**\n * Get the default library path\n * Uses ~/.reference-manager/csl.library.json\n */\nexport function getDefaultLibraryPath(): string {\n  return join(homedir(), \".reference-manager\", \"csl.library.json\");\n}\n\n/**\n * Get the default user config path\n * Uses ~/.reference-manager/config.toml\n */\nexport function getDefaultUserConfigPath(): string {\n  return join(homedir(), \".reference-manager\", \"config.toml\");\n}\n\n/**\n * Get the default current directory config filename\n * Uses .reference-manager.config.toml\n */\nexport function getDefaultCurrentDirConfigFilename(): string {\n  return \".reference-manager.config.toml\";\n}\n\n/**\n * Get the default CSL directory\n * Uses ~/.reference-manager/csl/\n */\nexport function getDefaultCslDirectory(): string {\n  return join(homedir(), \".reference-manager\", \"csl\");\n}\n\n/**\n * Get the default fulltext directory\n * Uses ~/.reference-manager/fulltext/\n */\nexport function getDefaultFulltextDirectory(): string {\n  return join(homedir(), \".reference-manager\", \"fulltext\");\n}\n\n/**\n * Default configuration\n */\nexport const defaultConfig: Config = {\n  library: getDefaultLibraryPath(),\n  logLevel: \"info\",\n  backup: {\n    maxGenerations: 50,\n    maxAgeDays: 365,\n    directory: getDefaultBackupDirectory(),\n  },\n  watch: {\n    enabled: true,\n    debounceMs: 500,\n    pollIntervalMs: 5000,\n    retryIntervalMs: 200,\n    maxRetries: 10,\n  },\n  server: {\n    autoStart: false,\n    autoStopMinutes: 0,\n  },\n  citation: {\n    defaultStyle: \"apa\",\n    cslDirectory: [getDefaultCslDirectory()],\n    defaultLocale: \"en-US\",\n    defaultFormat: \"text\",\n  },\n  pubmed: {\n    email: undefined,\n    apiKey: undefined,\n  },\n  fulltext: {\n    directory: getDefaultFulltextDirectory(),\n  },\n};\n","/**\n * Configuration loader\n */\n\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { homedir } from \"node:os\";\nimport { join } from \"node:path\";\nimport { parse as parseTOML } from \"@iarna/toml\";\nimport {\n  defaultConfig,\n  getDefaultCurrentDirConfigFilename,\n  getDefaultUserConfigPath,\n} from \"./defaults.js\";\nimport {\n  type Config,\n  type DeepPartialConfig,\n  type PartialConfig,\n  configSchema,\n  normalizePartialConfig,\n  partialConfigSchema,\n} from \"./schema.js\";\n\n/**\n * Options for loading configuration\n */\nexport interface LoadConfigOptions {\n  /** Current working directory (default: process.cwd()) */\n  cwd?: string;\n  /** User config path (default: ~/.reference-manager/config.toml) */\n  userConfigPath?: string;\n  /** CLI argument overrides */\n  overrides?: Partial<Config>;\n}\n\n/**\n * Load and parse a TOML config file\n */\nfunction loadTOMLFile(path: string): PartialConfig | null {\n  if (!existsSync(path)) {\n    return null;\n  }\n\n  try {\n    const content = readFileSync(path, \"utf-8\");\n    const parsed = parseTOML(content);\n\n    // Validate with partial schema\n    const validated = partialConfigSchema.parse(parsed);\n    return validated;\n  } catch (error) {\n    throw new Error(\n      `Failed to load config from ${path}: ${error instanceof Error ? error.message : String(error)}`\n    );\n  }\n}\n\n/**\n * Merge partial configurations\n * Later configs override earlier ones\n */\nfunction mergeConfigs(\n  base: DeepPartialConfig,\n  ...overrides: (DeepPartialConfig | null | undefined)[]\n): DeepPartialConfig {\n  const result: DeepPartialConfig = { ...base };\n\n  const sectionKeys = [\"backup\", \"watch\", \"server\", \"citation\", \"pubmed\", \"fulltext\"] as const;\n\n  for (const override of overrides) {\n    if (!override) continue;\n\n    // Merge top-level primitive fields\n    if (override.library !== undefined) {\n      result.library = override.library;\n    }\n    if (override.logLevel !== undefined) {\n      result.logLevel = override.logLevel;\n    }\n\n    // Merge section configs\n    for (const key of sectionKeys) {\n      if (override[key] !== undefined) {\n        result[key] = {\n          ...result[key],\n          ...override[key],\n        };\n      }\n    }\n  }\n\n  return result;\n}\n\n/**\n * Fill missing fields with defaults\n */\nfunction fillDefaults(partial: DeepPartialConfig): Config {\n  return {\n    library: partial.library ?? defaultConfig.library,\n    logLevel: partial.logLevel ?? defaultConfig.logLevel,\n    backup: {\n      maxGenerations: partial.backup?.maxGenerations ?? defaultConfig.backup.maxGenerations,\n      maxAgeDays: partial.backup?.maxAgeDays ?? defaultConfig.backup.maxAgeDays,\n      directory: partial.backup?.directory ?? defaultConfig.backup.directory,\n    },\n    watch: {\n      enabled: partial.watch?.enabled ?? defaultConfig.watch.enabled,\n      debounceMs: partial.watch?.debounceMs ?? defaultConfig.watch.debounceMs,\n      pollIntervalMs: partial.watch?.pollIntervalMs ?? defaultConfig.watch.pollIntervalMs,\n      retryIntervalMs: partial.watch?.retryIntervalMs ?? defaultConfig.watch.retryIntervalMs,\n      maxRetries: partial.watch?.maxRetries ?? defaultConfig.watch.maxRetries,\n    },\n    server: {\n      autoStart: partial.server?.autoStart ?? defaultConfig.server.autoStart,\n      autoStopMinutes: partial.server?.autoStopMinutes ?? defaultConfig.server.autoStopMinutes,\n    },\n    citation: fillCitationDefaults(partial.citation),\n    pubmed: fillPubmedDefaults(partial.pubmed),\n    fulltext: fillFulltextDefaults(partial.fulltext),\n  };\n}\n\n/**\n * Fill citation config with defaults\n */\nfunction fillCitationDefaults(partial: DeepPartialConfig[\"citation\"]): Config[\"citation\"] {\n  return {\n    defaultStyle: partial?.defaultStyle ?? defaultConfig.citation.defaultStyle,\n    cslDirectory: partial?.cslDirectory ?? defaultConfig.citation.cslDirectory,\n    defaultLocale: partial?.defaultLocale ?? defaultConfig.citation.defaultLocale,\n    defaultFormat: partial?.defaultFormat ?? defaultConfig.citation.defaultFormat,\n  };\n}\n\n/**\n * Fill pubmed config with defaults\n * Environment variables take priority over config file values\n */\nfunction fillPubmedDefaults(partial: DeepPartialConfig[\"pubmed\"]): Config[\"pubmed\"] {\n  // Environment variables take priority\n  const email = process.env.PUBMED_EMAIL ?? partial?.email ?? defaultConfig.pubmed.email;\n  const apiKey = process.env.PUBMED_API_KEY ?? partial?.apiKey ?? defaultConfig.pubmed.apiKey;\n\n  return {\n    email,\n    apiKey,\n  };\n}\n\n/**\n * Expand ~ to home directory\n */\nfunction expandTilde(path: string): string {\n  if (path.startsWith(\"~/\")) {\n    return join(homedir(), path.slice(2));\n  }\n  return path;\n}\n\n/**\n * Fill fulltext config with defaults\n *\n * Priority:\n * 1. Environment variable REFERENCE_MANAGER_FULLTEXT_DIR\n * 2. Config file setting\n * 3. Default value\n */\nfunction fillFulltextDefaults(partial: DeepPartialConfig[\"fulltext\"]): Config[\"fulltext\"] {\n  const envDir = process.env.REFERENCE_MANAGER_FULLTEXT_DIR;\n  const directory = envDir ?? partial?.directory ?? defaultConfig.fulltext.directory;\n  return {\n    directory: expandTilde(directory),\n  };\n}\n\n/**\n * Load configuration from multiple sources\n *\n * Priority (highest to lowest):\n * 1. CLI argument overrides\n * 2. Current directory config (.reference-manager.config.toml)\n * 3. Environment variable (REFERENCE_MANAGER_CONFIG)\n * 4. User config (~/.reference-manager/config.toml)\n * 5. Default values\n */\nexport function loadConfig(options: LoadConfigOptions = {}): Config {\n  const cwd = options.cwd ?? process.cwd();\n  const userConfigPath = options.userConfigPath ?? getDefaultUserConfigPath();\n\n  // 1. Load user config (lowest priority)\n  const userConfig = loadTOMLFile(userConfigPath);\n\n  // 2. Load environment variable config\n  const envConfigPath = process.env.REFERENCE_MANAGER_CONFIG;\n  const envConfig = envConfigPath ? loadTOMLFile(envConfigPath) : null;\n\n  // 3. Load current directory config (highest priority)\n  const currentConfigPath = join(cwd, getDefaultCurrentDirConfigFilename());\n  const currentConfig = loadTOMLFile(currentConfigPath);\n\n  // Normalize snake_case to camelCase\n  const normalizedUser = userConfig ? normalizePartialConfig(userConfig) : null;\n  const normalizedEnv = envConfig ? normalizePartialConfig(envConfig) : null;\n  const normalizedCurrent = currentConfig ? normalizePartialConfig(currentConfig) : null;\n\n  // Merge configs (priority: current > env > user > defaults)\n  const merged = mergeConfigs(\n    {},\n    normalizedUser,\n    normalizedEnv,\n    normalizedCurrent,\n    options.overrides\n  );\n\n  // Fill missing fields with defaults\n  const config = fillDefaults(merged);\n\n  // Validate final config\n  try {\n    return configSchema.parse(config);\n  } catch (error) {\n    throw new Error(\n      `Invalid configuration: ${error instanceof Error ? error.message : String(error)}`\n    );\n  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