@ncukondo/reference-manager 0.1.0 → 0.3.0

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sources":["../src/core/csl-json/validator.ts","../src/utils/logger.ts","../src/utils/file.ts","../src/utils/backup.ts","../src/features/merge/three-way.ts","../src/features/file-watcher/file-watcher.ts"],"sourcesContent":["import { CslItemSchema, CslLibrarySchema } from \"./types\";\nimport type { CslItem, CslLibrary } from \"./types\";\n\n/**\n * Validate CSL-JSON library structure\n * @param data - Data to validate (can be any type)\n * @returns Validated CSL-JSON library\n * @throws Error if validation fails\n */\nexport function validateCslJson(data: unknown): CslLibrary {\n  const parseResult = CslLibrarySchema.safeParse(data);\n\n  if (!parseResult.success) {\n    throw new Error(`Invalid CSL-JSON structure: ${parseResult.error.message}`);\n  }\n\n  return parseResult.data;\n}\n\n/**\n * Validate a single CSL-JSON item\n * @param data - Data to validate (can be any type)\n * @returns Validation result with valid flag and errors\n */\nexport function validateCslItem(data: unknown): {\n  valid: boolean;\n  data?: CslItem;\n  errors?: string[];\n} {\n  const parseResult = CslItemSchema.safeParse(data);\n\n  if (!parseResult.success) {\n    return {\n      valid: false,\n      errors: parseResult.error.issues.map((issue) => issue.message),\n    };\n  }\n\n  return {\n    valid: true,\n    data: parseResult.data,\n  };\n}\n","export type LogLevel = \"silent\" | \"info\" | \"debug\";\n\nexport interface Logger {\n  info(...args: unknown[]): void;\n  debug(...args: unknown[]): void;\n  error(...args: unknown[]): void;\n}\n\nexport function createLogger(level: LogLevel = \"info\"): Logger {\n  const shouldLogInfo = level === \"info\" || level === \"debug\";\n  const shouldLogDebug = level === \"debug\";\n\n  function formatMessage(...args: unknown[]): string {\n    return `${args.map((arg) => String(arg)).join(\" \")}\\n`;\n  }\n\n  return {\n    info(...args: unknown[]): void {\n      if (shouldLogInfo) {\n        process.stderr.write(formatMessage(...args));\n      }\n    },\n\n    debug(...args: unknown[]): void {\n      if (shouldLogDebug) {\n        process.stderr.write(formatMessage(...args));\n      }\n    },\n\n    error(...args: unknown[]): void {\n      process.stderr.write(formatMessage(...args));\n    },\n  };\n}\n","import { mkdir } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\nimport writeFileAtomicLib from \"write-file-atomic\";\n\n/**\n * Write file atomically with parent directory creation\n */\nexport async function writeFileAtomic(filePath: string, content: string): Promise<void> {\n  await ensureDirectoryExists(dirname(filePath));\n  await writeFileAtomicLib(filePath, content, { encoding: \"utf-8\" });\n}\n\n/**\n * Ensure directory exists, creating it recursively if necessary\n */\nexport async function ensureDirectoryExists(dirPath: string): Promise<void> {\n  await mkdir(dirPath, { recursive: true });\n}\n","import { existsSync } from \"node:fs\";\nimport { copyFile, readFile, readdir, stat, unlink } from \"node:fs/promises\";\nimport { tmpdir } from \"node:os\";\nimport { dirname, join } from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\nimport { ensureDirectoryExists } from \"./file\";\n\nexport interface BackupOptions {\n  maxGenerations?: number;\n  maxAgeMs?: number;\n}\n\nconst DEFAULT_MAX_GENERATIONS = 50;\nconst DEFAULT_MAX_AGE_MS = 365 * 24 * 60 * 60 * 1000; // 1 year\n\n/**\n * Get package name from package.json\n */\nasync function resolvePackageName(): Promise<string> {\n  try {\n    const currentFile = fileURLToPath(import.meta.url);\n    let currentDir = dirname(currentFile);\n\n    for (let i = 0; i < 10; i++) {\n      const packageJsonPath = join(currentDir, \"package.json\");\n      if (existsSync(packageJsonPath)) {\n        const content = await readFile(packageJsonPath, \"utf-8\");\n        const pkg = JSON.parse(content);\n        return pkg.name;\n      }\n      currentDir = dirname(currentDir);\n    }\n  } catch {\n    // Fall back to hardcoded name if package.json is not found\n  }\n\n  return \"reference-manager\";\n}\n\nconst packageName = await resolvePackageName();\n\n/**\n * Get backup directory path for a library\n */\nexport function getBackupDirectory(libraryName: string): string {\n  const pkgName = packageName ?? \"reference-manager\";\n  return join(tmpdir(), pkgName, \"backups\", libraryName);\n}\n\n/**\n * Create a backup of the given file\n */\nexport async function createBackup(sourceFile: string, libraryName: string): Promise<string> {\n  const backupDir = getBackupDirectory(libraryName);\n  await ensureDirectoryExists(backupDir);\n\n  const timestamp = Date.now();\n  const backupFileName = `${timestamp}.backup`;\n  const backupPath = join(backupDir, backupFileName);\n\n  await copyFile(sourceFile, backupPath);\n\n  return backupPath;\n}\n\n/**\n * List all backups for a library (sorted by modification time, newest first)\n */\nexport async function listBackups(libraryName: string): Promise<string[]> {\n  const backupDir = getBackupDirectory(libraryName);\n\n  if (!existsSync(backupDir)) {\n    return [];\n  }\n\n  const files = await readdir(backupDir);\n  const backupFiles = files.filter((f) => f.endsWith(\".backup\")).map((f) => join(backupDir, f));\n\n  const filesWithStats = await Promise.all(\n    backupFiles.map(async (file) => {\n      const stats = await stat(file);\n      return { file, mtime: stats.mtimeMs };\n    })\n  );\n\n  filesWithStats.sort((a, b) => b.mtime - a.mtime);\n\n  return filesWithStats.map((f) => f.file);\n}\n\n/**\n * Clean up old backups based on generation count and age\n */\nexport async function cleanupOldBackups(\n  libraryName: string,\n  options?: BackupOptions\n): Promise<void> {\n  const maxGenerations = options?.maxGenerations ?? DEFAULT_MAX_GENERATIONS;\n  const maxAgeMs = options?.maxAgeMs ?? DEFAULT_MAX_AGE_MS;\n\n  const backups = await listBackups(libraryName);\n  const now = Date.now();\n\n  const backupsToDelete: string[] = [];\n\n  for (let i = 0; i < backups.length; i++) {\n    const backupPath = backups[i];\n    if (!backupPath) continue;\n\n    const stats = await stat(backupPath);\n    const age = now - stats.mtimeMs;\n\n    if (i >= maxGenerations || age > maxAgeMs) {\n      backupsToDelete.push(backupPath);\n    }\n  }\n\n  await Promise.all(backupsToDelete.map((backup) => unlink(backup)));\n}\n","/**\n * 3-way merge implementation with Last-Write-Wins (LWW) strategy\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type {\n  FieldConflict,\n  ItemConflict,\n  MergeOptions,\n  MergeResult,\n  MergeStatus,\n} from \"./types.js\";\n\n/**\n * Get UUID from item, with fallback to id if uuid is missing\n */\nfunction getItemUuid(item: CslItem): string {\n  return item.custom?.uuid || item.id || \"unknown\";\n}\n\n/**\n * Get timestamp from item, with fallback to created_at\n */\nfunction getTimestamp(item: CslItem): string {\n  return item.custom?.timestamp || item.custom?.created_at || \"1970-01-01T00:00:00.000Z\";\n}\n\n/**\n * Deep equality check for field values\n */\nfunction deepEqual(a: unknown, b: unknown): boolean {\n  return JSON.stringify(a) === JSON.stringify(b);\n}\n\n/**\n * Resolve a field conflict using LWW or prefer option\n */\nfunction resolveFieldConflict(\n  localValue: unknown,\n  remoteValue: unknown,\n  localTimestamp: string,\n  remoteTimestamp: string,\n  options?: MergeOptions\n): unknown {\n  if (localTimestamp > remoteTimestamp) {\n    return localValue;\n  }\n  if (remoteTimestamp > localTimestamp) {\n    return remoteValue;\n  }\n  // Timestamps equal: use prefer option or default to local\n  if (options?.prefer === \"remote\") {\n    return remoteValue;\n  }\n  return localValue;\n}\n\n/**\n * Determine conflict resolution type\n */\nfunction determineResolution(\n  fieldConflicts: FieldConflict[],\n  localTimestamp: string,\n  remoteTimestamp: string,\n  options?: MergeOptions\n): ItemConflict[\"resolution\"] {\n  const hasRealConflicts = fieldConflicts.every((fc) => fc.resolved !== undefined);\n  const localIsNewer = fieldConflicts.some(\n    (fc) => fc.local !== fc.remote && localTimestamp > remoteTimestamp\n  );\n  const remoteIsNewer = fieldConflicts.some(\n    (fc) => fc.local !== fc.remote && remoteTimestamp > localTimestamp\n  );\n\n  if (hasRealConflicts && localIsNewer) return \"auto-lww\";\n  if (hasRealConflicts && remoteIsNewer) return \"auto-lww\";\n  if (options?.prefer === \"local\") return \"prefer-local\";\n  if (options?.prefer === \"remote\") return \"prefer-remote\";\n  return \"unresolved\";\n}\n\n/**\n * Merge a single field from base, local, and remote versions\n */\nfunction mergeField(\n  key: string,\n  baseValue: unknown,\n  localValue: unknown,\n  remoteValue: unknown,\n  localTimestamp: string,\n  remoteTimestamp: string,\n  options?: MergeOptions\n): { value: unknown; conflict: FieldConflict | null } {\n  const localChanged = !deepEqual(baseValue, localValue);\n  const remoteChanged = !deepEqual(baseValue, remoteValue);\n\n  if (!localChanged && !remoteChanged) {\n    return { value: baseValue, conflict: null };\n  }\n\n  if (localChanged && !remoteChanged) {\n    return { value: localValue, conflict: null };\n  }\n\n  if (!localChanged && remoteChanged) {\n    return { value: remoteValue, conflict: null };\n  }\n\n  // Both changed\n  if (deepEqual(localValue, remoteValue)) {\n    return { value: localValue, conflict: null };\n  }\n\n  // Both changed to different values\n  const resolved = resolveFieldConflict(\n    localValue,\n    remoteValue,\n    localTimestamp,\n    remoteTimestamp,\n    options\n  );\n\n  // Don't record conflicts for 'custom' metadata field\n  if (key === \"custom\") {\n    return { value: resolved, conflict: null };\n  }\n\n  return {\n    value: resolved,\n    conflict: {\n      field: key,\n      base: baseValue,\n      local: localValue,\n      remote: remoteValue,\n      resolved,\n    },\n  };\n}\n\n/**\n * Merge a single item from base, local, and remote versions\n */\nfunction mergeItem(\n  base: CslItem,\n  local: CslItem,\n  remote: CslItem,\n  options?: MergeOptions\n): { merged: CslItem; conflict: ItemConflict | null } {\n  const uuid = getItemUuid(base);\n  const localTimestamp = getTimestamp(local);\n  const remoteTimestamp = getTimestamp(remote);\n\n  const merged: CslItem = { ...base };\n  const fieldConflicts: FieldConflict[] = [];\n\n  // Get all unique keys from all three versions\n  const allKeys = new Set<string>([\n    ...Object.keys(base),\n    ...Object.keys(local),\n    ...Object.keys(remote),\n  ]);\n\n  for (const key of allKeys) {\n    const baseValue = (base as Record<string, unknown>)[key];\n    const localValue = (local as Record<string, unknown>)[key];\n    const remoteValue = (remote as Record<string, unknown>)[key];\n\n    const { value, conflict } = mergeField(\n      key,\n      baseValue,\n      localValue,\n      remoteValue,\n      localTimestamp,\n      remoteTimestamp,\n      options\n    );\n\n    (merged as Record<string, unknown>)[key] = value;\n\n    if (conflict) {\n      fieldConflicts.push(conflict);\n    }\n  }\n\n  // If there are field conflicts, create ItemConflict\n  if (fieldConflicts.length > 0) {\n    const resolution = determineResolution(\n      fieldConflicts,\n      localTimestamp,\n      remoteTimestamp,\n      options\n    );\n\n    return {\n      merged,\n      conflict: {\n        uuid,\n        id: base.id || \"unknown\",\n        fields: fieldConflicts,\n        localTimestamp,\n        remoteTimestamp,\n        resolution,\n      },\n    };\n  }\n\n  return { merged, conflict: null };\n}\n\n/**\n * Build UUID-indexed maps from item arrays\n */\nfunction buildItemMaps(base: CslItem[], local: CslItem[], remote: CslItem[]) {\n  const baseMap = new Map<string, CslItem>();\n  const localMap = new Map<string, CslItem>();\n  const remoteMap = new Map<string, CslItem>();\n\n  for (const item of base) {\n    baseMap.set(getItemUuid(item), item);\n  }\n  for (const item of local) {\n    localMap.set(getItemUuid(item), item);\n  }\n  for (const item of remote) {\n    remoteMap.set(getItemUuid(item), item);\n  }\n\n  return { baseMap, localMap, remoteMap };\n}\n\n/**\n * Handle items that exist in all three versions\n */\nfunction mergeExistingItem(\n  baseItem: CslItem,\n  localItem: CslItem,\n  remoteItem: CslItem,\n  options: MergeOptions | undefined,\n  merged: CslItem[],\n  conflicts: ItemConflict[]\n): void {\n  const { merged: mergedItem, conflict } = mergeItem(baseItem, localItem, remoteItem, options);\n  merged.push(mergedItem);\n  if (conflict) {\n    conflicts.push(conflict);\n  }\n}\n\n/**\n * Handle items added in both local and remote\n */\nfunction handleDualAddition(\n  uuid: string,\n  localItem: CslItem,\n  remoteItem: CslItem,\n  options: MergeOptions | undefined,\n  merged: CslItem[],\n  conflicts: ItemConflict[]\n): void {\n  if (deepEqual(localItem, remoteItem)) {\n    merged.push(localItem);\n  } else {\n    const syntheticBase: CslItem = {\n      id: uuid,\n      type: \"article\",\n      custom: {\n        uuid,\n        created_at: \"1970-01-01T00:00:00.000Z\",\n        timestamp: \"1970-01-01T00:00:00.000Z\",\n      },\n    };\n    const { merged: mergedItem, conflict } = mergeItem(\n      syntheticBase,\n      localItem,\n      remoteItem,\n      options\n    );\n    merged.push(mergedItem);\n    if (conflict) {\n      conflicts.push(conflict);\n    }\n  }\n}\n\n/**\n * Process a single UUID across all three versions\n */\nfunction processItem(\n  uuid: string,\n  baseMap: Map<string, CslItem>,\n  localMap: Map<string, CslItem>,\n  remoteMap: Map<string, CslItem>,\n  options: MergeOptions | undefined,\n  result: {\n    merged: CslItem[];\n    conflicts: ItemConflict[];\n    localOnly: CslItem[];\n    remoteOnly: CslItem[];\n    deletedInLocal: CslItem[];\n    deletedInRemote: CslItem[];\n  }\n): void {\n  const baseItem = baseMap.get(uuid);\n  const localItem = localMap.get(uuid);\n  const remoteItem = remoteMap.get(uuid);\n\n  if (baseItem && localItem && remoteItem) {\n    mergeExistingItem(baseItem, localItem, remoteItem, options, result.merged, result.conflicts);\n  } else if (!baseItem && localItem && remoteItem) {\n    handleDualAddition(uuid, localItem, remoteItem, options, result.merged, result.conflicts);\n  } else if (!baseItem && localItem && !remoteItem) {\n    result.merged.push(localItem);\n    result.localOnly.push(localItem);\n  } else if (!baseItem && !localItem && remoteItem) {\n    result.merged.push(remoteItem);\n    result.remoteOnly.push(remoteItem);\n  } else if (baseItem && !localItem && remoteItem) {\n    result.deletedInLocal.push(baseItem);\n  } else if (baseItem && localItem && !remoteItem) {\n    result.deletedInRemote.push(baseItem);\n  } else if (baseItem && !localItem && !remoteItem) {\n    result.deletedInLocal.push(baseItem);\n    result.deletedInRemote.push(baseItem);\n  }\n}\n\n/**\n * Performs a 3-way merge of CSL-JSON items\n *\n * @param base - Base version (common ancestor)\n * @param local - Local version (current working copy)\n * @param remote - Remote version (incoming changes)\n * @param options - Merge options (e.g., prefer local/remote for tie-breaking)\n * @returns Merge result with merged items and conflict information\n */\nexport function threeWayMerge(\n  base: CslItem[],\n  local: CslItem[],\n  remote: CslItem[],\n  options?: MergeOptions\n): MergeResult {\n  const { baseMap, localMap, remoteMap } = buildItemMaps(base, local, remote);\n\n  const result = {\n    merged: [] as CslItem[],\n    conflicts: [] as ItemConflict[],\n    localOnly: [] as CslItem[],\n    remoteOnly: [] as CslItem[],\n    deletedInLocal: [] as CslItem[],\n    deletedInRemote: [] as CslItem[],\n  };\n\n  const allUuids = new Set<string>([...baseMap.keys(), ...localMap.keys(), ...remoteMap.keys()]);\n\n  for (const uuid of allUuids) {\n    processItem(uuid, baseMap, localMap, remoteMap, options, result);\n  }\n\n  // Determine overall status\n  let status: MergeStatus = \"success\";\n  if (result.conflicts.length > 0) {\n    const hasUnresolved = result.conflicts.some((c) => c.resolution === \"unresolved\");\n    status = hasUnresolved ? \"conflict\" : \"auto-resolved\";\n  }\n\n  return {\n    status,\n    ...result,\n  };\n}\n","import { EventEmitter } from \"node:events\";\nimport * as fs from \"node:fs/promises\";\nimport * as path from \"node:path\";\nimport chokidar, { type FSWatcher } from \"chokidar\";\n\n/**\n * Options for FileWatcher\n */\nexport interface FileWatcherOptions {\n  /** Debounce time in milliseconds (default: 500) */\n  debounceMs?: number;\n  /** Poll interval in milliseconds for polling mode (default: 5000) */\n  pollIntervalMs?: number;\n  /** Use polling instead of native file system events */\n  usePolling?: boolean;\n  /** Retry delay in milliseconds for JSON parse (default: 200) */\n  retryDelayMs?: number;\n  /** Maximum number of retries for JSON parse (default: 10) */\n  maxRetries?: number;\n}\n\n// Default values from spec\nconst DEFAULT_DEBOUNCE_MS = 500;\nconst DEFAULT_POLL_INTERVAL_MS = 5000;\nconst DEFAULT_RETRY_DELAY_MS = 200;\nconst DEFAULT_MAX_RETRIES = 10;\n\n/**\n * Check if a file should be ignored based on spec patterns\n * Ignored patterns:\n * - *.tmp\n * - *.bak\n * - *.conflict.*\n * - *.lock\n * - editor swap files (.swp, ~)\n */\nfunction shouldIgnore(filePath: string): boolean {\n  const basename = path.basename(filePath);\n\n  // *.tmp files\n  if (basename.endsWith(\".tmp\")) return true;\n\n  // *.bak files\n  if (basename.endsWith(\".bak\")) return true;\n\n  // *.conflict.* files (contains .conflict. in name)\n  if (basename.includes(\".conflict.\")) return true;\n\n  // *.lock files\n  if (basename.endsWith(\".lock\")) return true;\n\n  // Vim swap files (.*.swp)\n  if (basename.startsWith(\".\") && basename.endsWith(\".swp\")) return true;\n\n  // Editor backup files (*~)\n  if (basename.endsWith(\"~\")) return true;\n\n  return false;\n}\n\n/**\n * FileWatcher watches a file or directory for changes and emits events.\n *\n * Events:\n * - 'change': Emitted when a watched file changes (after debounce)\n * - 'error': Emitted when a watch error occurs\n * - 'ready': Emitted when watching has started\n * - 'parsed': Emitted when JSON file is successfully parsed\n * - 'parseError': Emitted when JSON parse fails after all retries\n */\nexport class FileWatcher extends EventEmitter {\n  private readonly watchPath: string;\n  private readonly debounceMs: number;\n  private readonly pollIntervalMs: number;\n  private readonly usePolling: boolean;\n  private readonly retryDelayMs: number;\n  private readonly maxRetries: number;\n\n  private watcher: FSWatcher | null = null;\n  private watching = false;\n  private debounceTimers: Map<string, NodeJS.Timeout> = new Map();\n\n  constructor(watchPath: string, options?: FileWatcherOptions) {\n    super();\n    this.watchPath = watchPath;\n    this.debounceMs = options?.debounceMs ?? DEFAULT_DEBOUNCE_MS;\n    this.pollIntervalMs = options?.pollIntervalMs ?? DEFAULT_POLL_INTERVAL_MS;\n    this.usePolling = options?.usePolling ?? false;\n    this.retryDelayMs = options?.retryDelayMs ?? DEFAULT_RETRY_DELAY_MS;\n    this.maxRetries = options?.maxRetries ?? DEFAULT_MAX_RETRIES;\n  }\n\n  /**\n   * Start watching for file changes\n   */\n  async start(): Promise<void> {\n    if (this.watching) {\n      return;\n    }\n\n    return new Promise((resolve, reject) => {\n      this.watcher = chokidar.watch(this.watchPath, {\n        ignored: shouldIgnore,\n        persistent: true,\n        usePolling: this.usePolling,\n        interval: this.pollIntervalMs,\n        ignoreInitial: true,\n        awaitWriteFinish: false,\n      });\n\n      this.watcher.on(\"ready\", () => {\n        this.watching = true;\n        this.emit(\"ready\");\n        resolve();\n      });\n\n      this.watcher.on(\"error\", (error: unknown) => {\n        this.emit(\"error\", error);\n        if (!this.watching) {\n          reject(error);\n        }\n      });\n\n      this.watcher.on(\"change\", (filePath: string) => {\n        this.handleFileChange(filePath);\n      });\n\n      this.watcher.on(\"add\", (filePath: string) => {\n        this.handleFileChange(filePath);\n      });\n    });\n  }\n\n  /**\n   * Handle file change with debouncing\n   */\n  private handleFileChange(filePath: string): void {\n    // Clear existing timer for this file\n    const existingTimer = this.debounceTimers.get(filePath);\n    if (existingTimer) {\n      clearTimeout(existingTimer);\n    }\n\n    // Set new debounced timer\n    const timer = setTimeout(() => {\n      this.debounceTimers.delete(filePath);\n      this.emit(\"change\", filePath);\n      this.tryParseJsonFile(filePath);\n    }, this.debounceMs);\n\n    this.debounceTimers.set(filePath, timer);\n  }\n\n  /**\n   * Try to parse JSON file with retries\n   */\n  private async tryParseJsonFile(filePath: string): Promise<void> {\n    // Only parse .json files\n    if (path.extname(filePath).toLowerCase() !== \".json\") {\n      return;\n    }\n\n    let lastError: Error | null = null;\n\n    for (let attempt = 0; attempt <= this.maxRetries; attempt++) {\n      try {\n        const content = await fs.readFile(filePath, \"utf-8\");\n        const parsed = JSON.parse(content);\n        this.emit(\"parsed\", filePath, parsed);\n        return;\n      } catch (error) {\n        lastError = error as Error;\n        if (attempt < this.maxRetries) {\n          await this.delay(this.retryDelayMs);\n        }\n      }\n    }\n\n    this.emit(\"parseError\", filePath, lastError);\n  }\n\n  /**\n   * Delay helper\n   */\n  private delay(ms: number): Promise<void> {\n    return new Promise((resolve) => setTimeout(resolve, ms));\n  }\n\n  /**\n   * Stop watching for file changes\n   */\n  close(): void {\n    if (this.watcher) {\n      this.watcher.close();\n      this.watcher = null;\n    }\n\n    // Clear all debounce timers\n    for (const timer of this.debounceTimers.values()) {\n      clearTimeout(timer);\n    }\n    this.debounceTimers.clear();\n\n    this.watching = false;\n  }\n\n  /**\n   * Get the watched path\n   */\n  getPath(): string {\n    return this.watchPath;\n  }\n\n  /**\n   * Check if the watcher is currently active\n   */\n  isWatching(): boolean {\n    return this.watching;\n  }\n\n  /**\n   * Get the debounce time in milliseconds\n   */\n  getDebounceMs(): number {\n    return this.debounceMs;\n  }\n\n  /**\n   * Get the poll interval in milliseconds\n   */\n  getPollIntervalMs(): number {\n    return this.pollIntervalMs;\n  }\n\n  /**\n   * Get the retry delay in milliseconds\n   */\n  getRetryDelayMs(): number {\n    return this.retryDelayMs;\n  }\n\n  /**\n   * Get the maximum number of retries\n   */\n  getMaxRetries(): number {\n    return this.maxRetries;\n  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options?: MergeOptions\n): { value: unknown; conflict: FieldConflict | null } {\n  const localChanged = !deepEqual(baseValue, localValue);\n  const remoteChanged = !deepEqual(baseValue, remoteValue);\n\n  if (!localChanged && !remoteChanged) {\n    return { value: baseValue, conflict: null };\n  }\n\n  if (localChanged && !remoteChanged) {\n    return { value: localValue, conflict: null };\n  }\n\n  if (!localChanged && remoteChanged) {\n    return { value: remoteValue, conflict: null };\n  }\n\n  // Both changed\n  if (deepEqual(localValue, remoteValue)) {\n    return { value: localValue, conflict: null };\n  }\n\n  // Both changed to different values\n  const resolved = resolveFieldConflict(\n    localValue,\n    remoteValue,\n    localTimestamp,\n    remoteTimestamp,\n    options\n  );\n\n  // Don't record conflicts for 'custom' metadata field\n  if (key === \"custom\") {\n    return { value: resolved, conflict: null };\n  }\n\n  return {\n    value: resolved,\n    conflict: {\n     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const localMap = new Map<string, CslItem>();\n  const remoteMap = new Map<string, CslItem>();\n\n  for (const item of base) {\n    baseMap.set(getItemUuid(item), item);\n  }\n  for (const item of local) {\n    localMap.set(getItemUuid(item), item);\n  }\n  for (const item of remote) {\n    remoteMap.set(getItemUuid(item), item);\n  }\n\n  return { baseMap, localMap, remoteMap };\n}\n\n/**\n * Handle items that exist in all three versions\n */\nfunction mergeExistingItem(\n  baseItem: CslItem,\n  localItem: CslItem,\n  remoteItem: CslItem,\n  options: MergeOptions | undefined,\n  merged: CslItem[],\n  conflicts: ItemConflict[]\n): void {\n  const { merged: mergedItem, conflict } = mergeItem(baseItem, localItem, remoteItem, options);\n  merged.push(mergedItem);\n  if (conflict) {\n    conflicts.push(conflict);\n  }\n}\n\n/**\n * Handle items added in both local and remote\n */\nfunction handleDualAddition(\n  uuid: string,\n  localItem: CslItem,\n  remoteItem: CslItem,\n  options: MergeOptions | undefined,\n  merged: CslItem[],\n  conflicts: ItemConflict[]\n): void {\n  if (deepEqual(localItem, remoteItem)) {\n    merged.push(localItem);\n  } else {\n    const syntheticBase: CslItem = {\n      id: uuid,\n      type: \"article\",\n      custom: {\n        uuid,\n        created_at: \"1970-01-01T00:00:00.000Z\",\n        timestamp: \"1970-01-01T00:00:00.000Z\",\n      },\n    };\n    const { merged: mergedItem, conflict } = mergeItem(\n      syntheticBase,\n      localItem,\n      remoteItem,\n      options\n    );\n    merged.push(mergedItem);\n    if (conflict) {\n      conflicts.push(conflict);\n    }\n  }\n}\n\n/**\n * Process a single UUID across all three versions\n */\nfunction processItem(\n  uuid: string,\n  baseMap: Map<string, CslItem>,\n  localMap: Map<string, CslItem>,\n  remoteMap: Map<string, CslItem>,\n  options: MergeOptions | undefined,\n  result: {\n    merged: CslItem[];\n    conflicts: ItemConflict[];\n    localOnly: CslItem[];\n    remoteOnly: CslItem[];\n    deletedInLocal: CslItem[];\n    deletedInRemote: CslItem[];\n  }\n): void {\n  const baseItem = baseMap.get(uuid);\n  const localItem = localMap.get(uuid);\n  const remoteItem = remoteMap.get(uuid);\n\n  if (baseItem && localItem && remoteItem) {\n    mergeExistingItem(baseItem, localItem, remoteItem, options, result.merged, result.conflicts);\n  } else if (!baseItem && localItem && remoteItem) {\n    handleDualAddition(uuid, localItem, remoteItem, options, result.merged, result.conflicts);\n  } else if (!baseItem && localItem && !remoteItem) {\n    result.merged.push(localItem);\n    result.localOnly.push(localItem);\n  } else if (!baseItem && !localItem && remoteItem) {\n    result.merged.push(remoteItem);\n    result.remoteOnly.push(remoteItem);\n  } else if (baseItem && !localItem && remoteItem) {\n    result.deletedInLocal.push(baseItem);\n  } else if (baseItem && localItem && !remoteItem) {\n    result.deletedInRemote.push(baseItem);\n  } else if 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system events */\n  usePolling?: boolean;\n  /** Retry delay in milliseconds for JSON parse (default: 200) */\n  retryDelayMs?: number;\n  /** Maximum number of retries for JSON parse (default: 10) */\n  maxRetries?: number;\n}\n\n// Default values from spec\nconst DEFAULT_DEBOUNCE_MS = 500;\nconst DEFAULT_POLL_INTERVAL_MS = 5000;\nconst DEFAULT_RETRY_DELAY_MS = 200;\nconst DEFAULT_MAX_RETRIES = 10;\n\n/**\n * Check if a file should be ignored based on spec patterns\n * Ignored patterns:\n * - *.tmp\n * - *.bak\n * - *.conflict.*\n * - *.lock\n * - editor swap files (.swp, ~)\n */\nfunction shouldIgnore(filePath: string): boolean {\n  const basename = path.basename(filePath);\n\n  // *.tmp files\n  if (basename.endsWith(\".tmp\")) return true;\n\n  // *.bak files\n  if (basename.endsWith(\".bak\")) return true;\n\n  // *.conflict.* files (contains .conflict. in name)\n  if (basename.includes(\".conflict.\")) return true;\n\n  // *.lock files\n  if (basename.endsWith(\".lock\")) return 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this.handleFileChange(filePath);\n      });\n    });\n  }\n\n  /**\n   * Handle file change with debouncing\n   */\n  private handleFileChange(filePath: string): void {\n    // Clear existing timer for this file\n    const existingTimer = this.debounceTimers.get(filePath);\n    if (existingTimer) {\n      clearTimeout(existingTimer);\n    }\n\n    // Set new debounced timer\n    const timer = setTimeout(() => {\n      this.debounceTimers.delete(filePath);\n      this.emit(\"change\", filePath);\n      this.tryParseJsonFile(filePath);\n    }, this.debounceMs);\n\n    this.debounceTimers.set(filePath, timer);\n  }\n\n  /**\n   * Try to parse JSON file with retries\n   */\n  private async tryParseJsonFile(filePath: string): Promise<void> {\n    // Only parse .json files\n    if (path.extname(filePath).toLowerCase() !== \".json\") {\n      return;\n    }\n\n    let lastError: Error | null = null;\n\n    for (let attempt = 0; attempt <= this.maxRetries; attempt++) {\n      try {\n        const content = await fs.readFile(filePath, \"utf-8\");\n        const parsed = JSON.parse(content);\n        this.emit(\"parsed\", filePath, parsed);\n        return;\n      } catch (error) {\n        lastError = error as Error;\n        if (attempt < this.maxRetries) {\n          await this.delay(this.retryDelayMs);\n        }\n      }\n    }\n\n    this.emit(\"parseError\", filePath, lastError);\n  }\n\n  /**\n   * Delay helper\n   */\n  private delay(ms: number): Promise<void> {\n    return new Promise((resolve) => setTimeout(resolve, ms));\n  }\n\n  /**\n   * Stop watching for file changes\n   */\n  close(): void {\n    if (this.watcher) {\n      this.watcher.close();\n      this.watcher = null;\n    }\n\n    // Clear all debounce timers\n    for (const timer of this.debounceTimers.values()) {\n      clearTimeout(timer);\n    }\n    this.debounceTimers.clear();\n\n    this.watching = false;\n  }\n\n  /**\n   * Get the watched path\n   */\n  getPath(): string {\n    return 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package/dist/server/index.d.ts

@@ -1,9 +1,11 @@
 import { Hono } from "hono";
+import type { Config } from "../config/schema.js";
 import type { Library } from "../core/library.js";
 /**
  * Create the main Hono server application.
  * @param library - Library instance for the references API
+ * @param config - Configuration for the server
  * @returns Hono application
  */
-export declare function createServer(library: Library): Hono<import("hono/types").BlankEnv, import("hono/types").BlankSchema, "/">;
+export declare function createServer(library: Library, config: Config): Hono<import("hono/types").BlankEnv, import("hono/types").BlankSchema, "/">;
 //# sourceMappingURL=index.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/server/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAC5B,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAIlD;;;;GAIG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,OAAO,8EAW5C"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/server/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAC5B,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAClD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAQlD;;;;;GAKG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,8EA2B5D"}

package/dist/server/routes/add.d.ts

@@ -0,0 +1,11 @@
+import { Hono } from "hono";
+import type { Config } from "../../config/schema.js";
+import type { Library } from "../../core/library.js";
+/**
+ * Create add route for importing references.
+ * @param library - Library instance to use for operations
+ * @param config - Configuration with PubMed settings
+ * @returns Hono app with add route
+ */
+export declare function createAddRoute(library: Library, config: Config): Hono<import("hono/types").BlankEnv, import("hono/types").BlankSchema, "/">;
+//# sourceMappingURL=add.d.ts.map

package/dist/server/routes/add.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"add.d.ts","sourceRoot":"","sources":["../../../src/server/routes/add.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAC5B,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AAoBrD;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,8EAiD9D"}

package/dist/server/routes/cite.d.ts

@@ -0,0 +1,9 @@
+import { Hono } from "hono";
+import type { Library } from "../../core/library.js";
+/**
+ * Create cite route for generating citations.
+ * @param library - Library instance to use for operations
+ * @returns Hono app with cite route
+ */
+export declare function createCiteRoute(library: Library): Hono<import("hono/types").BlankEnv, import("hono/types").BlankSchema, "/">;
+//# sourceMappingURL=cite.d.ts.map

package/dist/server/routes/cite.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"cite.d.ts","sourceRoot":"","sources":["../../../src/server/routes/cite.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAE5B,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AAqCrD;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,OAAO,8EA2B/C"}

package/dist/server/routes/list.d.ts

@@ -0,0 +1,25 @@
+import { Hono } from "hono";
+import { z } from "zod";
+import type { Library } from "../../core/library.js";
+/**
+ * Request body schema for list endpoint
+ */
+declare const listRequestBodySchema: z.ZodObject<{
+    format: z.ZodOptional<z.ZodEnum<{
+        uuid: "uuid";
+        json: "json";
+        bibtex: "bibtex";
+        pretty: "pretty";
+        "ids-only": "ids-only";
+    }>>;
+}, z.core.$strip>;
+/**
+ * Request body type for list endpoint
+ */
+export type ListRequestBody = z.infer<typeof listRequestBodySchema>;
+/**
+ * Creates list route for HTTP server
+ */
+export declare function createListRoute(library: Library): Hono<import("hono/types").BlankEnv, import("hono/types").BlankSchema, "/">;
+export {};
+//# sourceMappingURL=list.d.ts.map

package/dist/server/routes/list.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"list.d.ts","sourceRoot":"","sources":["../../../src/server/routes/list.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAC5B,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AAGrD;;GAEG;AACH,QAAA,MAAM,qBAAqB;;;;;;;;iBAEzB,CAAC;AAEH;;GAEG;AACH,MAAM,MAAM,eAAe,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,qBAAqB,CAAC,CAAC;AAEpE;;GAEG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,OAAO,8EAkC/C"}

package/dist/server/routes/references.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"references.d.ts","sourceRoot":"","sources":["../../../src/server/routes/references.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAC5B,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AAErD;;;;GAIG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,OAAO,8EA4GrD"}
+{"version":3,"file":"references.d.ts","sourceRoot":"","sources":["../../../src/server/routes/references.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAC5B,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AAIrD;;;;GAIG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,OAAO,8EAmKrD"}

package/dist/server/routes/search.d.ts

@@ -0,0 +1,26 @@
+import { Hono } from "hono";
+import { z } from "zod";
+import type { Library } from "../../core/library.js";
+/**
+ * Request body schema for search endpoint
+ */
+declare const searchRequestBodySchema: z.ZodObject<{
+    query: z.ZodString;
+    format: z.ZodOptional<z.ZodEnum<{
+        uuid: "uuid";
+        json: "json";
+        bibtex: "bibtex";
+        pretty: "pretty";
+        "ids-only": "ids-only";
+    }>>;
+}, z.core.$strip>;
+/**
+ * Request body type for search endpoint
+ */
+export type SearchRequestBody = z.infer<typeof searchRequestBodySchema>;
+/**
+ * Creates search route for HTTP server
+ */
+export declare function createSearchRoute(library: Library): Hono<import("hono/types").BlankEnv, import("hono/types").BlankSchema, "/">;
+export {};
+//# sourceMappingURL=search.d.ts.map

package/dist/server/routes/search.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../../src/server/routes/search.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAC5B,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AAGrD;;GAEG;AACH,QAAA,MAAM,uBAAuB;;;;;;;;;iBAG3B,CAAC;AAEH;;GAEG;AACH,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,uBAAuB,CAAC,CAAC;AAExE;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,OAAO,8EAoCjD"}

package/dist/server.js

@@ -1,8 +1,116 @@
 import { Hono } from "hono";
+import { a as addReferences, c as citeReferences, l as listReferences, u as updateReference, r as removeReference, s as searchReferences } from "./chunks/search-Be9vzUIH.js";
+import { z } from "zod";
+function buildPubmedConfig(config) {
+  const pubmedConfig = {};
+  if (config.pubmed.email !== void 0) {
+    pubmedConfig.email = config.pubmed.email;
+  }
+  if (config.pubmed.apiKey !== void 0) {
+    pubmedConfig.apiKey = config.pubmed.apiKey;
+  }
+  return pubmedConfig;
+}
+function createAddRoute(library, config) {
+  const route = new Hono();
+  route.post("/", async (c) => {
+    let body;
+    try {
+      body = await c.req.json();
+    } catch {
+      return c.json({ error: "Invalid JSON" }, 400);
+    }
+    if (!body || typeof body !== "object") {
+      return c.json({ error: "Request body must be an object" }, 400);
+    }
+    const { inputs, options } = body;
+    if (!inputs || !Array.isArray(inputs) || inputs.length === 0) {
+      return c.json({ error: "inputs must be a non-empty array of strings" }, 400);
+    }
+    if (!inputs.every((input) => typeof input === "string")) {
+      return c.json({ error: "All inputs must be strings" }, 400);
+    }
+    const addOptions = {
+      force: options?.force ?? false,
+      pubmedConfig: buildPubmedConfig(config)
+    };
+    if (options?.format) {
+      addOptions.format = options.format;
+    }
+    const result = await addReferences(inputs, library, addOptions);
+    return c.json(result);
+  });
+  return route;
+}
+const CiteRequestSchema = z.object({
+  identifiers: z.array(z.string()).min(1, "identifiers must be a non-empty array"),
+  byUuid: z.boolean().optional(),
+  inText: z.boolean().optional(),
+  style: z.string().optional(),
+  cslFile: z.string().optional(),
+  locale: z.string().optional(),
+  format: z.enum(["text", "html"]).optional()
+});
+function buildCiteOptions(body) {
+  return {
+    identifiers: body.identifiers,
+    ...body.byUuid !== void 0 && { byUuid: body.byUuid },
+    ...body.inText !== void 0 && { inText: body.inText },
+    ...body.style !== void 0 && { style: body.style },
+    ...body.cslFile !== void 0 && { cslFile: body.cslFile },
+    ...body.locale !== void 0 && { locale: body.locale },
+    ...body.format !== void 0 && { format: body.format }
+  };
+}
+function createCiteRoute(library) {
+  const route = new Hono();
+  route.post("/", async (c) => {
+    let rawBody;
+    try {
+      rawBody = await c.req.json();
+    } catch {
+      return c.json({ error: "Invalid JSON" }, 400);
+    }
+    const parseResult = CiteRequestSchema.safeParse(rawBody);
+    if (!parseResult.success) {
+      const errorMessage = parseResult.error.issues[0]?.message ?? "Invalid request body";
+      return c.json({ error: errorMessage }, 400);
+    }
+    const result = await citeReferences(library, buildCiteOptions(parseResult.data));
+    return c.json(result);
+  });
+  return route;
+}
 const healthRoute = new Hono();
 healthRoute.get("/", (c) => {
   return c.json({ status: "ok" });
 });
+const listRequestBodySchema = z.object({
+  format: z.enum(["pretty", "json", "bibtex", "ids-only", "uuid"]).optional()
+});
+function createListRoute(library) {
+  const route = new Hono();
+  route.post("/", async (c) => {
+    let body;
+    try {
+      body = await c.req.json();
+    } catch {
+      return c.json({ error: "Invalid JSON" }, 400);
+    }
+    const parseResult = listRequestBodySchema.safeParse(body);
+    if (!parseResult.success) {
+      return c.json({ error: "Request body must be an object" }, 400);
+    }
+    const requestBody = parseResult.data;
+    const options = {};
+    if (requestBody.format !== void 0) {
+      options.format = requestBody.format;
+    }
+    const result = listReferences(library, options);
+    return c.json(result);
+  });
+  return route;
+}
 function createReferencesRoute(library) {
   const route = new Hono();
   route.get("/", (c) => {
@@ -10,7 +118,7 @@ function createReferencesRoute(library) {
     const items = references.map((ref) => ref.getItem());
     return c.json(items);
   });
-  route.get("/:uuid", (c) => {
+  route.get("/uuid/:uuid", (c) => {
     const uuid = c.req.param("uuid");
     const ref = library.findByUuid(uuid);
     if (!ref) {
@@ -18,6 +126,14 @@ function createReferencesRoute(library) {
     }
     return c.json(ref.getItem());
   });
+  route.get("/id/:id", (c) => {
+    const id = c.req.param("id");
+    const ref = library.findById(id);
+    if (!ref) {
+      return c.json({ error: "Reference not found" }, 404);
+    }
+    return c.json(ref.getItem());
+  });
   route.post("/", async (c) => {
     try {
       const body = await c.req.json();
@@ -38,51 +154,118 @@ function createReferencesRoute(library) {
       );
     }
   });
-  route.put("/:uuid", async (c) => {
+  route.put("/uuid/:uuid", async (c) => {
     const uuid = c.req.param("uuid");
-    const existing = library.findByUuid(uuid);
-    if (!existing) {
-      return c.json({ error: "Reference not found" }, 404);
+    let body;
+    try {
+      body = await c.req.json();
+    } catch {
+      return c.json({ error: "Invalid JSON" }, 400);
+    }
+    if (!body || typeof body !== "object") {
+      return c.json({ error: "Request body must be an object" }, 400);
     }
+    const result = await updateReference(library, {
+      identifier: uuid,
+      byUuid: true,
+      updates: body,
+      onIdCollision: "suffix"
+    });
+    if (!result.updated) {
+      const status = result.idCollision ? 409 : 404;
+      return c.json(result, status);
+    }
+    return c.json(result);
+  });
+  route.put("/id/:id", async (c) => {
+    const id = c.req.param("id");
+    let body;
     try {
-      const body = await c.req.json();
-      if (!body.custom) {
-        body.custom = {};
-      }
-      body.custom.uuid = uuid;
-      library.removeByUuid(uuid);
-      library.add(body);
-      const updatedRef = library.findByUuid(uuid);
-      if (!updatedRef) {
-        return c.json({ error: "Failed to update reference" }, 500);
-      }
-      return c.json(updatedRef.getItem());
-    } catch (error) {
-      return c.json(
-        {
-          error: "Invalid request body",
-          details: error instanceof Error ? error.message : String(error)
-        },
-        400
-      );
+      body = await c.req.json();
+    } catch {
+      return c.json({ error: "Invalid JSON" }, 400);
+    }
+    if (!body || typeof body !== "object") {
+      return c.json({ error: "Request body must be an object" }, 400);
     }
+    const result = await updateReference(library, {
+      identifier: id,
+      byUuid: false,
+      updates: body,
+      onIdCollision: "suffix"
+    });
+    if (!result.updated) {
+      const status = result.idCollision ? 409 : 404;
+      return c.json(result, status);
+    }
+    return c.json(result);
   });
-  route.delete("/:uuid", (c) => {
+  route.delete("/uuid/:uuid", async (c) => {
     const uuid = c.req.param("uuid");
-    const existing = library.findByUuid(uuid);
-    if (!existing) {
-      return c.json({ error: "Reference not found" }, 404);
+    const result = await removeReference(library, {
+      identifier: uuid,
+      byUuid: true
+    });
+    if (!result.removed) {
+      return c.json(result, 404);
+    }
+    return c.json(result);
+  });
+  route.delete("/id/:id", async (c) => {
+    const id = c.req.param("id");
+    const result = await removeReference(library, {
+      identifier: id,
+      byUuid: false
+    });
+    if (!result.removed) {
+      return c.json(result, 404);
+    }
+    return c.json(result);
+  });
+  return route;
+}
+const searchRequestBodySchema = z.object({
+  query: z.string(),
+  format: z.enum(["pretty", "json", "bibtex", "ids-only", "uuid"]).optional()
+});
+function createSearchRoute(library) {
+  const route = new Hono();
+  route.post("/", async (c) => {
+    let body;
+    try {
+      body = await c.req.json();
+    } catch {
+      return c.json({ error: "Invalid JSON" }, 400);
+    }
+    const parseResult = searchRequestBodySchema.safeParse(body);
+    if (!parseResult.success) {
+      return c.json({ error: "Invalid request body" }, 400);
+    }
+    const requestBody = parseResult.data;
+    const options = {
+      query: requestBody.query
+    };
+    if (requestBody.format !== void 0) {
+      options.format = requestBody.format;
     }
-    library.removeByUuid(uuid);
-    return c.body(null, 204);
+    const result = searchReferences(library, options);
+    return c.json(result);
   });
   return route;
 }
-function createServer(library) {
+function createServer(library, config) {
   const app = new Hono();
   app.route("/health", healthRoute);
   const referencesRoute = createReferencesRoute(library);
   app.route("/api/references", referencesRoute);
+  const addRoute = createAddRoute(library, config);
+  app.route("/api/add", addRoute);
+  const citeRoute = createCiteRoute(library);
+  app.route("/api/cite", citeRoute);
+  const listRoute = createListRoute(library);
+  app.route("/api/list", listRoute);
+  const searchRoute = createSearchRoute(library);
+  app.route("/api/search", searchRoute);
   return app;
 }
 export {