@ncukondo/reference-manager 0.1.0 → 0.3.0

package/dist/cli.js.map

@@ -1 +1 @@
-{"version":3,"file":"cli.js","sources":["../src/server/portfile.ts","../src/cli/commands/add.ts","../src/cli/output/bibtex.ts","../src/cli/output/json.ts","../src/cli/output/pretty.ts","../src/cli/commands/list.ts","../src/cli/commands/search.ts","../src/cli/commands/server.ts","../src/cli/commands/update.ts","../src/cli/helpers.ts","../src/cli/server-client.ts","../src/cli/server-detection.ts","../src/cli/index.ts"],"sourcesContent":["import { promises as fs } from \"node:fs\";\nimport * as os from \"node:os\";\nimport * as path from \"node:path\";\n\n/**\n * Get the default portfile path.\n * @returns The path to the portfile in the system's temp directory.\n */\nexport function getPortfilePath(): string {\n  const tmpDir = os.tmpdir();\n  return path.join(tmpDir, \"reference-manager\", \"server.port\");\n}\n\n/**\n * Write port, PID, library path, and optionally started_at to the portfile.\n * @param portfilePath - Path to the portfile\n * @param port - Server port number\n * @param pid - Server process ID\n * @param library - Path to the library file\n * @param started_at - Optional ISO 8601 timestamp of when the server started\n */\nexport async function writePortfile(\n  portfilePath: string,\n  port: number,\n  pid: number,\n  library: string,\n  started_at?: string\n): Promise<void> {\n  // Create parent directory if it doesn't exist\n  const dir = path.dirname(portfilePath);\n  await fs.mkdir(dir, { recursive: true });\n\n  // Write portfile with port, pid, library, and optionally started_at\n  const data: Record<string, unknown> = { port, pid, library };\n  if (started_at !== undefined) {\n    data.started_at = started_at;\n  }\n  const content = JSON.stringify(data, null, 2);\n  await fs.writeFile(portfilePath, content, \"utf-8\");\n}\n\n/**\n * Read port, PID, library, and optionally started_at from the portfile.\n * @param portfilePath - Path to the portfile\n * @returns Object with port, pid, library (if present), and started_at (if present), or null if file doesn't exist or is invalid\n */\nexport async function readPortfile(portfilePath: string): Promise<{\n  port: number;\n  pid: number;\n  library?: string;\n  started_at?: string;\n} | null> {\n  try {\n    const content = await fs.readFile(portfilePath, \"utf-8\");\n    const data = JSON.parse(content);\n\n    // Validate required fields (port and pid are always required)\n    if (typeof data.port !== \"number\" || typeof data.pid !== \"number\") {\n      return null;\n    }\n\n    // Build result with required fields\n    const result: {\n      port: number;\n      pid: number;\n      library?: string;\n      started_at?: string;\n    } = {\n      port: data.port,\n      pid: data.pid,\n    };\n\n    // Add optional fields if present\n    if (typeof data.library === \"string\") {\n      result.library = data.library;\n    }\n    if (typeof data.started_at === \"string\") {\n      result.started_at = data.started_at;\n    }\n\n    return result;\n  } catch {\n    // File doesn't exist or invalid JSON\n    return null;\n  }\n}\n\n/**\n * Check if the portfile exists.\n * @param portfilePath - Path to the portfile\n * @returns True if portfile exists, false otherwise\n */\nexport async function portfileExists(portfilePath: string): Promise<boolean> {\n  try {\n    await fs.access(portfilePath);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Remove the portfile.\n * @param portfilePath - Path to the portfile\n */\nexport async function removePortfile(portfilePath: string): Promise<void> {\n  try {\n    await fs.unlink(portfilePath);\n  } catch {\n    // Ignore if file doesn't exist\n  }\n}\n\n/**\n * Check if a process with the given PID is running.\n * @param pid - Process ID to check\n * @returns True if process is running, false otherwise\n */\nexport function isProcessRunning(pid: number): boolean {\n  if (pid <= 0) {\n    return false;\n  }\n\n  try {\n    // Sending signal 0 checks if the process exists without killing it\n    process.kill(pid, 0);\n    return true;\n  } catch {\n    return false;\n  }\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport { detectDuplicate } from \"../../features/duplicate/detector.js\";\nimport type { DuplicateMatch } from \"../../features/duplicate/types.js\";\n\nexport interface AddOptions {\n  force: boolean;\n}\n\nexport interface AddResult {\n  added: boolean;\n  item: CslItem;\n  idChanged: boolean;\n  originalId?: string | undefined;\n  duplicate?: DuplicateMatch | undefined;\n}\n\n/**\n * Generate suffix for ID collision (a, b, c, ..., z, aa, ab, ...)\n */\nfunction generateSuffix(index: number): string {\n  const alphabet = \"abcdefghijklmnopqrstuvwxyz\";\n  let suffix = \"\";\n  let n = index;\n\n  do {\n    suffix = alphabet[n % 26] + suffix;\n    n = Math.floor(n / 26) - 1;\n  } while (n >= 0);\n\n  return suffix;\n}\n\n/**\n * Resolve ID collision by appending suffix\n */\nfunction resolveIdCollision(baseId: string, existing: CslItem[]): { id: string; changed: boolean } {\n  const existingIds = new Set(existing.map((item) => item.id));\n\n  if (!existingIds.has(baseId)) {\n    return { id: baseId, changed: false };\n  }\n\n  // Find next available suffix\n  let index = 0;\n  let newId: string;\n\n  do {\n    const suffix = generateSuffix(index);\n    newId = `${baseId}${suffix}`;\n    index++;\n  } while (existingIds.has(newId));\n\n  return { id: newId, changed: true };\n}\n\n/**\n * Add a new reference to the library.\n *\n * @param existing - Existing library items\n * @param newItem - New item to add\n * @param options - Add options\n * @returns Add result\n */\nexport async function add(\n  existing: CslItem[],\n  newItem: CslItem,\n  options: AddOptions\n): Promise<AddResult> {\n  // 1. Check for content duplicate (unless force=true)\n  if (!options.force) {\n    const duplicateResult = detectDuplicate(newItem, existing);\n\n    if (duplicateResult.matches.length > 0) {\n      // Duplicate found, reject\n      return {\n        added: false,\n        item: newItem,\n        idChanged: false,\n        duplicate: duplicateResult.matches[0],\n      };\n    }\n  }\n\n  // 2. Resolve ID collision\n  const originalId = newItem.id;\n  const { id, changed } = resolveIdCollision(originalId, existing);\n\n  const finalItem: CslItem = {\n    ...newItem,\n    id,\n  };\n\n  return {\n    added: true,\n    item: finalItem,\n    idChanged: changed,\n    originalId: changed ? originalId : undefined,\n  };\n}\n","import type { CslItem } from \"../../core/csl-json/types\";\nimport type { Reference } from \"../../core/reference\";\n\n/**\n * Map CSL-JSON type to BibTeX entry type\n */\nfunction mapEntryType(cslType: string): string {\n  const typeMap: Record<string, string> = {\n    article: \"article\",\n    \"article-journal\": \"article\",\n    \"article-magazine\": \"article\",\n    \"article-newspaper\": \"article\",\n    book: \"book\",\n    chapter: \"inbook\",\n    \"paper-conference\": \"inproceedings\",\n    thesis: \"phdthesis\",\n    report: \"techreport\",\n    webpage: \"misc\",\n  };\n\n  return typeMap[cslType] || \"misc\";\n}\n\n/**\n * Format a single author as \"Family, Given\"\n */\nfunction formatBibtexAuthor(author: {\n  family?: string | undefined;\n  given?: string | undefined;\n  literal?: string | undefined;\n}): string {\n  if (author.literal) {\n    return author.literal;\n  }\n  const family = author.family || \"\";\n  const given = author.given || \"\";\n  return given ? `${family}, ${given}` : family;\n}\n\n/**\n * Format authors for BibTeX as \"Family1, Given1 and Family2, Given2\"\n */\nfunction formatBibtexAuthors(\n  authors: Array<{\n    family?: string | undefined;\n    given?: string | undefined;\n    literal?: string | undefined;\n    \"dropping-particle\"?: string | undefined;\n    \"non-dropping-particle\"?: string | undefined;\n    suffix?: string | undefined;\n  }>\n): string {\n  return authors.map(formatBibtexAuthor).join(\" and \");\n}\n\n/**\n * Format a BibTeX field\n */\nfunction formatField(name: string, value: string): string {\n  return `  ${name} = {${value}},`;\n}\n\n/**\n * Add basic bibliographic fields to BibTeX entry\n */\nfunction addBasicFields(lines: string[], item: CslItem): void {\n  // Title\n  if (item.title) {\n    lines.push(formatField(\"title\", item.title));\n  }\n\n  // Authors\n  if (item.author && item.author.length > 0) {\n    lines.push(formatField(\"author\", formatBibtexAuthors(item.author)));\n  }\n\n  // Year\n  const year = item.issued?.[\"date-parts\"]?.[0]?.[0];\n  if (year) {\n    lines.push(formatField(\"year\", String(year)));\n  }\n}\n\n/**\n * Add publication details to BibTeX entry\n */\nfunction addPublicationDetails(lines: string[], item: CslItem, entryType: string): void {\n  // Container-title (journal or booktitle depending on type)\n  if (item[\"container-title\"]) {\n    if (entryType === \"article\") {\n      lines.push(formatField(\"journal\", item[\"container-title\"]));\n    } else if (entryType === \"inbook\" || entryType === \"inproceedings\") {\n      lines.push(formatField(\"booktitle\", item[\"container-title\"]));\n    }\n  }\n\n  // Volume\n  if (item.volume) {\n    lines.push(formatField(\"volume\", item.volume));\n  }\n\n  // Issue -> number\n  if (item.issue) {\n    lines.push(formatField(\"number\", item.issue));\n  }\n\n  // Pages\n  if (item.page) {\n    lines.push(formatField(\"pages\", item.page));\n  }\n\n  // Publisher\n  if (item.publisher) {\n    lines.push(formatField(\"publisher\", item.publisher));\n  }\n}\n\n/**\n * Add identifier fields to BibTeX entry\n */\nfunction addIdentifierFields(lines: string[], item: CslItem): void {\n  // DOI\n  if (item.DOI) {\n    lines.push(formatField(\"doi\", item.DOI));\n  }\n\n  // URL\n  if (item.URL) {\n    lines.push(formatField(\"url\", item.URL));\n  }\n\n  // PMID or PMCID in note field\n  if (item.PMID) {\n    lines.push(formatField(\"note\", `PMID: ${item.PMID}`));\n  } else if (item.PMCID) {\n    lines.push(formatField(\"note\", `PMCID: ${item.PMCID}`));\n  }\n}\n\n/**\n * Format a single reference as BibTeX entry\n */\nfunction formatSingleBibtexEntry(ref: Reference): string {\n  const item: CslItem = ref.getItem();\n  const entryType = mapEntryType(item.type);\n  const lines: string[] = [];\n\n  // Opening line: @type{citation-key,\n  lines.push(`@${entryType}{${item.id},`);\n\n  // Add fields in sections\n  addBasicFields(lines, item);\n  addPublicationDetails(lines, item, entryType);\n  addIdentifierFields(lines, item);\n\n  // Closing brace\n  lines.push(\"}\");\n\n  return lines.join(\"\\n\");\n}\n\n/**\n * Format references as BibTeX\n */\nexport function formatBibtex(references: Reference[]): string {\n  if (references.length === 0) {\n    return \"\";\n  }\n\n  return references.map(formatSingleBibtexEntry).join(\"\\n\\n\");\n}\n","import type { Reference } from \"../../core/reference\";\n\n/**\n * Format references as compact JSON\n */\nexport function formatJson(references: Reference[]): string {\n  const items = references.map((ref) => ref.getItem());\n  return JSON.stringify(items);\n}\n","import type { Reference } from \"../../core/reference\";\n\n/**\n * Format a single author as \"Family, Given-Initial.\"\n */\nfunction formatAuthor(author: {\n  family?: string | undefined;\n  given?: string | undefined;\n}): string {\n  const family = author.family || \"\";\n  const givenInitial = author.given ? `${author.given.charAt(0)}.` : \"\";\n  return givenInitial ? `${family}, ${givenInitial}` : family;\n}\n\n/**\n * Format authors array as \"Family1, G.; Family2, G.\"\n */\nfunction formatAuthors(\n  authors: Array<{\n    family?: string | undefined;\n    given?: string | undefined;\n    literal?: string | undefined;\n    \"dropping-particle\"?: string | undefined;\n    \"non-dropping-particle\"?: string | undefined;\n    suffix?: string | undefined;\n  }>\n): string {\n  return authors.map(formatAuthor).join(\"; \");\n}\n\n/**\n * Format a single reference in pretty format\n */\nfunction formatSingleReference(ref: Reference): string {\n  const item = ref.getItem();\n  const lines: string[] = [];\n\n  // Header line: [id] title\n  const header = item.title ? `[${item.id}] ${item.title}` : `[${item.id}]`;\n  lines.push(header);\n\n  // Authors (if present)\n  if (item.author && item.author.length > 0) {\n    lines.push(`  Authors: ${formatAuthors(item.author)}`);\n  }\n\n  // Year\n  const year = item.issued?.[\"date-parts\"]?.[0]?.[0];\n  lines.push(`  Year: ${year || \"(no year)\"}`);\n\n  // Type\n  lines.push(`  Type: ${item.type}`);\n\n  // DOI (if present)\n  if (item.DOI) {\n    lines.push(`  DOI: ${item.DOI}`);\n  }\n\n  // PMID (if present)\n  if (item.PMID) {\n    lines.push(`  PMID: ${item.PMID}`);\n  }\n\n  // PMCID (if present)\n  if (item.PMCID) {\n    lines.push(`  PMCID: ${item.PMCID}`);\n  }\n\n  // URL (if present)\n  if (item.URL) {\n    lines.push(`  URL: ${item.URL}`);\n  }\n\n  // UUID (always)\n  lines.push(`  UUID: ${ref.getUuid()}`);\n\n  return lines.join(\"\\n\");\n}\n\n/**\n * Format references in pretty-printed format\n */\nexport function formatPretty(references: Reference[]): string {\n  if (references.length === 0) {\n    return \"\";\n  }\n\n  return references.map(formatSingleReference).join(\"\\n\\n\");\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport { Reference } from \"../../core/reference.js\";\nimport { formatBibtex } from \"../output/bibtex.js\";\nimport { formatJson } from \"../output/json.js\";\nimport { formatPretty } from \"../output/pretty.js\";\n\nexport interface ListOptions {\n  json?: boolean;\n  idsOnly?: boolean;\n  uuid?: boolean;\n  bibtex?: boolean;\n}\n\n/**\n * List all references in the library.\n *\n * @param items - Array of CSL items\n * @param options - Output format options\n */\nexport async function list(items: CslItem[], options: ListOptions): Promise<void> {\n  // Check for conflicting output options\n  const outputOptions = [options.json, options.idsOnly, options.uuid, options.bibtex].filter(\n    Boolean\n  );\n\n  if (outputOptions.length > 1) {\n    throw new Error(\n      \"Multiple output formats specified. Only one of --json, --ids-only, --uuid, --bibtex can be used.\"\n    );\n  }\n\n  // Convert CslItems to References for output formatters\n  const references = items.map((item) => new Reference(item));\n\n  // Output based on selected format\n  if (options.json) {\n    process.stdout.write(formatJson(references));\n  } else if (options.idsOnly) {\n    for (const item of items) {\n      process.stdout.write(`${item.id}\\n`);\n    }\n  } else if (options.uuid) {\n    for (const item of items) {\n      if (item.custom) {\n        process.stdout.write(`${item.custom.uuid}\\n`);\n      }\n    }\n  } else if (options.bibtex) {\n    process.stdout.write(formatBibtex(references));\n  } else {\n    // Default: pretty format\n    process.stdout.write(formatPretty(references));\n  }\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport { Reference } from \"../../core/reference.js\";\nimport { search as searchReferences } from \"../../features/search/matcher.js\";\nimport { sortResults } from \"../../features/search/sorter.js\";\nimport { tokenize } from \"../../features/search/tokenizer.js\";\nimport { formatBibtex } from \"../output/bibtex.js\";\nimport { formatJson } from \"../output/json.js\";\nimport { formatPretty } from \"../output/pretty.js\";\n\nexport interface SearchOptions {\n  json?: boolean;\n  idsOnly?: boolean;\n  uuid?: boolean;\n  bibtex?: boolean;\n}\n\n/**\n * Search references in the library.\n *\n * @param items - Array of CSL items\n * @param query - Search query string\n * @param options - Output format options\n */\nexport async function search(\n  items: CslItem[],\n  query: string,\n  options: SearchOptions\n): Promise<void> {\n  // Check for conflicting output options\n  const outputOptions = [options.json, options.idsOnly, options.uuid, options.bibtex].filter(\n    Boolean\n  );\n\n  if (outputOptions.length > 1) {\n    throw new Error(\n      \"Multiple output formats specified. Only one of --json, --ids-only, --uuid, --bibtex can be used.\"\n    );\n  }\n\n  // Tokenize query\n  const searchQuery = tokenize(query);\n\n  // Search\n  const results = searchReferences(items, searchQuery.tokens);\n\n  // Sort results\n  const sorted = sortResults(results);\n\n  // Extract items from results\n  const matchedItems = sorted.map((result) => result.reference);\n\n  // Convert to References for output formatters\n  const references = matchedItems.map((item) => new Reference(item));\n\n  // Output based on selected format\n  if (options.json) {\n    process.stdout.write(formatJson(references));\n  } else if (options.idsOnly) {\n    for (const item of matchedItems) {\n      process.stdout.write(`${item.id}\\n`);\n    }\n  } else if (options.uuid) {\n    for (const item of matchedItems) {\n      if (item.custom) {\n        process.stdout.write(`${item.custom.uuid}\\n`);\n      }\n    }\n  } else if (options.bibtex) {\n    process.stdout.write(formatBibtex(references));\n  } else {\n    // Default: pretty format\n    process.stdout.write(formatPretty(references));\n  }\n}\n","import {\n  isProcessRunning,\n  readPortfile,\n  removePortfile,\n  writePortfile,\n} from \"../../server/portfile.js\";\n\nexport interface ServerStartOptions {\n  port?: number;\n  daemon?: boolean;\n  library: string;\n  portfilePath: string;\n}\n\nexport interface ServerInfo {\n  port: number;\n  pid: number;\n  library: string;\n  started_at?: string;\n}\n\n/**\n * Start HTTP server.\n *\n * @param options - Server start options\n */\nexport async function serverStart(options: ServerStartOptions): Promise<void> {\n  // Check if server is already running\n  const existingStatus = await serverStatus(options.portfilePath);\n  if (existingStatus !== null) {\n    throw new Error(\"Server is already running\");\n  }\n\n  // Determine port (use provided port or default to 3000 for testing)\n  const port = options.port ?? 3000;\n\n  // For daemon mode, create portfile with current process PID\n  // (In real implementation, this would be the spawned server process PID)\n  const pid = process.pid;\n  const started_at = new Date().toISOString();\n\n  await writePortfile(options.portfilePath, port, pid, options.library, started_at);\n\n  // In real implementation, this would spawn the server process\n  // For now, we just create the portfile for testing purposes\n}\n\n/**\n * Stop running server.\n *\n * @param portfilePath - Path to the portfile\n */\nexport async function serverStop(portfilePath: string): Promise<void> {\n  // Check if server is running\n  const status = await serverStatus(portfilePath);\n  if (status === null) {\n    throw new Error(\"Server is not running\");\n  }\n\n  // In real implementation, send SIGTERM to the server process\n  // For testing, we just remove the portfile\n  await removePortfile(portfilePath);\n\n  process.stdout.write(\"Server stopped successfully\\n\");\n}\n\n/**\n * Get server status.\n *\n * @param portfilePath - Path to the portfile\n * @returns Server info if running, null otherwise\n */\nexport async function serverStatus(portfilePath: string): Promise<ServerInfo | null> {\n  // Read portfile\n  const portfileData = await readPortfile(portfilePath);\n  if (portfileData === null) {\n    return null;\n  }\n\n  // Check if process is still running\n  if (!isProcessRunning(portfileData.pid)) {\n    // Process not found, cleanup stale portfile\n    await removePortfile(portfilePath);\n    return null;\n  }\n\n  // Return server info\n  const result: ServerInfo = {\n    port: portfileData.port,\n    pid: portfileData.pid,\n    library: portfileData.library ?? \"\",\n  };\n\n  if (portfileData.started_at !== undefined) {\n    result.started_at = portfileData.started_at;\n  }\n\n  return result;\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\n\nexport interface UpdateOptions {\n  byUuid: boolean;\n}\n\nexport interface UpdateResult {\n  updated: boolean;\n  item?: CslItem | undefined;\n  items: CslItem[];\n}\n\n/**\n * Update a reference in the library.\n *\n * @param items - Library items\n * @param identifier - Reference ID or UUID\n * @param updates - Partial updates to apply\n * @param options - Update options\n * @returns Update result\n */\nexport async function update(\n  items: CslItem[],\n  identifier: string,\n  updates: Partial<CslItem>,\n  options: UpdateOptions\n): Promise<UpdateResult> {\n  let foundIndex = -1;\n\n  if (options.byUuid) {\n    // Find by UUID\n    foundIndex = items.findIndex((item) => item.custom?.uuid === identifier);\n  } else {\n    // Find by ID\n    foundIndex = items.findIndex((item) => item.id === identifier);\n  }\n\n  if (foundIndex === -1) {\n    // Not found\n    return {\n      updated: false,\n      items,\n    };\n  }\n\n  const existingItem = items[foundIndex];\n  if (!existingItem) {\n    // Should not happen, but TypeScript needs this\n    return {\n      updated: false,\n      items,\n    };\n  }\n\n  // Merge updates with existing item\n  const updatedItem: CslItem = {\n    ...existingItem,\n    ...updates,\n    // Ensure required fields\n    id: updates.id ?? existingItem.id,\n    type: updates.type ?? existingItem.type,\n    // Preserve UUID and created_at\n    custom: {\n      ...(existingItem.custom || {}),\n      ...(updates.custom || {}),\n      uuid: existingItem.custom?.uuid || \"\",\n      created_at: existingItem.custom?.created_at || new Date().toISOString(),\n      // Update timestamp\n      timestamp: new Date().toISOString(),\n    },\n  };\n\n  const updatedItems = [...items.slice(0, foundIndex), updatedItem, ...items.slice(foundIndex + 1)];\n\n  return {\n    updated: true,\n    item: updatedItem,\n    items: updatedItems,\n  };\n}\n","/**\n * CLI Helper Functions\n */\n\nimport { readFileSync } from \"node:fs\";\nimport { stdin, stdout } from \"node:process\";\nimport { loadConfig } from \"../config/loader.js\";\nimport type { Config } from \"../config/schema.js\";\n\n/**\n * Output format type\n */\nexport type OutputFormat = \"pretty\" | \"json\" | \"ids-only\" | \"uuid\" | \"bibtex\";\n\n/**\n * CLI options interface\n */\nexport interface CliOptions {\n  library?: string;\n  logLevel?: \"silent\" | \"info\" | \"debug\";\n  config?: string;\n  quiet?: boolean;\n  verbose?: boolean;\n  backup?: boolean;\n  backupDir?: string;\n  json?: boolean;\n  idsOnly?: boolean;\n  uuid?: boolean;\n  bibtex?: boolean;\n}\n\n/**\n * Read JSON input from file or stdin\n * @param file - File path (optional, defaults to stdin)\n * @returns JSON string\n */\nexport async function readJsonInput(file?: string): Promise<string> {\n  if (file) {\n    // Read from file\n    try {\n      return readFileSync(file, \"utf-8\");\n    } catch (error) {\n      throw new Error(\n        `I/O error: Cannot read file ${file}: ${error instanceof Error ? error.message : String(error)}`\n      );\n    }\n  }\n\n  // Read from stdin\n  const chunks: Buffer[] = [];\n  for await (const chunk of stdin) {\n    chunks.push(chunk as Buffer);\n  }\n  return Buffer.concat(chunks).toString(\"utf-8\");\n}\n\n/**\n * Parse JSON input\n * @param input - JSON string\n * @returns Parsed JSON object or array\n */\nexport function parseJsonInput(input: string): unknown {\n  if (!input || input.trim() === \"\") {\n    throw new Error(\"Parse error: Empty input\");\n  }\n\n  try {\n    return JSON.parse(input);\n  } catch (error) {\n    throw new Error(\n      `Parse error: Invalid JSON: ${error instanceof Error ? error.message : String(error)}`\n    );\n  }\n}\n\n/**\n * Load config with CLI argument overrides\n * @param options - CLI options\n * @returns Config with overrides applied\n */\nexport async function loadConfigWithOverrides(options: CliOptions): Promise<Config> {\n  // Load base config\n  // Note: options.config is currently ignored as loadConfig uses cwd and userConfigPath\n  const config = await loadConfig();\n\n  // Apply CLI overrides\n  const overrides: Partial<Config> = {};\n\n  // Library path\n  if (options.library) {\n    overrides.library = options.library;\n  }\n\n  // Log level\n  if (options.quiet) {\n    overrides.logLevel = \"silent\";\n  } else if (options.verbose) {\n    overrides.logLevel = \"debug\";\n  } else if (options.logLevel) {\n    overrides.logLevel = options.logLevel;\n  }\n\n  // Backup settings\n  if (options.backup !== undefined || options.backupDir) {\n    overrides.backup = {\n      ...config.backup,\n      ...(options.backup !== undefined && { enabled: options.backup }),\n      ...(options.backupDir && { directory: options.backupDir }),\n    };\n  }\n\n  return { ...config, ...overrides };\n}\n\n/**\n * Get output format from options\n * @param options - CLI options\n * @returns Output format\n * @throws Error if multiple formats specified\n */\nexport function getOutputFormat(options: CliOptions): OutputFormat {\n  const formats: OutputFormat[] = [];\n\n  if (options.json) formats.push(\"json\");\n  if (options.idsOnly) formats.push(\"ids-only\");\n  if (options.uuid) formats.push(\"uuid\");\n  if (options.bibtex) formats.push(\"bibtex\");\n\n  if (formats.length > 1) {\n    throw new Error(\n      \"Multiple output formats specified. Only one of --json, --ids-only, --uuid, --bibtex can be used.\"\n    );\n  }\n\n  return formats[0] || \"pretty\";\n}\n\n/**\n * Check if running in TTY\n * @returns True if stdin and stdout are TTY\n */\nexport function isTTY(): boolean {\n  return Boolean(stdin.isTTY && stdout.isTTY);\n}\n\n/**\n * Read confirmation from user (y/N)\n * @param prompt - Confirmation prompt message\n * @returns True if user confirmed (y/yes), false otherwise\n */\nexport async function readConfirmation(prompt: string): Promise<boolean> {\n  // If not TTY, auto-confirm\n  if (!isTTY()) {\n    return true;\n  }\n\n  // Display prompt\n  stdout.write(`${prompt} (y/N): `);\n\n  // Read input\n  const chunks: Buffer[] = [];\n  for await (const chunk of stdin) {\n    chunks.push(chunk as Buffer);\n    // Break after first line\n    const input = Buffer.concat(chunks).toString(\"utf-8\");\n    if (input.includes(\"\\n\")) {\n      break;\n    }\n  }\n\n  const input = Buffer.concat(chunks).toString(\"utf-8\").trim().toLowerCase();\n  return input === \"y\" || input === \"yes\";\n}\n","import type { CslItem } from \"../core/csl-json/types.js\";\n\n/**\n * Client for communicating with the reference-manager HTTP server.\n */\nexport class ServerClient {\n  constructor(private baseUrl: string) {}\n\n  /**\n   * Get all references from the server.\n   * @returns Array of CSL items\n   */\n  async getAll(): Promise<CslItem[]> {\n    const url = `${this.baseUrl}/api/references`;\n    const response = await fetch(url);\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as CslItem[];\n  }\n\n  /**\n   * Find reference by UUID.\n   * @param uuid - Reference UUID\n   * @returns CSL item or null if not found\n   */\n  async findByUuid(uuid: string): Promise<CslItem | null> {\n    const url = `${this.baseUrl}/api/references/${uuid}`;\n    const response = await fetch(url);\n\n    if (response.status === 404) {\n      return null;\n    }\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as CslItem;\n  }\n\n  /**\n   * Add new reference to the library.\n   * @param item - CSL item to add\n   * @returns Created CSL item with UUID\n   */\n  async add(item: CslItem): Promise<CslItem> {\n    const url = `${this.baseUrl}/api/references`;\n    const response = await fetch(url, {\n      method: \"POST\",\n      headers: { \"Content-Type\": \"application/json\" },\n      body: JSON.stringify(item),\n    });\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as CslItem;\n  }\n\n  /**\n   * Update existing reference.\n   * @param uuid - Reference UUID\n   * @param item - Updated CSL item\n   * @returns Updated CSL item\n   */\n  async update(uuid: string, item: CslItem): Promise<CslItem> {\n    const url = `${this.baseUrl}/api/references/${uuid}`;\n    const response = await fetch(url, {\n      method: \"PUT\",\n      headers: { \"Content-Type\": \"application/json\" },\n      body: JSON.stringify(item),\n    });\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as CslItem;\n  }\n\n  /**\n   * Remove reference by UUID.\n   * @param uuid - Reference UUID\n   */\n  async remove(uuid: string): Promise<void> {\n    const url = `${this.baseUrl}/api/references/${uuid}`;\n    const response = await fetch(url, {\n      method: \"DELETE\",\n    });\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n  }\n}\n","import { spawn } from \"node:child_process\";\nimport type { Config } from \"../config/schema.js\";\nimport {\n  getPortfilePath,\n  isProcessRunning,\n  portfileExists,\n  readPortfile,\n  removePortfile,\n} from \"../server/portfile.js\";\n\n/**\n * Server connection information.\n */\nexport interface ServerConnection {\n  baseUrl: string;\n  pid: number;\n}\n\n/**\n * Get server connection if available.\n * @param libraryPath - Path to the library file\n * @param config - Configuration\n * @returns Server connection or null if not available\n */\nexport async function getServerConnection(\n  libraryPath: string,\n  config: Config\n): Promise<ServerConnection | null> {\n  const portfilePath = getPortfilePath();\n  const portfileData = await readPortfile(portfilePath);\n\n  // Check if portfile exists\n  if (!portfileData) {\n    // No server running\n    if (config.server.autoStart) {\n      // Auto-start server\n      await startServerDaemon(libraryPath, config);\n      await waitForPortfile(5000); // 5 second timeout\n      // Retry connection\n      return await getServerConnection(libraryPath, config);\n    }\n    return null;\n  }\n\n  // Check if process is running\n  if (!isProcessRunning(portfileData.pid)) {\n    // Stale portfile, remove it\n    await removePortfile(portfilePath);\n    return null;\n  }\n\n  // Check if library path matches\n  if (!portfileData.library || portfileData.library !== libraryPath) {\n    // Server is serving a different library\n    return null;\n  }\n\n  // Server is running and serving our library\n  return {\n    baseUrl: `http://localhost:${portfileData.port}`,\n    pid: portfileData.pid,\n  };\n}\n\n/**\n * Start server in daemon mode.\n * @param libraryPath - Path to the library file\n * @param _config - Configuration (reserved for future use)\n */\nexport async function startServerDaemon(libraryPath: string, _config: Config): Promise<void> {\n  // Get the binary path (argv[1] is the script being executed)\n  const binaryPath = process.argv[1] || process.execPath;\n\n  // Spawn server in detached daemon mode\n  const child = spawn(\n    process.execPath,\n    [binaryPath, \"server\", \"start\", \"--daemon\", \"--library\", libraryPath],\n    {\n      detached: true,\n      stdio: \"ignore\",\n    }\n  );\n\n  child.unref(); // Allow parent to exit\n}\n\n/**\n * Wait for portfile to appear.\n * @param timeoutMs - Timeout in milliseconds\n */\nexport async function waitForPortfile(timeoutMs: number): Promise<void> {\n  const portfilePath = getPortfilePath();\n  const startTime = Date.now();\n  const checkInterval = 50; // Check every 50ms\n\n  while (Date.now() - startTime < timeoutMs) {\n    if (await portfileExists(portfilePath)) {\n      return;\n    }\n    // Wait before next check\n    await new Promise((resolve) => setTimeout(resolve, checkInterval));\n  }\n\n  throw new Error(`Server failed to start: portfile not created within ${timeoutMs}ms`);\n}\n","/**\n * CLI Entry Point\n */\n\nimport { Command } from \"commander\";\nimport { z } from \"zod\";\nimport type { CslItem } from \"../core/csl-json/types.js\";\nimport { Library } from \"../core/library.js\";\nimport { getPortfilePath } from \"../server/portfile.js\";\nimport { add as addCommand } from \"./commands/add.js\";\nimport { list } from \"./commands/list.js\";\nimport { search as searchCommand } from \"./commands/search.js\";\nimport { serverStart, serverStatus, serverStop } from \"./commands/server.js\";\nimport { update as updateCommand } from \"./commands/update.js\";\nimport type { CliOptions } from \"./helpers.js\";\nimport {\n  isTTY,\n  loadConfigWithOverrides,\n  parseJsonInput,\n  readConfirmation,\n  readJsonInput,\n} from \"./helpers.js\";\nimport { ServerClient } from \"./server-client.js\";\nimport { getServerConnection } from \"./server-detection.js\";\n\n// Import package.json for version and description\nimport packageJson from \"../../package.json\" with { type: \"json\" };\n\n/**\n * Create Commander program instance\n */\nexport function createProgram(): Command {\n  const program = new Command();\n\n  program\n    .name(\"reference-manager\")\n    .version(packageJson.version)\n    .description(packageJson.description);\n\n  // Global options\n  program\n    .option(\"--library <path>\", \"Override library file path\")\n    .option(\"--log-level <level>\", \"Override log level (silent|info|debug)\")\n    .option(\"--config <path>\", \"Use specific config file\")\n    .option(\"--quiet\", \"Suppress all non-error output\")\n    .option(\"--verbose\", \"Enable verbose output\")\n    .option(\"--no-backup\", \"Disable backup creation\")\n    .option(\"--backup-dir <path>\", \"Override backup directory\");\n\n  // Register commands\n  registerListCommand(program);\n  registerSearchCommand(program);\n  registerAddCommand(program);\n  registerRemoveCommand(program);\n  registerUpdateCommand(program);\n  registerServerCommand(program);\n\n  return program;\n}\n\n/**\n * Register 'list' command\n */\nfunction registerListCommand(program: Command): void {\n  program\n    .command(\"list\")\n    .description(\"List all references in the library\")\n    .option(\"--json\", \"Output in JSON format\")\n    .option(\"--ids-only\", \"Output only citation keys\")\n    .option(\"--uuid\", \"Output only UUIDs\")\n    .option(\"--bibtex\", \"Output in BibTeX format\")\n    .action(async (options) => {\n      try {\n        const globalOpts = program.opts();\n        const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n        // Get items (server or direct)\n        const server = await getServerConnection(config.library, config);\n        let items: CslItem[];\n\n        if (server) {\n          // Use server API\n          const client = new ServerClient(server.baseUrl);\n          items = await client.getAll();\n        } else {\n          // Direct file access\n          const library = await Library.load(config.library);\n          items = library.getAll().map((ref) => ref.getItem());\n        }\n\n        // Execute list command\n        await list(items, {\n          json: options.json,\n          idsOnly: options.idsOnly,\n          uuid: options.uuid,\n          bibtex: options.bibtex,\n        });\n\n        process.exit(0);\n      } catch (error) {\n        process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}\\n`);\n        process.exit(4);\n      }\n    });\n}\n\n/**\n * Register 'search' command\n */\nfunction registerSearchCommand(program: Command): void {\n  program\n    .command(\"search\")\n    .description(\"Search references\")\n    .argument(\"<query>\", \"Search query\")\n    .option(\"--json\", \"Output in JSON format\")\n    .option(\"--ids-only\", \"Output only citation keys\")\n    .option(\"--uuid\", \"Output only UUIDs\")\n    .option(\"--bibtex\", \"Output in BibTeX format\")\n    .action(async (query: string, options) => {\n      try {\n        const globalOpts = program.opts();\n        const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n        // Get items (server or direct)\n        const server = await getServerConnection(config.library, config);\n        let items: CslItem[];\n\n        if (server) {\n          // Use server API\n          const client = new ServerClient(server.baseUrl);\n          items = await client.getAll();\n        } else {\n          // Direct file access\n          const library = await Library.load(config.library);\n          items = library.getAll().map((ref) => ref.getItem());\n        }\n\n        // Execute search command (handles search and output)\n        await searchCommand(items, query, {\n          json: options.json,\n          idsOnly: options.idsOnly,\n          uuid: options.uuid,\n          bibtex: options.bibtex,\n        });\n\n        process.exit(0);\n      } catch (error) {\n        process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}\\n`);\n        process.exit(4);\n      }\n    });\n}\n\n/**\n * Register 'add' command\n */\nasync function addViaServer(\n  items: CslItem[],\n  server: { baseUrl: string },\n  force: boolean\n): Promise<void> {\n  const client = new ServerClient(server.baseUrl);\n\n  for (const item of items) {\n    try {\n      await client.add(item);\n      process.stderr.write(`Added reference: [${item.id}]\\n`);\n    } catch (error) {\n      if (!force && error instanceof Error && error.message.includes(\"Duplicate\")) {\n        process.stderr.write(`Error: ${error.message}\\n`);\n        process.exit(1);\n      }\n      throw error;\n    }\n  }\n}\n\nasync function addViaLibrary(items: CslItem[], libraryPath: string, force: boolean): Promise<void> {\n  const library = await Library.load(libraryPath);\n  const existingItems = library.getAll().map((ref) => ref.getItem());\n\n  for (const item of items) {\n    const result = await addCommand(existingItems, item, { force });\n\n    if (result.added) {\n      library.add(result.item);\n      process.stderr.write(`Added reference: [${result.item.id}]\\n`);\n      existingItems.push(result.item);\n    } else if (result.duplicate) {\n      throw new Error(\n        `Duplicate detected: ${result.duplicate.type} match with existing reference [${result.duplicate.existing.id}]`\n      );\n    }\n  }\n\n  await library.save();\n}\n\nfunction handleAddError(error: unknown): never {\n  const message = error instanceof Error ? error.message : String(error);\n  if (message.includes(\"Parse error\")) {\n    process.stderr.write(`Error: ${message}\\n`);\n    process.exit(3);\n  }\n  if (message.includes(\"Duplicate\")) {\n    process.stderr.write(`Error: ${message}\\n`);\n    process.exit(1);\n  }\n  process.stderr.write(`Error: ${message}\\n`);\n  process.exit(4);\n}\n\nasync function handleAddAction(\n  file: string | undefined,\n  options: CliOptions & { force?: boolean },\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n    const inputStr = await readJsonInput(file);\n    const input = parseJsonInput(inputStr);\n    const items: CslItem[] = Array.isArray(input) ? input : [input as CslItem];\n\n    const server = await getServerConnection(config.library, config);\n\n    if (server) {\n      await addViaServer(items, server, options.force ?? false);\n    } else {\n      await addViaLibrary(items, config.library, options.force ?? false);\n    }\n\n    process.exit(0);\n  } catch (error) {\n    handleAddError(error);\n  }\n}\n\nfunction registerAddCommand(program: Command): void {\n  program\n    .command(\"add\")\n    .description(\"Add new reference(s) to the library\")\n    .argument(\"[file]\", \"JSON file to add (or use stdin)\")\n    .option(\"-f, --force\", \"Skip duplicate detection\")\n    .action(async (file: string | undefined, options) => {\n      await handleAddAction(file, options, program);\n    });\n}\n\n/**\n * Register 'remove' command\n */\nasync function findReferenceToRemove(\n  identifier: string,\n  byUuid: boolean,\n  server: { baseUrl: string } | null,\n  libraryPath: string\n): Promise<CslItem | undefined> {\n  if (server) {\n    const client = new ServerClient(server.baseUrl);\n    const items = await client.getAll();\n    return byUuid\n      ? items.find((item) => item.custom?.uuid === identifier)\n      : items.find((item) => item.id === identifier);\n  }\n\n  const library = await Library.load(libraryPath);\n  const ref = byUuid ? library.findByUuid(identifier) : library.findById(identifier);\n  return ref?.getItem();\n}\n\nasync function confirmRemoval(refToRemove: CslItem, force: boolean): Promise<boolean> {\n  if (force || !isTTY()) {\n    return true;\n  }\n\n  const authors = Array.isArray(refToRemove.author)\n    ? refToRemove.author.map((a) => `${a.family || \"\"}, ${a.given?.[0] || \"\"}.`).join(\"; \")\n    : \"(no authors)\";\n  const confirmMsg = `Remove reference [${refToRemove.id}]?\\nTitle: ${refToRemove.title || \"(no title)\"}\\nAuthors: ${authors}\\nContinue?`;\n\n  return await readConfirmation(confirmMsg);\n}\n\nasync function removeReference(\n  identifier: string,\n  refToRemove: CslItem,\n  byUuid: boolean,\n  server: { baseUrl: string } | null,\n  libraryPath: string\n): Promise<void> {\n  if (server) {\n    const client = new ServerClient(server.baseUrl);\n    if (!refToRemove.custom?.uuid) {\n      throw new Error(\"Reference missing UUID\");\n    }\n    await client.remove(refToRemove.custom.uuid);\n    return;\n  }\n\n  const library = await Library.load(libraryPath);\n  const removed = byUuid ? library.removeByUuid(identifier) : library.removeById(identifier);\n\n  if (!removed) {\n    throw new Error(\"Reference not found\");\n  }\n\n  await library.save();\n}\n\nfunction handleRemoveError(error: unknown): never {\n  const message = error instanceof Error ? error.message : String(error);\n  if (message.includes(\"not found\")) {\n    process.stderr.write(`Error: ${message}\\n`);\n    process.exit(1);\n  }\n  process.stderr.write(`Error: ${message}\\n`);\n  process.exit(4);\n}\n\nasync function handleRemoveAction(\n  identifier: string,\n  options: { uuid?: boolean; force?: boolean },\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n    const server = await getServerConnection(config.library, config);\n\n    const refToRemove = await findReferenceToRemove(\n      identifier,\n      options.uuid ?? false,\n      server,\n      config.library\n    );\n\n    if (!refToRemove) {\n      process.stderr.write(`Error: Reference not found: ${identifier}\\n`);\n      process.exit(1);\n    }\n\n    const confirmed = await confirmRemoval(refToRemove, options.force ?? false);\n    if (!confirmed) {\n      process.stderr.write(\"Cancelled.\\n\");\n      process.exit(2);\n    }\n\n    await removeReference(identifier, refToRemove, options.uuid ?? false, server, config.library);\n\n    process.stderr.write(`Removed reference: [${refToRemove.id}]\\n`);\n    process.exit(0);\n  } catch (error) {\n    handleRemoveError(error);\n  }\n}\n\nfunction registerRemoveCommand(program: Command): void {\n  program\n    .command(\"remove\")\n    .description(\"Remove a reference from the library\")\n    .argument(\"<identifier>\", \"Citation key or UUID\")\n    .option(\"--uuid\", \"Interpret identifier as UUID\")\n    .option(\"-f, --force\", \"Skip confirmation prompt\")\n    .action(async (identifier: string, options) => {\n      await handleRemoveAction(identifier, options, program);\n    });\n}\n\n/**\n * Register 'update' command\n */\nasync function updateViaServer(\n  identifier: string,\n  updates: Record<string, unknown>,\n  byUuid: boolean,\n  server: { baseUrl: string }\n): Promise<void> {\n  const client = new ServerClient(server.baseUrl);\n  const items = await client.getAll();\n  const refToUpdate = byUuid\n    ? items.find((item) => item.custom?.uuid === identifier)\n    : items.find((item) => item.id === identifier);\n\n  if (!refToUpdate || !refToUpdate.custom?.uuid) {\n    process.stderr.write(`Error: Reference not found: ${identifier}\\n`);\n    process.exit(1);\n  }\n\n  const updatedItem = { ...refToUpdate, ...updates } as CslItem;\n  await client.update(refToUpdate.custom.uuid, updatedItem);\n}\n\nasync function updateViaLibrary(\n  identifier: string,\n  updates: Partial<CslItem>,\n  byUuid: boolean,\n  libraryPath: string\n): Promise<void> {\n  const library = await Library.load(libraryPath);\n  const items = library.getAll().map((ref) => ref.getItem());\n\n  const result = await updateCommand(items, identifier, updates, { byUuid });\n\n  if (!result.updated || !result.item) {\n    throw new Error(\"Reference not found\");\n  }\n\n  if (result.item.custom?.uuid) {\n    library.removeByUuid(result.item.custom.uuid);\n    library.add(result.item);\n  }\n\n  await library.save();\n}\n\nfunction handleUpdateError(error: unknown): never {\n  const message = error instanceof Error ? error.message : String(error);\n  if (message.includes(\"Parse error\")) {\n    process.stderr.write(`Error: ${message}\\n`);\n    process.exit(3);\n  }\n  if (message.includes(\"not found\") || message.includes(\"validation\")) {\n    process.stderr.write(`Error: ${message}\\n`);\n    process.exit(1);\n  }\n  process.stderr.write(`Error: ${message}\\n`);\n  process.exit(4);\n}\n\nasync function handleUpdateAction(\n  identifier: string,\n  file: string | undefined,\n  options: { uuid?: boolean },\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n    const inputStr = await readJsonInput(file);\n    const updates = parseJsonInput(inputStr);\n\n    // Validate that updates is a non-null object using zod\n    const updatesSchema = z.record(z.string(), z.unknown());\n    const validatedUpdates = updatesSchema.parse(updates);\n\n    const server = await getServerConnection(config.library, config);\n\n    if (server) {\n      await updateViaServer(identifier, validatedUpdates, options.uuid ?? false, server);\n    } else {\n      await updateViaLibrary(\n        identifier,\n        validatedUpdates as Partial<CslItem>,\n        options.uuid ?? false,\n        config.library\n      );\n    }\n\n    process.stderr.write(`Updated reference: [${identifier}]\\n`);\n    process.exit(0);\n  } catch (error) {\n    handleUpdateError(error);\n  }\n}\n\nfunction registerUpdateCommand(program: Command): void {\n  program\n    .command(\"update\")\n    .description(\"Update fields of an existing reference\")\n    .argument(\"<identifier>\", \"Citation key or UUID\")\n    .argument(\"[file]\", \"JSON file with updates (or use stdin)\")\n    .option(\"--uuid\", \"Interpret identifier as UUID\")\n    .action(async (identifier: string, file: string | undefined, options) => {\n      await handleUpdateAction(identifier, file, options, program);\n    });\n}\n\n/**\n * Register 'server' command\n */\nfunction registerServerCommand(program: Command): void {\n  const serverCmd = program.command(\"server\").description(\"Manage HTTP server for library access\");\n\n  serverCmd\n    .command(\"start\")\n    .description(\"Start HTTP server\")\n    .option(\"--port <port>\", \"Specify port number\")\n    .option(\"-d, --daemon\", \"Run in background\")\n    .action(async (options) => {\n      try {\n        const globalOpts = program.opts();\n        const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n        const portfilePath = getPortfilePath();\n\n        const startOptions = {\n          library: config.library,\n          portfilePath,\n          daemon: options.daemon,\n          ...(options.port && { port: Number.parseInt(options.port, 10) }),\n        };\n\n        await serverStart(startOptions);\n\n        process.exit(0);\n      } catch (error) {\n        const message = error instanceof Error ? error.message : String(error);\n        if (message.includes(\"already running\") || message.includes(\"conflict\")) {\n          process.stderr.write(`Error: ${message}\\n`);\n          process.exit(1);\n        }\n        process.stderr.write(`Error: ${message}\\n`);\n        process.exit(4);\n      }\n    });\n\n  serverCmd\n    .command(\"stop\")\n    .description(\"Stop running server\")\n    .action(async () => {\n      try {\n        const portfilePath = getPortfilePath();\n        await serverStop(portfilePath);\n\n        process.stderr.write(\"Server stopped.\\n\");\n        process.exit(0);\n      } catch (error) {\n        const message = error instanceof Error ? error.message : String(error);\n        if (message.includes(\"not running\")) {\n          process.stderr.write(`Error: ${message}\\n`);\n          process.exit(1);\n        }\n        process.stderr.write(`Error: ${message}\\n`);\n        process.exit(4);\n      }\n    });\n\n  serverCmd\n    .command(\"status\")\n    .description(\"Check server 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Path to the portfile\n * @returns True if portfile exists, false otherwise\n */\nexport async function portfileExists(portfilePath: string): Promise<boolean> {\n  try {\n    await fs.access(portfilePath);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Remove the portfile.\n * @param portfilePath - Path to the portfile\n */\nexport async function removePortfile(portfilePath: string): Promise<void> {\n  try {\n    await fs.unlink(portfilePath);\n  } catch {\n    // Ignore if file doesn't exist\n  }\n}\n\n/**\n * Check if a process with the given PID is running.\n * @param pid - Process ID to check\n * @returns True if process is running, false otherwise\n */\nexport function isProcessRunning(pid: number): boolean {\n  if (pid <= 0) {\n    return false;\n  }\n\n  try {\n    // Sending signal 0 checks if the process exists without killing it\n    process.kill(pid, 0);\n    return true;\n  } catch {\n    return false;\n  }\n}\n","import type { InputFormat } from \"../../features/import/detector.js\";\nimport type { PubmedConfig } from \"../../features/import/fetcher.js\";\nimport {\n  type AddReferencesOptions,\n  type AddReferencesResult,\n  type AddedItem,\n  type FailedItem,\n  type SkippedItem,\n  addReferences,\n} from \"../../features/operations/add.js\";\nimport type { ExecutionContext } from \"../execution-context.js\";\n\n/**\n * Options for the add command.\n */\nexport interface AddCommandOptions {\n  /** Input strings (file paths, PMIDs, DOIs) */\n  inputs: string[];\n  /** Skip duplicate detection */\n  force: boolean;\n  /** Explicit input format */\n  format?: string;\n  /** PubMed API configuration */\n  pubmedConfig?: PubmedConfig;\n  /** Show verbose error output */\n  verbose?: boolean;\n  /** Content from stdin */\n  stdinContent?: string;\n}\n\n/**\n * Result from add command execution.\n */\nexport type AddCommandResult = AddReferencesResult;\n\n// Re-export types for convenience\nexport type { AddedItem, FailedItem, SkippedItem };\n\n/** Maximum error message length in non-verbose mode */\nconst MAX_ERROR_LENGTH = 80;\n\n/**\n * Execute add command.\n * Routes to server API or direct library operation based on execution context.\n *\n * @param options - Add command options\n * @param context - Execution context (server or local)\n * @returns Add result containing added, failed, and skipped items\n */\nexport async function executeAdd(\n  options: AddCommandOptions,\n  context: ExecutionContext\n): Promise<AddCommandResult> {\n  const { inputs, force, format, pubmedConfig, stdinContent } = options;\n\n  if (context.type === \"server\") {\n    // Route through server - build options without undefined values\n    const serverOptions: { force: boolean; format?: string; stdinContent?: string } = { force };\n    if (format !== undefined) {\n      serverOptions.format = format;\n    }\n    if (stdinContent !== undefined) {\n      serverOptions.stdinContent = stdinContent;\n    }\n    return context.client.addFromInputs(inputs, serverOptions);\n  }\n\n  // Direct library operation - build options without undefined values\n  const addOptions: AddReferencesOptions = { force };\n  if (format !== undefined) {\n    addOptions.format = format as InputFormat | \"auto\";\n  }\n  if (pubmedConfig !== undefined) {\n    addOptions.pubmedConfig = pubmedConfig;\n  }\n  if (stdinContent !== undefined) {\n    addOptions.stdinContent = stdinContent;\n  }\n\n  return addReferences(inputs, context.library, addOptions);\n}\n\n/**\n * Format a single added item for output.\n */\nfunction formatAddedItem(item: AddedItem): string {\n  const idPart = item.idChanged ? `${item.id} (was: ${item.originalId})` : item.id;\n  const title = item.title ?? \"(no title)\";\n  return `  - ${idPart}: \"${title}\"`;\n}\n\n/**\n * Format a single failed item for output.\n */\nfunction formatFailedItem(item: FailedItem, verbose: boolean): string {\n  let error = item.error;\n  if (!verbose && error.length > MAX_ERROR_LENGTH) {\n    error = `${error.substring(0, MAX_ERROR_LENGTH - 3)}...`;\n  }\n  // In verbose mode, preserve multi-line errors; in non-verbose mode, take first line\n  if (!verbose && error.includes(\"\\n\")) {\n    error = error.split(\"\\n\")[0] ?? error;\n  }\n  return `  - ${item.source}: ${error}`;\n}\n\n/**\n * Format a single skipped item for output.\n */\nfunction formatSkippedItem(item: SkippedItem): string {\n  return `  - ${item.source}: matches existing '${item.existingId}'`;\n}\n\n/**\n * Format add result for CLI output.\n *\n * @param result - Add result\n * @param verbose - Show verbose error output\n * @returns Formatted output string\n */\nexport function formatAddOutput(result: AddCommandResult, verbose: boolean): string {\n  const lines: string[] = [];\n\n  // Added section\n  if (result.added.length > 0) {\n    lines.push(`Added ${result.added.length} reference(s):`);\n    for (const item of result.added) {\n      lines.push(formatAddedItem(item));\n    }\n  } else if (result.failed.length === 0 && result.skipped.length === 0) {\n    lines.push(\"Added 0 reference(s).\");\n  }\n\n  // Failed section\n  if (result.failed.length > 0) {\n    if (lines.length > 0) lines.push(\"\");\n    lines.push(`Failed to add ${result.failed.length} item(s):`);\n    for (const item of result.failed) {\n      lines.push(formatFailedItem(item, verbose));\n    }\n  }\n\n  // Skipped section\n  if (result.skipped.length > 0) {\n    if (lines.length > 0) lines.push(\"\");\n    lines.push(`Skipped ${result.skipped.length} duplicate(s):`);\n    for (const item of result.skipped) {\n      lines.push(formatSkippedItem(item));\n    }\n  }\n\n  return lines.join(\"\\n\");\n}\n\n/**\n * Determine exit code based on result.\n *\n * @param result - Add result\n * @returns Exit code (0 for success/partial success, 1 for complete failure)\n */\nexport function getExitCode(result: AddCommandResult): number {\n  // Success if anything was added\n  if (result.added.length > 0) {\n    return 0;\n  }\n\n  // Complete failure if nothing added and there were failures\n  if (result.failed.length > 0) {\n    return 1;\n  }\n\n  // All skipped or empty input is considered success\n  return 0;\n}\n","import { type CiteResult, citeReferences } from \"../../features/operations/cite.js\";\nimport type { ExecutionContext } from \"../execution-context.js\";\nimport type { ServerClient } from \"../server-client.js\";\n\n/**\n * Options for the cite command.\n */\nexport interface CiteCommandOptions {\n  identifiers: string[];\n  uuid?: boolean;\n  style?: string;\n  cslFile?: string;\n  locale?: string;\n  format?: \"text\" | \"html\" | \"rtf\";\n  inText?: boolean;\n}\n\n/**\n * Result from cite command execution.\n */\nexport type CiteCommandResult = CiteResult;\n\n/**\n * Validate citation options.\n */\nasync function validateOptions(options: CiteCommandOptions): Promise<void> {\n  if (options.format && ![\"text\", \"html\", \"rtf\"].includes(options.format)) {\n    throw new Error(`Invalid format '${options.format}'. Must be one of: text, html, rtf`);\n  }\n\n  if (options.cslFile) {\n    const fs = await import(\"node:fs\");\n    if (!fs.existsSync(options.cslFile)) {\n      throw new Error(`CSL file '${options.cslFile}' not found`);\n    }\n  }\n}\n\n/**\n * Build server cite options from command options.\n */\nfunction buildServerCiteOptions(options: CiteCommandOptions): Parameters<ServerClient[\"cite\"]>[0] {\n  return {\n    identifiers: options.identifiers,\n    ...(options.uuid !== undefined && { byUuid: options.uuid }),\n    ...(options.inText !== undefined && { inText: options.inText }),\n    ...(options.style !== undefined && { style: options.style }),\n    ...(options.cslFile !== undefined && { cslFile: options.cslFile }),\n    ...(options.locale !== undefined && { locale: options.locale }),\n    ...(options.format !== undefined && {\n      format: options.format === \"rtf\" ? \"text\" : options.format,\n    }),\n  };\n}\n\n/**\n * Build operation cite options from command options.\n */\nfunction buildOperationCiteOptions(\n  options: CiteCommandOptions\n): Parameters<typeof citeReferences>[1] {\n  return {\n    identifiers: options.identifiers,\n    ...(options.uuid !== undefined && { byUuid: options.uuid }),\n    ...(options.style !== undefined && { style: options.style }),\n    ...(options.cslFile !== undefined && { cslFile: options.cslFile }),\n    ...(options.locale !== undefined && { locale: options.locale }),\n    ...(options.format !== undefined && { format: options.format }),\n    ...(options.inText !== undefined && { inText: options.inText }),\n  };\n}\n\n/**\n * Execute cite command.\n * Routes to server API or direct library operation based on execution context.\n *\n * @param options - Cite command options\n * @param context - Execution context (server or local)\n * @returns Cite result containing per-identifier results\n */\nexport async function executeCite(\n  options: CiteCommandOptions,\n  context: ExecutionContext\n): Promise<CiteCommandResult> {\n  await validateOptions(options);\n\n  if (context.type === \"server\") {\n    return context.client.cite(buildServerCiteOptions(options));\n  }\n\n  return citeReferences(context.library, buildOperationCiteOptions(options));\n}\n\n/**\n * Format cite result for CLI output.\n *\n * @param result - Cite result\n * @returns Formatted output string (for stdout)\n */\nexport function formatCiteOutput(result: CiteCommandResult): string {\n  const lines: string[] = [];\n  for (const r of result.results) {\n    if (r.success) {\n      lines.push(r.citation);\n    }\n  }\n  return lines.join(\"\\n\");\n}\n\n/**\n * Format cite errors for stderr.\n *\n * @param result - Cite result\n * @returns Error messages to write to stderr\n */\nexport function formatCiteErrors(result: CiteCommandResult): string {\n  const lines: string[] = [];\n  for (const r of result.results) {\n    if (!r.success) {\n      lines.push(`Error for '${r.identifier}': ${r.error}`);\n    }\n  }\n  return lines.join(\"\\n\");\n}\n\n/**\n * Determine exit code based on result.\n *\n * @param result - Cite result\n * @returns Exit code (0 for success/partial success, 1 for complete failure)\n */\nexport function getCiteExitCode(result: CiteCommandResult): number {\n  const hasSuccess = result.results.some((r) => r.success);\n  const hasError = result.results.some((r) => !r.success);\n\n  if (hasSuccess) {\n    return 0;\n  }\n  if (hasError) {\n    return 1;\n  }\n  return 0;\n}\n","/**\n * Fulltext management types\n */\n\n/**\n * Supported fulltext file types\n */\nexport type FulltextType = \"pdf\" | \"markdown\";\n\n/**\n * File extensions for each fulltext type\n */\nexport const FULLTEXT_EXTENSIONS: Record<FulltextType, string> = {\n  pdf: \".pdf\",\n  markdown: \".md\",\n};\n","/**\n * Fulltext filename generation\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { FULLTEXT_EXTENSIONS, type FulltextType } from \"./types.js\";\n\n/**\n * Generate a filename for a fulltext file.\n *\n * Format: {id}[-PMID{PMID}]-{uuid}.{ext}\n *\n * @param item - CSL item to generate filename for\n * @param type - Fulltext type (pdf or markdown)\n * @returns Generated filename\n * @throws Error if custom.uuid is missing\n */\nexport function generateFulltextFilename(item: CslItem, type: FulltextType): string {\n  const uuid = item.custom?.uuid;\n  if (!uuid) {\n    throw new Error(\"Missing uuid in custom field\");\n  }\n\n  const parts: string[] = [item.id];\n\n  // Add PMID if present and non-empty\n  if (item.PMID && item.PMID.length > 0) {\n    parts.push(`PMID${item.PMID}`);\n  }\n\n  // Add UUID\n  parts.push(uuid);\n\n  // Join with hyphens and add extension\n  return parts.join(\"-\") + FULLTEXT_EXTENSIONS[type];\n}\n","/**\n * Fulltext file management\n */\n\nimport { existsSync } from \"node:fs\";\nimport { copyFile, mkdir, rename, unlink } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { generateFulltextFilename } from \"./filename.js\";\nimport type { FulltextType } from \"./types.js\";\n\n/**\n * Error thrown when fulltext I/O operation fails\n */\nexport class FulltextIOError extends Error {\n  constructor(\n    message: string,\n    public readonly cause?: Error\n  ) {\n    super(message);\n    this.name = \"FulltextIOError\";\n  }\n}\n\n/**\n * Error thrown when trying to detach non-attached fulltext\n */\nexport class FulltextNotAttachedError extends Error {\n  constructor(\n    public readonly itemId: string,\n    public readonly type: FulltextType\n  ) {\n    super(`No ${type} attached to reference ${itemId}`);\n    this.name = \"FulltextNotAttachedError\";\n  }\n}\n\n/**\n * Options for attachFile\n */\nexport interface AttachOptions {\n  /** Move file instead of copy (default: false) */\n  move?: boolean;\n  /** Overwrite existing attachment without confirmation (default: false) */\n  force?: boolean;\n}\n\n/**\n * Result of attachFile operation\n */\nexport interface AttachResult {\n  /** Generated filename */\n  filename: string;\n  /** Existing filename if already attached (when force=false) */\n  existingFile?: string;\n  /** Whether existing file was overwritten */\n  overwritten: boolean;\n  /** Old filename that was deleted (when force=true and filename changed) */\n  deletedOldFile?: string;\n}\n\n/**\n * Options for detachFile\n */\nexport interface DetachOptions {\n  /** Delete file from disk (default: false, metadata-only detach) */\n  delete?: boolean;\n}\n\n/**\n * Result of detachFile operation\n */\nexport interface DetachResult {\n  /** Detached filename */\n  filename: string;\n  /** Whether file was deleted from disk */\n  deleted: boolean;\n}\n\n/**\n * Manages fulltext file operations\n */\nexport class FulltextManager {\n  constructor(private readonly fulltextDirectory: string) {}\n\n  /**\n   * Ensure the fulltext directory exists\n   */\n  async ensureDirectory(): Promise<void> {\n    await mkdir(this.fulltextDirectory, { recursive: true });\n  }\n\n  /**\n   * Attach a file to a reference\n   */\n  async attachFile(\n    item: CslItem,\n    sourcePath: string,\n    type: FulltextType,\n    options?: AttachOptions\n  ): Promise<AttachResult> {\n    const { move = false, force = false } = options ?? {};\n\n    // Generate new filename based on current item state\n    const newFilename = generateFulltextFilename(item, type);\n\n    // Validate source file exists\n    this.validateSourceFile(sourcePath);\n\n    // Get existing filename from metadata\n    const existingFilename = this.getExistingFilename(item, type);\n\n    // If already attached and not force, return existing info\n    if (existingFilename && !force) {\n      return {\n        filename: newFilename,\n        existingFile: existingFilename,\n        overwritten: false,\n      };\n    }\n\n    // Ensure directory exists\n    await this.ensureDirectory();\n\n    // Delete old file if force and filename changed\n    const deletedOldFile = await this.deleteOldFileIfNeeded(existingFilename, newFilename, force);\n\n    // Copy or move file to destination\n    const destPath = join(this.fulltextDirectory, newFilename);\n    await this.copyOrMoveFile(sourcePath, destPath, move);\n\n    const result: AttachResult = {\n      filename: newFilename,\n      overwritten: existingFilename !== undefined,\n    };\n    if (deletedOldFile) {\n      result.deletedOldFile = deletedOldFile;\n    }\n    return result;\n  }\n\n  /**\n   * Validate that source file exists\n   */\n  private validateSourceFile(sourcePath: string): void {\n    if (!existsSync(sourcePath)) {\n      throw new FulltextIOError(`Source file not found: ${sourcePath}`);\n    }\n  }\n\n  /**\n   * Delete old file if force mode and filename changed\n   * @returns Deleted filename or undefined\n   */\n  private async deleteOldFileIfNeeded(\n    existingFilename: string | undefined,\n    newFilename: string,\n    force: boolean\n  ): Promise<string | undefined> {\n    if (!force || !existingFilename || existingFilename === newFilename) {\n      return undefined;\n    }\n\n    const oldPath = join(this.fulltextDirectory, existingFilename);\n    try {\n      await unlink(oldPath);\n    } catch {\n      // Ignore if old file doesn't exist\n    }\n    return existingFilename;\n  }\n\n  /**\n   * Copy or move file to destination\n   */\n  private async copyOrMoveFile(sourcePath: string, destPath: string, move: boolean): Promise<void> {\n    try {\n      if (move) {\n        await rename(sourcePath, destPath);\n      } else {\n        await copyFile(sourcePath, destPath);\n      }\n    } catch (error) {\n      const operation = move ? \"move\" : \"copy\";\n      throw new FulltextIOError(\n        `Failed to ${operation} file to ${destPath}`,\n        error instanceof Error ? error : undefined\n      );\n    }\n  }\n\n  /**\n   * Get the full path for an attached file\n   * @returns Full path or null if not attached\n   */\n  getFilePath(item: CslItem, type: FulltextType): string | null {\n    const filename = this.getExistingFilename(item, type);\n    if (!filename) {\n      return null;\n    }\n    return join(this.fulltextDirectory, filename);\n  }\n\n  /**\n   * Detach a file from a reference\n   */\n  async detachFile(\n    item: CslItem,\n    type: FulltextType,\n    options?: DetachOptions\n  ): Promise<DetachResult> {\n    const { delete: deleteFile = false } = options ?? {};\n\n    const filename = this.getExistingFilename(item, type);\n    if (!filename) {\n      throw new FulltextNotAttachedError(item.id, type);\n    }\n\n    if (deleteFile) {\n      const filePath = join(this.fulltextDirectory, filename);\n      try {\n        await unlink(filePath);\n      } catch {\n        // Ignore if file doesn't exist (orphaned metadata)\n      }\n    }\n\n    return {\n      filename,\n      deleted: deleteFile,\n    };\n  }\n\n  /**\n   * Get list of attached fulltext types\n   */\n  getAttachedTypes(item: CslItem): FulltextType[] {\n    const types: FulltextType[] = [];\n    const fulltext = item.custom?.fulltext;\n\n    if (fulltext?.pdf) {\n      types.push(\"pdf\");\n    }\n    if (fulltext?.markdown) {\n      types.push(\"markdown\");\n    }\n\n    return types;\n  }\n\n  /**\n   * Check if item has attachment\n   * @param type Optional type to check; if omitted, checks for any attachment\n   */\n  hasAttachment(item: CslItem, type?: FulltextType): boolean {\n    if (type) {\n      return this.getExistingFilename(item, type) !== undefined;\n    }\n    return this.getAttachedTypes(item).length > 0;\n  }\n\n  /**\n   * Get existing filename from item metadata\n   */\n  private getExistingFilename(item: CslItem, type: FulltextType): string | undefined {\n    const fulltext = item.custom?.fulltext;\n    if (!fulltext) {\n      return undefined;\n    }\n    return fulltext[type];\n  }\n}\n","/**\n * Fulltext CLI commands: attach, get, detach\n */\n\nimport { mkdtempSync, writeFileSync } from \"node:fs\";\nimport { readFile, rm } from \"node:fs/promises\";\nimport { tmpdir } from \"node:os\";\nimport { extname, join } from \"node:path\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport {\n  FulltextIOError,\n  FulltextManager,\n  FulltextNotAttachedError,\n  type FulltextType,\n} from \"../../features/fulltext/index.js\";\nimport { updateReference } from \"../../features/operations/update.js\";\nimport type { ExecutionContext } from \"../execution-context.js\";\n\n/**\n * Options for fulltext attach command\n */\nexport interface FulltextAttachOptions {\n  identifier: string;\n  filePath?: string;\n  type?: FulltextType;\n  move?: boolean;\n  force?: boolean;\n  byUuid?: boolean;\n  fulltextDirectory: string;\n  // For stdin support\n  stdinContent?: Buffer;\n}\n\n/**\n * Result from fulltext attach command\n */\nexport interface FulltextAttachResult {\n  success: boolean;\n  filename?: string;\n  type?: FulltextType;\n  overwritten?: boolean;\n  existingFile?: string;\n  requiresConfirmation?: boolean;\n  error?: string;\n}\n\n/**\n * Options for fulltext get command\n */\nexport interface FulltextGetOptions {\n  identifier: string;\n  type?: FulltextType;\n  stdout?: boolean;\n  byUuid?: boolean;\n  fulltextDirectory: string;\n}\n\n/**\n * Result from fulltext get command\n */\nexport interface FulltextGetResult {\n  success: boolean;\n  paths?: {\n    pdf?: string;\n    markdown?: string;\n  };\n  content?: Buffer;\n  error?: string;\n}\n\n/**\n * Options for fulltext detach command\n */\nexport interface FulltextDetachOptions {\n  identifier: string;\n  type?: FulltextType;\n  delete?: boolean;\n  force?: boolean;\n  byUuid?: boolean;\n  fulltextDirectory: string;\n}\n\n/**\n * Result from fulltext detach command\n */\nexport interface FulltextDetachResult {\n  success: boolean;\n  detached?: FulltextType[];\n  deleted?: FulltextType[];\n  error?: string;\n}\n\n/**\n * Detect fulltext type from file extension\n */\nfunction detectType(filePath: string): FulltextType | undefined {\n  const ext = extname(filePath).toLowerCase();\n  if (ext === \".pdf\") return \"pdf\";\n  if (ext === \".md\" || ext === \".markdown\") return \"markdown\";\n  return undefined;\n}\n\n/**\n * Find reference by identifier\n */\nasync function findReference(\n  identifier: string,\n  context: ExecutionContext,\n  byUuid: boolean\n): Promise<CslItem | null> {\n  if (context.type === \"server\") {\n    return context.client.find(identifier, { byUuid });\n  }\n  const ref = byUuid\n    ? context.library.findByUuid(identifier)\n    : context.library.findById(identifier);\n  return ref?.getItem() ?? null;\n}\n\n/**\n * Update reference metadata with fulltext info\n */\nasync function updateFulltextMetadata(\n  identifier: string,\n  fulltext: { pdf?: string; markdown?: string } | undefined,\n  context: ExecutionContext,\n  byUuid: boolean\n): Promise<void> {\n  // Build updates with fulltext only - other custom fields preserved by merge in updateReference\n  const updates = {\n    custom: { fulltext },\n  } as Partial<CslItem>;\n\n  if (context.type === \"server\") {\n    await context.client.update(identifier, updates, { byUuid });\n  } else {\n    await updateReference(context.library, {\n      identifier,\n      updates,\n      byUuid,\n    });\n  }\n}\n\n/**\n * Clean up temp directory\n */\nasync function cleanupTempDir(tempDir: string | undefined): Promise<void> {\n  if (tempDir) {\n    await rm(tempDir, { recursive: true, force: true }).catch(() => {});\n  }\n}\n\n/**\n * Prepare source path from stdin content\n */\nfunction prepareStdinSource(\n  stdinContent: Buffer,\n  fileType: FulltextType\n): { sourcePath: string; tempDir: string } | { error: string } {\n  try {\n    const tempDir = mkdtempSync(join(tmpdir(), \"refmgr-\"));\n    const ext = fileType === \"pdf\" ? \".pdf\" : \".md\";\n    const sourcePath = join(tempDir, `stdin${ext}`);\n    writeFileSync(sourcePath, stdinContent);\n    return { sourcePath, tempDir };\n  } catch (error) {\n    return {\n      error: `Failed to write stdin content: ${error instanceof Error ? error.message : String(error)}`,\n    };\n  }\n}\n\n/**\n * Build new fulltext metadata\n */\nfunction buildNewFulltext(\n  currentFulltext: { pdf?: string | undefined; markdown?: string | undefined },\n  fileType: FulltextType,\n  filename: string\n): { pdf?: string; markdown?: string } {\n  const newFulltext: { pdf?: string; markdown?: string } = {};\n  if (currentFulltext.pdf) newFulltext.pdf = currentFulltext.pdf;\n  if (currentFulltext.markdown) newFulltext.markdown = currentFulltext.markdown;\n  newFulltext[fileType] = filename;\n  return newFulltext;\n}\n\n/**\n * Resolve file type from options\n */\nfunction resolveFileType(\n  explicitType: FulltextType | undefined,\n  filePath: string | undefined,\n  stdinContent: Buffer | undefined\n): FulltextType | { error: string } {\n  let fileType = explicitType;\n  if (!fileType && filePath) {\n    fileType = detectType(filePath);\n  }\n\n  if (stdinContent && !fileType) {\n    return {\n      error: \"File type must be specified with --pdf or --markdown when reading from stdin.\",\n    };\n  }\n\n  if (!fileType) {\n    return { error: \"Cannot detect file type. Use --pdf or --markdown to specify the type.\" };\n  }\n\n  return fileType;\n}\n\n/**\n * Execute fulltext attach command\n */\nexport async function executeFulltextAttach(\n  options: FulltextAttachOptions,\n  context: ExecutionContext\n): Promise<FulltextAttachResult> {\n  const {\n    identifier,\n    filePath,\n    type: explicitType,\n    move,\n    force,\n    byUuid = false,\n    fulltextDirectory,\n    stdinContent,\n  } = options;\n\n  // Find reference\n  const item = await findReference(identifier, context, byUuid);\n  if (!item) {\n    return { success: false, error: `Reference '${identifier}' not found` };\n  }\n\n  // Resolve file type\n  const fileTypeResult = resolveFileType(explicitType, filePath, stdinContent);\n  if (typeof fileTypeResult === \"object\" && \"error\" in fileTypeResult) {\n    return { success: false, error: fileTypeResult.error };\n  }\n  const fileType = fileTypeResult;\n\n  // Prepare source path\n  let sourcePath = filePath;\n  let tempDir: string | undefined;\n\n  if (stdinContent) {\n    const stdinResult = prepareStdinSource(stdinContent, fileType);\n    if (\"error\" in stdinResult) {\n      return { success: false, error: stdinResult.error };\n    }\n    sourcePath = stdinResult.sourcePath;\n    tempDir = stdinResult.tempDir;\n  }\n\n  if (!sourcePath) {\n    return { success: false, error: \"No file path or stdin content provided.\" };\n  }\n\n  // Attach file\n  const manager = new FulltextManager(fulltextDirectory);\n\n  try {\n    const attachOptions = {\n      ...(move !== undefined && { move }),\n      ...(force !== undefined && { force }),\n    };\n    const result = await manager.attachFile(item, sourcePath, fileType, attachOptions);\n\n    // If existing file and not force, return confirmation required\n    if (result.existingFile && !result.overwritten) {\n      await cleanupTempDir(tempDir);\n      return { success: false, existingFile: result.existingFile, requiresConfirmation: true };\n    }\n\n    // Update metadata\n    const newFulltext = buildNewFulltext(item.custom?.fulltext ?? {}, fileType, result.filename);\n    await updateFulltextMetadata(identifier, newFulltext, context, byUuid);\n    await cleanupTempDir(tempDir);\n\n    return {\n      success: true,\n      filename: result.filename,\n      type: fileType,\n      overwritten: result.overwritten,\n    };\n  } catch (error) {\n    await cleanupTempDir(tempDir);\n    if (error instanceof FulltextIOError) {\n      return { success: false, error: error.message };\n    }\n    throw error;\n  }\n}\n\n/**\n * Get file content for stdout mode\n */\nasync function getFileContent(\n  manager: FulltextManager,\n  item: CslItem,\n  type: FulltextType,\n  identifier: string\n): Promise<FulltextGetResult> {\n  const filePath = manager.getFilePath(item, type);\n  if (!filePath) {\n    return { success: false, error: `No ${type} fulltext attached to '${identifier}'` };\n  }\n\n  try {\n    const content = await readFile(filePath);\n    return { success: true, content };\n  } catch (error) {\n    return {\n      success: false,\n      error: `Failed to read file: ${error instanceof Error ? error.message : String(error)}`,\n    };\n  }\n}\n\n/**\n * Get file paths for path mode\n */\nfunction getFilePaths(\n  manager: FulltextManager,\n  item: CslItem,\n  types: FulltextType[],\n  identifier: string\n): FulltextGetResult {\n  const paths: { pdf?: string; markdown?: string } = {};\n  for (const t of types) {\n    const filePath = manager.getFilePath(item, t);\n    if (filePath) {\n      paths[t] = filePath;\n    }\n  }\n\n  if (Object.keys(paths).length === 0) {\n    return { success: false, error: `No fulltext attached to '${identifier}'` };\n  }\n\n  return { success: true, paths };\n}\n\n/**\n * Execute fulltext get command\n */\nexport async function executeFulltextGet(\n  options: FulltextGetOptions,\n  context: ExecutionContext\n): Promise<FulltextGetResult> {\n  const { identifier, type, stdout, byUuid = false, fulltextDirectory } = options;\n\n  const item = await findReference(identifier, context, byUuid);\n  if (!item) {\n    return { success: false, error: `Reference '${identifier}' not found` };\n  }\n\n  const manager = new FulltextManager(fulltextDirectory);\n\n  // Stdout mode with specific type\n  if (stdout && type) {\n    return getFileContent(manager, item, type, identifier);\n  }\n\n  // Path mode\n  const attachedTypes = type ? [type] : manager.getAttachedTypes(item);\n  if (attachedTypes.length === 0) {\n    return { success: false, error: `No fulltext attached to '${identifier}'` };\n  }\n\n  return getFilePaths(manager, item, attachedTypes, identifier);\n}\n\n/**\n * Perform detach operations for specified types\n */\nasync function performDetachOperations(\n  manager: FulltextManager,\n  item: CslItem,\n  typesToDetach: FulltextType[],\n  deleteFile: boolean | undefined\n): Promise<{ detached: FulltextType[]; deleted: FulltextType[] }> {\n  const detached: FulltextType[] = [];\n  const deleted: FulltextType[] = [];\n\n  for (const t of typesToDetach) {\n    const detachOptions = deleteFile ? { delete: deleteFile } : {};\n    const result = await manager.detachFile(item, t, detachOptions);\n    detached.push(t);\n    if (result.deleted) {\n      deleted.push(t);\n    }\n  }\n\n  return { detached, deleted };\n}\n\n/**\n * Build remaining fulltext metadata after detach\n */\nfunction buildRemainingFulltext(\n  currentFulltext: { pdf?: string | undefined; markdown?: string | undefined },\n  detached: FulltextType[]\n): { pdf?: string; markdown?: string } | undefined {\n  const newFulltext: { pdf?: string; markdown?: string } = {};\n  if (currentFulltext.pdf && !detached.includes(\"pdf\")) {\n    newFulltext.pdf = currentFulltext.pdf;\n  }\n  if (currentFulltext.markdown && !detached.includes(\"markdown\")) {\n    newFulltext.markdown = currentFulltext.markdown;\n  }\n  return Object.keys(newFulltext).length > 0 ? newFulltext : undefined;\n}\n\n/**\n * Handle detach errors\n */\nfunction handleDetachError(error: unknown): FulltextDetachResult {\n  if (error instanceof FulltextNotAttachedError || error instanceof FulltextIOError) {\n    return { success: false, error: error.message };\n  }\n  throw error;\n}\n\n/**\n * Execute fulltext detach command\n */\nexport async function executeFulltextDetach(\n  options: FulltextDetachOptions,\n  context: ExecutionContext\n): Promise<FulltextDetachResult> {\n  const { identifier, type, delete: deleteFile, byUuid = false, fulltextDirectory } = options;\n\n  const item = await findReference(identifier, context, byUuid);\n  if (!item) {\n    return { success: false, error: `Reference '${identifier}' not found` };\n  }\n\n  const manager = new FulltextManager(fulltextDirectory);\n  const typesToDetach: FulltextType[] = type ? [type] : manager.getAttachedTypes(item);\n\n  if (typesToDetach.length === 0) {\n    return { success: false, error: `No fulltext attached to '${identifier}'` };\n  }\n\n  try {\n    const { detached, deleted } = await performDetachOperations(\n      manager,\n      item,\n      typesToDetach,\n      deleteFile\n    );\n\n    const updatedFulltext = buildRemainingFulltext(item.custom?.fulltext ?? {}, detached);\n    await updateFulltextMetadata(identifier, updatedFulltext, context, byUuid);\n\n    const resultData: FulltextDetachResult = { success: true, detached };\n    if (deleted.length > 0) {\n      resultData.deleted = deleted;\n    }\n    return resultData;\n  } catch (error) {\n    return handleDetachError(error);\n  }\n}\n\n/**\n * Format fulltext attach output\n */\nexport function formatFulltextAttachOutput(result: FulltextAttachResult): string {\n  if (result.requiresConfirmation) {\n    return `File already attached: ${result.existingFile}\\nUse --force to overwrite.`;\n  }\n\n  if (!result.success) {\n    return `Error: ${result.error}`;\n  }\n\n  const parts: string[] = [];\n  if (result.overwritten) {\n    parts.push(`Attached ${result.type} (overwritten): ${result.filename}`);\n  } else {\n    parts.push(`Attached ${result.type}: ${result.filename}`);\n  }\n\n  return parts.join(\"\\n\");\n}\n\n/**\n * Format fulltext get output\n */\nexport function formatFulltextGetOutput(result: FulltextGetResult): string {\n  if (!result.success) {\n    return `Error: ${result.error}`;\n  }\n\n  // If content mode (stdout), the content is returned as Buffer, handled by CLI\n  if (result.content) {\n    return result.content.toString();\n  }\n\n  // Path mode\n  const lines: string[] = [];\n  if (result.paths?.pdf) {\n    lines.push(`pdf: ${result.paths.pdf}`);\n  }\n  if (result.paths?.markdown) {\n    lines.push(`markdown: ${result.paths.markdown}`);\n  }\n\n  return lines.join(\"\\n\");\n}\n\n/**\n * Format fulltext detach output\n */\nexport function formatFulltextDetachOutput(result: FulltextDetachResult): string {\n  if (!result.success) {\n    return `Error: ${result.error}`;\n  }\n\n  const lines: string[] = [];\n  for (const type of result.detached ?? []) {\n    if (result.deleted?.includes(type)) {\n      lines.push(`Detached and deleted ${type}`);\n    } else {\n      lines.push(`Detached ${type}`);\n    }\n  }\n\n  return lines.join(\"\\n\");\n}\n\n/**\n * Get exit code for fulltext command result\n */\nexport function getFulltextExitCode(\n  result: FulltextAttachResult | FulltextGetResult | FulltextDetachResult\n): number {\n  return result.success ? 0 : 1;\n}\n","import {\n  type ListFormat,\n  type ListResult,\n  listReferences,\n} from \"../../features/operations/list.js\";\nimport type { ExecutionContext } from \"../execution-context.js\";\n\n/**\n * Options for the list command.\n */\nexport interface ListCommandOptions {\n  json?: boolean;\n  idsOnly?: boolean;\n  uuid?: boolean;\n  bibtex?: boolean;\n}\n\n/**\n * Result from list command execution.\n */\nexport type ListCommandResult = ListResult;\n\n/**\n * Convert CLI options to ListFormat.\n */\nfunction getListFormat(options: ListCommandOptions): ListFormat {\n  if (options.json) return \"json\";\n  if (options.idsOnly) return \"ids-only\";\n  if (options.uuid) return \"uuid\";\n  if (options.bibtex) return \"bibtex\";\n  return \"pretty\";\n}\n\n/**\n * Validate that only one output format is specified.\n */\nfunction validateOptions(options: ListCommandOptions): void {\n  const outputOptions = [options.json, options.idsOnly, options.uuid, options.bibtex].filter(\n    Boolean\n  );\n\n  if (outputOptions.length > 1) {\n    throw new Error(\n      \"Multiple output formats specified. Only one of --json, --ids-only, --uuid, --bibtex can be used.\"\n    );\n  }\n}\n\n/**\n * Execute list command.\n * Routes to server API or direct library operation based on execution context.\n *\n * @param options - List command options\n * @param context - Execution context (server or local)\n * @returns List result containing formatted items\n */\nexport async function executeList(\n  options: ListCommandOptions,\n  context: ExecutionContext\n): Promise<ListCommandResult> {\n  validateOptions(options);\n  const format = getListFormat(options);\n\n  if (context.type === \"server\") {\n    // Use server's list API with format option\n    return context.client.list({ format });\n  }\n\n  // Direct library operation\n  return listReferences(context.library, { format });\n}\n\n/**\n * Format list result for CLI output.\n *\n * @param result - List result\n * @returns Formatted output string\n */\nexport function formatListOutput(result: ListCommandResult): string {\n  if (result.items.length === 0) {\n    return \"\";\n  }\n  return result.items.join(\"\\n\");\n}\n","import { unlink } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { FulltextType } from \"../../features/fulltext/index.js\";\nimport { type RemoveResult, removeReference } from \"../../features/operations/remove.js\";\nimport type { ExecutionContext } from \"../execution-context.js\";\n\n/**\n * Options for the remove command.\n */\nexport interface RemoveCommandOptions {\n  identifier: string;\n  byUuid?: boolean;\n}\n\n/**\n * Result from remove command execution.\n */\nexport type RemoveCommandResult = RemoveResult;\n\n/**\n * Execute remove command.\n * Routes to server API or direct library operation based on execution context.\n *\n * @param options - Remove command options\n * @param context - Execution context (server or local)\n * @returns Remove result\n */\nexport async function executeRemove(\n  options: RemoveCommandOptions,\n  context: ExecutionContext\n): Promise<RemoveCommandResult> {\n  const { identifier, byUuid = false } = options;\n\n  if (context.type === \"server\") {\n    // Server mode: use client with byUuid option for direct ID or UUID lookup\n    return context.client.remove(identifier, { byUuid });\n  }\n\n  // Local mode: direct library operation\n  return removeReference(context.library, { identifier, byUuid });\n}\n\n/**\n * Format remove result for CLI output.\n *\n * @param result - Remove result\n * @param identifier - The identifier that was used\n * @returns Formatted output string\n */\nexport function formatRemoveOutput(result: RemoveCommandResult, identifier: string): string {\n  if (!result.removed) {\n    return `Reference not found: ${identifier}`;\n  }\n\n  const item = result.item;\n  if (item) {\n    return `Removed: [${item.id}] ${item.title || \"(no title)\"}`;\n  }\n\n  return `Removed reference: ${identifier}`;\n}\n\n/**\n * Get fulltext attachment types from a CSL item.\n *\n * @param item - CSL item to check\n * @returns Array of attached fulltext types\n */\nexport function getFulltextAttachmentTypes(item: CslItem): FulltextType[] {\n  const types: FulltextType[] = [];\n  const fulltext = item.custom?.fulltext;\n\n  if (fulltext?.pdf) {\n    types.push(\"pdf\");\n  }\n  if (fulltext?.markdown) {\n    types.push(\"markdown\");\n  }\n\n  return types;\n}\n\n/**\n * Format fulltext warning message for remove confirmation.\n *\n * @param types - Attached fulltext types\n * @returns Warning message string\n */\nexport function formatFulltextWarning(types: FulltextType[]): string {\n  const typeLabels = types.map((t) => (t === \"pdf\" ? \"PDF\" : \"Markdown\"));\n  const fileTypes = typeLabels.join(\" and \");\n  return `Warning: This reference has fulltext files attached (${fileTypes}). Use --force to also delete the fulltext files.`;\n}\n\n/**\n * Delete fulltext files associated with a CSL item.\n *\n * @param item - CSL item with fulltext attachments\n * @param fulltextDirectory - Directory containing fulltext files\n */\nexport async function deleteFulltextFiles(item: CslItem, fulltextDirectory: string): Promise<void> {\n  const fulltext = item.custom?.fulltext;\n  if (!fulltext) {\n    return;\n  }\n\n  const filesToDelete: string[] = [];\n\n  if (fulltext.pdf) {\n    filesToDelete.push(join(fulltextDirectory, fulltext.pdf));\n  }\n  if (fulltext.markdown) {\n    filesToDelete.push(join(fulltextDirectory, fulltext.markdown));\n  }\n\n  for (const filePath of filesToDelete) {\n    try {\n      await unlink(filePath);\n    } catch {\n      // Ignore errors (file might not exist)\n    }\n  }\n}\n","import {\n  type SearchFormat,\n  type SearchResult,\n  searchReferences,\n} from \"../../features/operations/search.js\";\nimport type { ExecutionContext } from \"../execution-context.js\";\n\n/**\n * Options for the search command.\n */\nexport interface SearchCommandOptions {\n  query: string;\n  json?: boolean;\n  idsOnly?: boolean;\n  uuid?: boolean;\n  bibtex?: boolean;\n}\n\n/**\n * Result from search command execution.\n */\nexport type SearchCommandResult = SearchResult;\n\n/**\n * Convert CLI options to SearchFormat.\n */\nfunction getSearchFormat(options: SearchCommandOptions): SearchFormat {\n  if (options.json) return \"json\";\n  if (options.idsOnly) return \"ids-only\";\n  if (options.uuid) return \"uuid\";\n  if (options.bibtex) return \"bibtex\";\n  return \"pretty\";\n}\n\n/**\n * Validate that only one output format is specified.\n */\nfunction validateOptions(options: SearchCommandOptions): void {\n  const outputOptions = [options.json, options.idsOnly, options.uuid, options.bibtex].filter(\n    Boolean\n  );\n\n  if (outputOptions.length > 1) {\n    throw new Error(\n      \"Multiple output formats specified. Only one of --json, --ids-only, --uuid, --bibtex can be used.\"\n    );\n  }\n}\n\n/**\n * Execute search command.\n * Routes to server API or direct library operation based on execution context.\n *\n * @param options - Search command options\n * @param context - Execution context (server or local)\n * @returns Search result containing formatted items\n */\nexport async function executeSearch(\n  options: SearchCommandOptions,\n  context: ExecutionContext\n): Promise<SearchCommandResult> {\n  validateOptions(options);\n  const format = getSearchFormat(options);\n\n  if (context.type === \"server\") {\n    // Use server's search API with format option\n    return context.client.search({ query: options.query, format });\n  }\n\n  // Direct library operation\n  return searchReferences(context.library, { query: options.query, format });\n}\n\n/**\n * Format search result for CLI output.\n *\n * @param result - Search result\n * @returns Formatted output string\n */\nexport function formatSearchOutput(result: SearchCommandResult): string {\n  if (result.items.length === 0) {\n    return \"\";\n  }\n  return result.items.join(\"\\n\");\n}\n","import {\n  isProcessRunning,\n  readPortfile,\n  removePortfile,\n  writePortfile,\n} from \"../../server/portfile.js\";\n\nexport interface ServerStartOptions {\n  port?: number;\n  daemon?: boolean;\n  library: string;\n  portfilePath: string;\n}\n\nexport interface ServerInfo {\n  port: number;\n  pid: number;\n  library: string;\n  started_at?: string;\n}\n\n/**\n * Start HTTP server.\n *\n * @param options - Server start options\n */\nexport async function serverStart(options: ServerStartOptions): Promise<void> {\n  // Check if server is already running\n  const existingStatus = await serverStatus(options.portfilePath);\n  if (existingStatus !== null) {\n    throw new Error(\"Server is already running\");\n  }\n\n  // Determine port (use provided port or default to 3000 for testing)\n  const port = options.port ?? 3000;\n\n  // For daemon mode, create portfile with current process PID\n  // (In real implementation, this would be the spawned server process PID)\n  const pid = process.pid;\n  const started_at = new Date().toISOString();\n\n  await writePortfile(options.portfilePath, port, pid, options.library, started_at);\n\n  // In real implementation, this would spawn the server process\n  // For now, we just create the portfile for testing purposes\n}\n\n/**\n * Stop running server.\n *\n * @param portfilePath - Path to the portfile\n */\nexport async function serverStop(portfilePath: string): Promise<void> {\n  // Check if server is running\n  const status = await serverStatus(portfilePath);\n  if (status === null) {\n    throw new Error(\"Server is not running\");\n  }\n\n  // In real implementation, send SIGTERM to the server process\n  // For testing, we just remove the portfile\n  await removePortfile(portfilePath);\n\n  process.stdout.write(\"Server stopped successfully\\n\");\n}\n\n/**\n * Get server status.\n *\n * @param portfilePath - Path to the portfile\n * @returns Server info if running, null otherwise\n */\nexport async function serverStatus(portfilePath: string): Promise<ServerInfo | null> {\n  // Read portfile\n  const portfileData = await readPortfile(portfilePath);\n  if (portfileData === null) {\n    return null;\n  }\n\n  // Check if process is still running\n  if (!isProcessRunning(portfileData.pid)) {\n    // Process not found, cleanup stale portfile\n    await removePortfile(portfilePath);\n    return null;\n  }\n\n  // Return server info\n  const result: ServerInfo = {\n    port: portfileData.port,\n    pid: portfileData.pid,\n    library: portfileData.library ?? \"\",\n  };\n\n  if (portfileData.started_at !== undefined) {\n    result.started_at = portfileData.started_at;\n  }\n\n  return result;\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport { type UpdateOperationResult, updateReference } from \"../../features/operations/update.js\";\nimport type { ExecutionContext } from \"../execution-context.js\";\n\n/**\n * Options for the update command.\n */\nexport interface UpdateCommandOptions {\n  identifier: string;\n  updates: Partial<CslItem>;\n  byUuid?: boolean;\n}\n\n/**\n * Result from update command execution.\n */\nexport type UpdateCommandResult = UpdateOperationResult;\n\n/**\n * Execute update command.\n * Routes to server API or direct library operation based on execution context.\n *\n * @param options - Update command options\n * @param context - Execution context (server or local)\n * @returns Update result\n */\nexport async function executeUpdate(\n  options: UpdateCommandOptions,\n  context: ExecutionContext\n): Promise<UpdateCommandResult> {\n  const { identifier, updates, byUuid = false } = options;\n\n  if (context.type === \"server\") {\n    // Server mode: use client with byUuid option for direct ID or UUID lookup\n    return context.client.update(identifier, updates, { byUuid });\n  }\n\n  // Local mode: direct library operation\n  return updateReference(context.library, { identifier, updates, byUuid });\n}\n\n/**\n * Format update result for CLI output.\n *\n * @param result - Update result\n * @param identifier - The identifier that was used\n * @returns Formatted output string\n */\nexport function formatUpdateOutput(result: UpdateCommandResult, identifier: string): string {\n  if (!result.updated) {\n    if (result.idCollision) {\n      return `Update failed: ID collision for ${identifier}`;\n    }\n    return `Reference not found: ${identifier}`;\n  }\n\n  const item = result.item;\n  const parts: string[] = [];\n\n  if (item) {\n    parts.push(`Updated: [${item.id}] ${item.title || \"(no title)\"}`);\n  } else {\n    parts.push(`Updated reference: ${identifier}`);\n  }\n\n  if (result.idChanged && result.newId) {\n    parts.push(`ID changed to: ${result.newId}`);\n  }\n\n  return parts.join(\"\\n\");\n}\n","import type { CslItem } from \"../core/csl-json/types.js\";\nimport type { AddReferencesResult } from \"../features/operations/add.js\";\nimport type { CiteResult } from \"../features/operations/cite.js\";\nimport type { ListOptions, ListResult } from \"../features/operations/list.js\";\nimport type { RemoveResult } from \"../features/operations/remove.js\";\nimport type { SearchOperationOptions, SearchResult } from \"../features/operations/search.js\";\nimport type { UpdateOperationResult } from \"../features/operations/update.js\";\n\n/**\n * Options for addFromInputs method.\n */\nexport interface AddFromInputsOptions {\n  force?: boolean;\n  format?: string;\n}\n\n/**\n * Options for cite method.\n */\nexport interface CiteOptions {\n  identifiers: string[];\n  byUuid?: boolean;\n  inText?: boolean;\n  style?: string;\n  cslFile?: string;\n  locale?: string;\n  format?: \"text\" | \"html\";\n}\n\n/**\n * Client for communicating with the reference-manager HTTP server.\n */\nexport class ServerClient {\n  constructor(private baseUrl: string) {}\n\n  /**\n   * Get all references from the server.\n   * @returns Array of CSL items\n   */\n  async getAll(): Promise<CslItem[]> {\n    const url = `${this.baseUrl}/api/references`;\n    const response = await fetch(url);\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as CslItem[];\n  }\n\n  /**\n   * Find reference by identifier.\n   * @param identifier - Citation ID or UUID\n   * @param options - Options object\n   * @param options.byUuid - If true, treat identifier as UUID; otherwise as citation ID\n   * @returns CSL item or null if not found\n   */\n  async find(identifier: string, options?: { byUuid?: boolean }): Promise<CslItem | null> {\n    const path = options?.byUuid\n      ? `/api/references/uuid/${identifier}`\n      : `/api/references/id/${identifier}`;\n    const url = `${this.baseUrl}${path}`;\n    const response = await fetch(url);\n\n    if (response.status === 404) {\n      return null;\n    }\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as CslItem;\n  }\n\n  /**\n   * Add new reference to the library.\n   * @param item - CSL item to add\n   * @returns Created CSL item with UUID\n   */\n  async add(item: CslItem): Promise<CslItem> {\n    const url = `${this.baseUrl}/api/references`;\n    const response = await fetch(url, {\n      method: \"POST\",\n      headers: { \"Content-Type\": \"application/json\" },\n      body: JSON.stringify(item),\n    });\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as CslItem;\n  }\n\n  /**\n   * Update existing reference.\n   * @param identifier - Citation ID or UUID\n   * @param updates - Partial CSL item with fields to update\n   * @param options - Options object\n   * @param options.byUuid - If true, treat identifier as UUID; otherwise as citation ID\n   * @returns Update operation result\n   */\n  async update(\n    identifier: string,\n    updates: Partial<CslItem>,\n    options?: { byUuid?: boolean }\n  ): Promise<UpdateOperationResult> {\n    const path = options?.byUuid\n      ? `/api/references/uuid/${identifier}`\n      : `/api/references/id/${identifier}`;\n    const url = `${this.baseUrl}${path}`;\n    const response = await fetch(url, {\n      method: \"PUT\",\n      headers: { \"Content-Type\": \"application/json\" },\n      body: JSON.stringify(updates),\n    });\n\n    if (!response.ok && response.status !== 404 && response.status !== 409) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as UpdateOperationResult;\n  }\n\n  /**\n   * Remove reference by identifier.\n   * @param identifier - Citation ID or UUID\n   * @param options - Options object\n   * @param options.byUuid - If true, treat identifier as UUID; otherwise as citation ID\n   * @returns Remove operation result\n   */\n  async remove(identifier: string, options?: { byUuid?: boolean }): Promise<RemoveResult> {\n    const path = options?.byUuid\n      ? `/api/references/uuid/${identifier}`\n      : `/api/references/id/${identifier}`;\n    const url = `${this.baseUrl}${path}`;\n    const response = await fetch(url, {\n      method: \"DELETE\",\n    });\n\n    if (!response.ok && response.status !== 404) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as RemoveResult;\n  }\n\n  /**\n   * Add references from various input formats.\n   * @param inputs - Array of inputs (file paths, PMIDs, DOIs)\n   * @param options - Options for add operation\n   * @returns Result containing added, failed, and skipped items\n   */\n  async addFromInputs(\n    inputs: string[],\n    options?: AddFromInputsOptions\n  ): Promise<AddReferencesResult> {\n    const url = `${this.baseUrl}/api/add`;\n    const response = await fetch(url, {\n      method: \"POST\",\n      headers: { \"Content-Type\": \"application/json\" },\n      body: JSON.stringify({ inputs, options }),\n    });\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as AddReferencesResult;\n  }\n\n  /**\n   * Generate citations for references.\n   * @param options - Cite options including identifiers and formatting\n   * @returns Cite result with per-identifier results\n   */\n  async cite(options: CiteOptions): Promise<CiteResult> {\n    const url = `${this.baseUrl}/api/cite`;\n    const response = await fetch(url, {\n      method: \"POST\",\n      headers: { \"Content-Type\": \"application/json\" },\n      body: JSON.stringify(options),\n    });\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as CiteResult;\n  }\n\n  /**\n   * List all references with optional formatting.\n   * @param options - List options including format\n   * @returns List result with formatted items\n   */\n  async list(options?: ListOptions): Promise<ListResult> {\n    const url = `${this.baseUrl}/api/list`;\n    const response = await fetch(url, {\n      method: \"POST\",\n      headers: { \"Content-Type\": \"application/json\" },\n      body: JSON.stringify(options ?? {}),\n    });\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as ListResult;\n  }\n\n  /**\n   * Search references with query.\n   * @param options - Search options including query and format\n   * @returns Search result with formatted items\n   */\n  async search(options: SearchOperationOptions): Promise<SearchResult> {\n    const url = `${this.baseUrl}/api/search`;\n    const response = await fetch(url, {\n      method: \"POST\",\n      headers: { \"Content-Type\": \"application/json\" },\n      body: JSON.stringify(options),\n    });\n\n    if (!response.ok) {\n      throw new Error(await response.text());\n    }\n\n    return (await response.json()) as SearchResult;\n  }\n}\n","import { spawn } from \"node:child_process\";\nimport type { Config } from \"../config/schema.js\";\nimport {\n  getPortfilePath,\n  isProcessRunning,\n  portfileExists,\n  readPortfile,\n  removePortfile,\n} from \"../server/portfile.js\";\n\n/**\n * Server connection information.\n */\nexport interface ServerConnection {\n  baseUrl: string;\n  pid: number;\n}\n\n/**\n * Get server connection if available.\n * @param libraryPath - Path to the library file\n * @param config - Configuration\n * @returns Server connection or null if not available\n */\nexport async function getServerConnection(\n  libraryPath: string,\n  config: Config\n): Promise<ServerConnection | null> {\n  const portfilePath = getPortfilePath();\n  const portfileData = await readPortfile(portfilePath);\n\n  // Check if portfile exists\n  if (!portfileData) {\n    // No server running\n    if (config.server.autoStart) {\n      // Auto-start server\n      await startServerDaemon(libraryPath, config);\n      await waitForPortfile(5000); // 5 second timeout\n      // Retry connection\n      return await getServerConnection(libraryPath, config);\n    }\n    return null;\n  }\n\n  // Check if process is running\n  if (!isProcessRunning(portfileData.pid)) {\n    // Stale portfile, remove it\n    await removePortfile(portfilePath);\n    return null;\n  }\n\n  // Check if library path matches\n  if (!portfileData.library || portfileData.library !== libraryPath) {\n    // Server is serving a different library\n    return null;\n  }\n\n  // Server is running and serving our library\n  return {\n    baseUrl: `http://localhost:${portfileData.port}`,\n    pid: portfileData.pid,\n  };\n}\n\n/**\n * Start server in daemon mode.\n * @param libraryPath - Path to the library file\n * @param _config - Configuration (reserved for future use)\n */\nexport async function startServerDaemon(libraryPath: string, _config: Config): Promise<void> {\n  // Get the binary path (argv[1] is the script being executed)\n  const binaryPath = process.argv[1] || process.execPath;\n\n  // Spawn server in detached daemon mode\n  const child = spawn(\n    process.execPath,\n    [binaryPath, \"server\", \"start\", \"--daemon\", \"--library\", libraryPath],\n    {\n      detached: true,\n      stdio: \"ignore\",\n    }\n  );\n\n  child.unref(); // Allow parent to exit\n}\n\n/**\n * Wait for portfile to appear.\n * @param timeoutMs - Timeout in milliseconds\n */\nexport async function waitForPortfile(timeoutMs: number): Promise<void> {\n  const portfilePath = getPortfilePath();\n  const startTime = Date.now();\n  const checkInterval = 50; // Check every 50ms\n\n  while (Date.now() - startTime < timeoutMs) {\n    if (await portfileExists(portfilePath)) {\n      return;\n    }\n    // Wait before next check\n    await new Promise((resolve) => setTimeout(resolve, checkInterval));\n  }\n\n  throw new Error(`Server failed to start: portfile not created within ${timeoutMs}ms`);\n}\n","/**\n * Execution Context for CLI Commands\n *\n * Provides a discriminated union type to distinguish between server and local execution modes.\n * This enables CLI commands to avoid redundant library loading when a server is available.\n */\n\nimport type { Config } from \"../config/schema.js\";\nimport type { Library } from \"../core/library.js\";\nimport { ServerClient } from \"./server-client.js\";\nimport { getServerConnection } from \"./server-detection.js\";\n\n/**\n * Server execution context - uses ServerClient for operations\n */\nexport interface ServerExecutionContext {\n  type: \"server\";\n  client: ServerClient;\n}\n\n/**\n * Local execution context - uses Library directly\n */\nexport interface LocalExecutionContext {\n  type: \"local\";\n  library: Library;\n}\n\n/**\n * Discriminated union type for execution context.\n * Commands can use this to determine whether to use server or local operations.\n *\n * @example\n * ```typescript\n * if (context.type === \"server\") {\n *   // Use context.client for server operations\n *   const result = await context.client.list(options);\n * } else {\n *   // Use context.library for local operations\n *   const items = context.library.getAll();\n * }\n * ```\n */\nexport type ExecutionContext = ServerExecutionContext | LocalExecutionContext;\n\n/**\n * Creates an execution context based on the current configuration.\n *\n * This function checks for an available server connection first.\n * If a server is available, it returns a server context to avoid loading the library.\n * Otherwise, it loads the library and returns a local context.\n *\n * @param config - The application configuration\n * @param loadLibrary - Function to load the library (injected for testability)\n * @returns Promise resolving to either a server or local execution context\n */\nexport async function createExecutionContext(\n  config: Config,\n  loadLibrary: (path: string) => Promise<Library>\n): Promise<ExecutionContext> {\n  // Check for server connection first\n  const server = await getServerConnection(config.library, config);\n\n  if (server) {\n    // Server is available - use server context to avoid loading library\n    return {\n      type: \"server\",\n      client: new ServerClient(server.baseUrl),\n    };\n  }\n\n  // No server available - load library for local operations\n  const library = await loadLibrary(config.library);\n  return {\n    type: \"local\",\n    library,\n  };\n}\n\n/**\n * Type guard to check if context is a server context\n */\nexport function isServerContext(context: ExecutionContext): context is ServerExecutionContext {\n  return context.type === \"server\";\n}\n\n/**\n * Type guard to check if context is a local context\n */\nexport function isLocalContext(context: ExecutionContext): context is LocalExecutionContext {\n  return context.type === \"local\";\n}\n","/**\n * CLI Helper Functions\n */\n\nimport { readFileSync } from \"node:fs\";\nimport { stdin, stdout } from \"node:process\";\nimport { loadConfig } from \"../config/loader.js\";\nimport type { Config } from \"../config/schema.js\";\n\n/**\n * Output format type\n */\nexport type OutputFormat = \"pretty\" | \"json\" | \"ids-only\" | \"uuid\" | \"bibtex\";\n\n/**\n * CLI options interface\n */\nexport interface CliOptions {\n  library?: string;\n  logLevel?: \"silent\" | \"info\" | \"debug\";\n  config?: string;\n  quiet?: boolean;\n  verbose?: boolean;\n  backup?: boolean;\n  backupDir?: string;\n  json?: boolean;\n  idsOnly?: boolean;\n  uuid?: boolean;\n  bibtex?: boolean;\n}\n\n/**\n * Read JSON input from file or stdin\n * @param file - File path (optional, defaults to stdin)\n * @returns JSON string\n */\nexport async function readJsonInput(file?: string): Promise<string> {\n  if (file) {\n    // Read from file\n    try {\n      return readFileSync(file, \"utf-8\");\n    } catch (error) {\n      throw new Error(\n        `I/O error: Cannot read file ${file}: ${error instanceof Error ? error.message : String(error)}`\n      );\n    }\n  }\n\n  // Read from stdin\n  const chunks: Buffer[] = [];\n  for await (const chunk of stdin) {\n    chunks.push(chunk as Buffer);\n  }\n  return Buffer.concat(chunks).toString(\"utf-8\");\n}\n\n/**\n * Parse JSON input\n * @param input - JSON string\n * @returns Parsed JSON object or array\n */\nexport function parseJsonInput(input: string): unknown {\n  if (!input || input.trim() === \"\") {\n    throw new Error(\"Parse error: Empty input\");\n  }\n\n  try {\n    return JSON.parse(input);\n  } catch (error) {\n    throw new Error(\n      `Parse error: Invalid JSON: ${error instanceof Error ? error.message : String(error)}`\n    );\n  }\n}\n\n/**\n * Load config with CLI argument overrides\n * @param options - CLI options\n * @returns Config with overrides applied\n */\nexport async function loadConfigWithOverrides(options: CliOptions): Promise<Config> {\n  // Load base config\n  // Note: options.config is currently ignored as loadConfig uses cwd and userConfigPath\n  const config = await loadConfig();\n\n  // Apply CLI overrides\n  const overrides: Partial<Config> = {};\n\n  // Library path\n  if (options.library) {\n    overrides.library = options.library;\n  }\n\n  // Log level\n  if (options.quiet) {\n    overrides.logLevel = \"silent\";\n  } else if (options.verbose) {\n    overrides.logLevel = \"debug\";\n  } else if (options.logLevel) {\n    overrides.logLevel = options.logLevel;\n  }\n\n  // Backup settings\n  if (options.backup !== undefined || options.backupDir) {\n    overrides.backup = {\n      ...config.backup,\n      ...(options.backup !== undefined && { enabled: options.backup }),\n      ...(options.backupDir && { directory: options.backupDir }),\n    };\n  }\n\n  return { ...config, ...overrides };\n}\n\n/**\n * Get output format from options\n * @param options - CLI options\n * @returns Output format\n * @throws Error if multiple formats specified\n */\nexport function getOutputFormat(options: CliOptions): OutputFormat {\n  const formats: OutputFormat[] = [];\n\n  if (options.json) formats.push(\"json\");\n  if (options.idsOnly) formats.push(\"ids-only\");\n  if (options.uuid) formats.push(\"uuid\");\n  if (options.bibtex) formats.push(\"bibtex\");\n\n  if (formats.length > 1) {\n    throw new Error(\n      \"Multiple output formats specified. Only one of --json, --ids-only, --uuid, --bibtex can be used.\"\n    );\n  }\n\n  return formats[0] || \"pretty\";\n}\n\n/**\n * Check if running in TTY\n * @returns True if stdin and stdout are TTY\n */\nexport function isTTY(): boolean {\n  return Boolean(stdin.isTTY && stdout.isTTY);\n}\n\n/**\n * Read confirmation from user (y/N)\n * @param prompt - Confirmation prompt message\n * @returns True if user confirmed (y/yes), false otherwise\n */\nexport async function readConfirmation(prompt: string): Promise<boolean> {\n  // If not TTY, auto-confirm\n  if (!isTTY()) {\n    return true;\n  }\n\n  // Display prompt\n  stdout.write(`${prompt} (y/N): `);\n\n  // Read input\n  const chunks: Buffer[] = [];\n  for await (const chunk of stdin) {\n    chunks.push(chunk as Buffer);\n    // Break after first line\n    const input = Buffer.concat(chunks).toString(\"utf-8\");\n    if (input.includes(\"\\n\")) {\n      break;\n    }\n  }\n\n  const input = Buffer.concat(chunks).toString(\"utf-8\").trim().toLowerCase();\n  return input === \"y\" || input === \"yes\";\n}\n\n/**\n * Read stdin content and split into inputs.\n * Used for reading identifiers from stdin.\n * @returns Array of input strings (split by whitespace)\n */\nexport async function readStdinInputs(): Promise<string[]> {\n  const content = await readStdinContent();\n\n  if (!content) {\n    return [];\n  }\n\n  // Split by whitespace (space, tab, newline)\n  return content.split(/\\s+/).filter((s) => s.length > 0);\n}\n\n/**\n * Read raw stdin content without splitting.\n * Used for reading file content (JSON, BibTeX, RIS) from stdin.\n * @returns Raw stdin content as string\n */\nexport async function readStdinContent(): Promise<string> {\n  const chunks: Buffer[] = [];\n  for await (const chunk of stdin) {\n    chunks.push(chunk as Buffer);\n  }\n  return Buffer.concat(chunks).toString(\"utf-8\").trim();\n}\n\n/**\n * Read raw stdin content as Buffer.\n * Used for reading binary file content (PDF) from stdin.\n * @returns Raw stdin content as Buffer\n */\nexport async function readStdinBuffer(): Promise<Buffer> {\n  const chunks: Buffer[] = [];\n  for await (const chunk of stdin) {\n    chunks.push(chunk as Buffer);\n  }\n  return Buffer.concat(chunks);\n}\n","/**\n * CLI Entry Point\n */\n\nimport { Command } from \"commander\";\nimport { z } from \"zod\";\n// Import package.json for version and description\nimport packageJson from \"../../package.json\" with { type: \"json\" };\nimport type { CslItem } from \"../core/csl-json/types.js\";\nimport { Library } from \"../core/library.js\";\nimport { getPortfilePath } from \"../server/portfile.js\";\nimport { executeAdd, formatAddOutput, getExitCode } from \"./commands/add.js\";\nimport {\n  type CiteCommandOptions,\n  executeCite,\n  formatCiteErrors,\n  formatCiteOutput,\n  getCiteExitCode,\n} from \"./commands/cite.js\";\nimport {\n  type FulltextAttachOptions,\n  type FulltextDetachOptions,\n  type FulltextGetOptions,\n  executeFulltextAttach,\n  executeFulltextDetach,\n  executeFulltextGet,\n  formatFulltextAttachOutput,\n  formatFulltextDetachOutput,\n  formatFulltextGetOutput,\n  getFulltextExitCode,\n} from \"./commands/fulltext.js\";\nimport { type ListCommandOptions, executeList, formatListOutput } from \"./commands/list.js\";\nimport {\n  type RemoveCommandOptions,\n  deleteFulltextFiles,\n  executeRemove,\n  formatFulltextWarning,\n  formatRemoveOutput,\n  getFulltextAttachmentTypes,\n} from \"./commands/remove.js\";\nimport { type SearchCommandOptions, executeSearch, formatSearchOutput } from \"./commands/search.js\";\nimport { serverStart, serverStatus, serverStop } from \"./commands/server.js\";\nimport { type UpdateCommandOptions, executeUpdate, formatUpdateOutput } from \"./commands/update.js\";\nimport { type ExecutionContext, createExecutionContext } from \"./execution-context.js\";\nimport type { CliOptions } from \"./helpers.js\";\nimport {\n  isTTY,\n  loadConfigWithOverrides,\n  parseJsonInput,\n  readConfirmation,\n  readJsonInput,\n  readStdinBuffer,\n  readStdinContent,\n} from \"./helpers.js\";\n\n/**\n * Create Commander program instance\n */\nexport function createProgram(): Command {\n  const program = new Command();\n\n  program\n    .name(\"reference-manager\")\n    .version(packageJson.version)\n    .description(packageJson.description);\n\n  // Global options\n  program\n    .option(\"--library <path>\", \"Override library file path\")\n    .option(\"--log-level <level>\", \"Override log level (silent|info|debug)\")\n    .option(\"--config <path>\", \"Use specific config file\")\n    .option(\"--quiet\", \"Suppress all non-error output\")\n    .option(\"--verbose\", \"Enable verbose output\")\n    .option(\"--no-backup\", \"Disable backup creation\")\n    .option(\"--backup-dir <path>\", \"Override backup directory\");\n\n  // Register commands\n  registerListCommand(program);\n  registerSearchCommand(program);\n  registerAddCommand(program);\n  registerRemoveCommand(program);\n  registerUpdateCommand(program);\n  registerCiteCommand(program);\n  registerServerCommand(program);\n  registerFulltextCommand(program);\n\n  return program;\n}\n\n/**\n * Handle 'list' command action\n */\nasync function handleListAction(options: ListCommandOptions, program: Command): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n    const context = await createExecutionContext(config, Library.load);\n    const result = await executeList(options, context);\n    const output = formatListOutput(result);\n\n    if (output) {\n      process.stdout.write(`${output}\\n`);\n    }\n\n    process.exit(0);\n  } catch (error) {\n    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}\\n`);\n    process.exit(4);\n  }\n}\n\n/**\n * Register 'list' command\n */\nfunction registerListCommand(program: Command): void {\n  program\n    .command(\"list\")\n    .description(\"List all references in the library\")\n    .option(\"--json\", \"Output in JSON format\")\n    .option(\"--ids-only\", \"Output only citation keys\")\n    .option(\"--uuid\", \"Output only UUIDs\")\n    .option(\"--bibtex\", \"Output in BibTeX format\")\n    .action(async (options) => {\n      await handleListAction(options, program);\n    });\n}\n\n/**\n * Handle 'search' command action\n */\nasync function handleSearchAction(\n  query: string,\n  options: Omit<SearchCommandOptions, \"query\">,\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n    const context = await createExecutionContext(config, Library.load);\n    const result = await executeSearch({ ...options, query }, context);\n    const output = formatSearchOutput(result);\n\n    if (output) {\n      process.stdout.write(`${output}\\n`);\n    }\n\n    process.exit(0);\n  } catch (error) {\n    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}\\n`);\n    process.exit(4);\n  }\n}\n\n/**\n * Register 'search' command\n */\nfunction registerSearchCommand(program: Command): void {\n  program\n    .command(\"search\")\n    .description(\"Search references\")\n    .argument(\"<query>\", \"Search query\")\n    .option(\"--json\", \"Output in JSON format\")\n    .option(\"--ids-only\", \"Output only citation keys\")\n    .option(\"--uuid\", \"Output only UUIDs\")\n    .option(\"--bibtex\", \"Output in BibTeX format\")\n    .action(async (query: string, options) => {\n      await handleSearchAction(query, options, program);\n    });\n}\n\n/**\n * Register 'add' command\n */\ninterface AddCommandOptions extends CliOptions {\n  force?: boolean;\n  format?: string;\n  verbose?: boolean;\n}\n\nasync function handleAddAction(\n  inputs: string[],\n  options: AddCommandOptions,\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n    // If no inputs provided, read content from stdin\n    let stdinContent: string | undefined;\n    if (inputs.length === 0) {\n      stdinContent = await readStdinContent();\n    }\n\n    // Create execution context\n    const context = await createExecutionContext(config, Library.load);\n\n    // Build add options - avoid undefined values for exactOptionalPropertyTypes\n    const addOptions: Parameters<typeof executeAdd>[0] = {\n      inputs,\n      force: options.force ?? false,\n    };\n    if (options.format !== undefined) {\n      addOptions.format = options.format;\n    }\n    if (options.verbose !== undefined) {\n      addOptions.verbose = options.verbose;\n    }\n    if (stdinContent?.trim()) {\n      addOptions.stdinContent = stdinContent;\n    }\n    // Build pubmedConfig only if values exist\n    const pubmedConfig: { email?: string; apiKey?: string } = {};\n    if (config.pubmed.email !== undefined) {\n      pubmedConfig.email = config.pubmed.email;\n    }\n    if (config.pubmed.apiKey !== undefined) {\n      pubmedConfig.apiKey = config.pubmed.apiKey;\n    }\n    if (Object.keys(pubmedConfig).length > 0) {\n      addOptions.pubmedConfig = pubmedConfig;\n    }\n\n    // Execute add command\n    const result = await executeAdd(addOptions, context);\n\n    // Format and output result\n    const output = formatAddOutput(result, options.verbose ?? false);\n    process.stderr.write(`${output}\\n`);\n\n    // Exit with appropriate code\n    process.exit(getExitCode(result));\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    process.stderr.write(`Error: ${message}\\n`);\n    process.exit(1);\n  }\n}\n\nfunction registerAddCommand(program: Command): void {\n  program\n    .command(\"add\")\n    .description(\"Add new reference(s) to the library\")\n    .argument(\"[input...]\", \"File paths or identifiers (PMID/DOI), or use stdin\")\n    .option(\"-f, --force\", \"Skip duplicate detection\")\n    .option(\"--format <format>\", \"Explicit input format: json|bibtex|ris|pmid|doi|auto\", \"auto\")\n    .option(\"--verbose\", \"Show detailed error information\")\n    .action(async (inputs: string[], options: AddCommandOptions) => {\n      await handleAddAction(inputs, options, program);\n    });\n}\n\n/**\n * Register 'remove' command\n */\nasync function findReferenceToRemove(\n  identifier: string,\n  byUuid: boolean,\n  context: ExecutionContext\n): Promise<CslItem | undefined> {\n  if (context.type === \"server\") {\n    const item = await context.client.find(identifier, { byUuid });\n    return item ?? undefined;\n  }\n\n  const ref = byUuid\n    ? context.library.findByUuid(identifier)\n    : context.library.findById(identifier);\n  return ref?.getItem();\n}\n\nasync function confirmRemoval(\n  refToRemove: CslItem,\n  force: boolean,\n  fulltextWarning?: string\n): Promise<boolean> {\n  if (force || !isTTY()) {\n    return true;\n  }\n\n  const authors = Array.isArray(refToRemove.author)\n    ? refToRemove.author.map((a) => `${a.family || \"\"}, ${a.given?.[0] || \"\"}.`).join(\"; \")\n    : \"(no authors)\";\n  let confirmMsg = `Remove reference [${refToRemove.id}]?\\nTitle: ${refToRemove.title || \"(no title)\"}\\nAuthors: ${authors}`;\n\n  if (fulltextWarning) {\n    confirmMsg += `\\n\\n${fulltextWarning}`;\n  }\n\n  confirmMsg += \"\\nContinue?\";\n\n  return await readConfirmation(confirmMsg);\n}\n\nfunction handleRemoveError(error: unknown): never {\n  const message = error instanceof Error ? error.message : String(error);\n  if (message.includes(\"not found\")) {\n    process.stderr.write(`Error: ${message}\\n`);\n    process.exit(1);\n  }\n  process.stderr.write(`Error: ${message}\\n`);\n  process.exit(4);\n}\n\n/**\n * Format type labels for fulltext files.\n */\nfunction formatTypeLabels(types: (\"pdf\" | \"markdown\")[]): string {\n  return types.map((t) => (t === \"pdf\" ? \"PDF\" : \"Markdown\")).join(\" and \");\n}\n\n/**\n * Handle fulltext deletion and output.\n */\nasync function handleFulltextDeletion(\n  item: CslItem,\n  fulltextDirectory: string,\n  types: (\"pdf\" | \"markdown\")[],\n  output: string\n): Promise<void> {\n  await deleteFulltextFiles(item, fulltextDirectory);\n  const typeLabels = formatTypeLabels(types);\n  process.stderr.write(`${output}\\n`);\n  process.stderr.write(`Deleted fulltext files: ${typeLabels}\\n`);\n}\n\nasync function handleRemoveAction(\n  identifier: string,\n  options: { uuid?: boolean; force?: boolean },\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n    const context = await createExecutionContext(config, Library.load);\n\n    // Find reference for confirmation display\n    const refToRemove = await findReferenceToRemove(identifier, options.uuid ?? false, context);\n\n    if (!refToRemove) {\n      process.stderr.write(`Error: Reference not found: ${identifier}\\n`);\n      process.exit(1);\n    }\n\n    // Check for fulltext attachments\n    const fulltextTypes = getFulltextAttachmentTypes(refToRemove);\n    const hasFulltext = fulltextTypes.length > 0;\n\n    // If fulltext attached and not TTY without --force, require --force\n    if (hasFulltext && !isTTY() && !options.force) {\n      const warning = formatFulltextWarning(fulltextTypes);\n      process.stderr.write(`Error: ${warning}\\n`);\n      process.exit(1);\n    }\n\n    // Interactive confirmation (with fulltext warning if applicable)\n    const fulltextWarning =\n      hasFulltext && !options.force ? formatFulltextWarning(fulltextTypes) : undefined;\n    const confirmed = await confirmRemoval(refToRemove, options.force ?? false, fulltextWarning);\n    if (!confirmed) {\n      process.stderr.write(\"Cancelled.\\n\");\n      process.exit(2);\n    }\n\n    // Execute removal using unified pattern\n    const removeOptions: RemoveCommandOptions = {\n      identifier,\n    };\n    if (options.uuid !== undefined) {\n      removeOptions.byUuid = options.uuid;\n    }\n\n    const result = await executeRemove(removeOptions, context);\n    const output = formatRemoveOutput(result, identifier);\n\n    if (!result.removed) {\n      process.stderr.write(`${output}\\n`);\n      process.exit(1);\n    }\n\n    // Delete fulltext files if --force and fulltext was attached\n    if (hasFulltext && options.force) {\n      await handleFulltextDeletion(refToRemove, config.fulltext.directory, fulltextTypes, output);\n    } else {\n      process.stderr.write(`${output}\\n`);\n    }\n    process.exit(0);\n  } catch (error) {\n    handleRemoveError(error);\n  }\n}\n\nfunction registerRemoveCommand(program: Command): void {\n  program\n    .command(\"remove\")\n    .description(\"Remove a reference from the library\")\n    .argument(\"<identifier>\", \"Citation key or UUID\")\n    .option(\"--uuid\", \"Interpret identifier as UUID\")\n    .option(\"-f, --force\", \"Skip confirmation prompt\")\n    .action(async (identifier: string, options) => {\n      await handleRemoveAction(identifier, options, program);\n    });\n}\n\nfunction handleUpdateError(error: unknown): never {\n  const message = error instanceof Error ? error.message : String(error);\n  if (message.includes(\"Parse error\")) {\n    process.stderr.write(`Error: ${message}\\n`);\n    process.exit(3);\n  }\n  if (message.includes(\"not found\") || message.includes(\"validation\")) {\n    process.stderr.write(`Error: ${message}\\n`);\n    process.exit(1);\n  }\n  process.stderr.write(`Error: ${message}\\n`);\n  process.exit(4);\n}\n\nasync function handleUpdateAction(\n  identifier: string,\n  file: string | undefined,\n  options: { uuid?: boolean },\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n    const inputStr = await readJsonInput(file);\n    const updates = parseJsonInput(inputStr);\n\n    // Validate that updates is a non-null object using zod\n    const updatesSchema = z.record(z.string(), z.unknown());\n    const validatedUpdates = updatesSchema.parse(updates);\n\n    const context = await createExecutionContext(config, Library.load);\n\n    const updateOptions: UpdateCommandOptions = {\n      identifier,\n      updates: validatedUpdates as Partial<CslItem>,\n    };\n    if (options.uuid !== undefined) {\n      updateOptions.byUuid = options.uuid;\n    }\n\n    const result = await executeUpdate(updateOptions, context);\n    const output = formatUpdateOutput(result, identifier);\n\n    if (result.updated) {\n      process.stderr.write(`${output}\\n`);\n      process.exit(0);\n    } else {\n      process.stderr.write(`${output}\\n`);\n      process.exit(1);\n    }\n  } catch (error) {\n    handleUpdateError(error);\n  }\n}\n\nfunction registerUpdateCommand(program: Command): void {\n  program\n    .command(\"update\")\n    .description(\"Update fields of an existing reference\")\n    .argument(\"<identifier>\", \"Citation key or UUID\")\n    .argument(\"[file]\", \"JSON file with updates (or use stdin)\")\n    .option(\"--uuid\", \"Interpret identifier as UUID\")\n    .action(async (identifier: string, file: string | undefined, options) => {\n      await handleUpdateAction(identifier, file, options, program);\n    });\n}\n\n/**\n * Handle 'cite' command action\n */\nasync function handleCiteAction(\n  identifiers: string[],\n  options: Omit<CiteCommandOptions, \"identifiers\">,\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n    const context = await createExecutionContext(config, Library.load);\n    const result = await executeCite({ ...options, identifiers }, context);\n\n    // Output successful citations\n    const output = formatCiteOutput(result);\n    if (output) {\n      process.stdout.write(`${output}\\n`);\n    }\n\n    // Output errors\n    const errors = formatCiteErrors(result);\n    if (errors) {\n      process.stderr.write(`${errors}\\n`);\n    }\n\n    process.exit(getCiteExitCode(result));\n  } catch (error) {\n    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}\\n`);\n    process.exit(4);\n  }\n}\n\n/**\n * Register 'cite' command\n */\nfunction registerCiteCommand(program: Command): void {\n  program\n    .command(\"cite\")\n    .description(\"Generate formatted citations for references\")\n    .argument(\"<id-or-uuid...>\", \"Citation keys or UUIDs to cite\")\n    .option(\"--uuid\", \"Treat arguments as UUIDs instead of IDs\")\n    .option(\"--style <style>\", \"CSL style name\")\n    .option(\"--csl-file <path>\", \"Path to custom CSL file\")\n    .option(\"--locale <locale>\", \"Locale code (e.g., en-US, ja-JP)\")\n    .option(\"--format <format>\", \"Output format: text|html|rtf\")\n    .option(\"--in-text\", \"Generate in-text citations instead of bibliography entries\")\n    .action(async (identifiers: string[], options) => {\n      await handleCiteAction(identifiers, options, program);\n    });\n}\n\n/**\n * Register 'server' command\n */\nfunction registerServerCommand(program: Command): void {\n  const serverCmd = program.command(\"server\").description(\"Manage HTTP server for library access\");\n\n  serverCmd\n    .command(\"start\")\n    .description(\"Start HTTP server\")\n    .option(\"--port <port>\", \"Specify port number\")\n    .option(\"-d, --daemon\", \"Run in background\")\n    .action(async (options) => {\n      try {\n        const globalOpts = program.opts();\n        const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n        const portfilePath = getPortfilePath();\n\n        const startOptions = {\n          library: config.library,\n          portfilePath,\n          daemon: options.daemon,\n          ...(options.port && { port: Number.parseInt(options.port, 10) }),\n        };\n\n        await serverStart(startOptions);\n\n        process.exit(0);\n      } catch (error) {\n        const message = error instanceof Error ? error.message : String(error);\n        if (message.includes(\"already running\") || message.includes(\"conflict\")) {\n          process.stderr.write(`Error: ${message}\\n`);\n          process.exit(1);\n        }\n        process.stderr.write(`Error: ${message}\\n`);\n        process.exit(4);\n      }\n    });\n\n  serverCmd\n    .command(\"stop\")\n    .description(\"Stop running server\")\n    .action(async () => {\n      try {\n        const portfilePath = getPortfilePath();\n        await serverStop(portfilePath);\n\n        process.stderr.write(\"Server stopped.\\n\");\n        process.exit(0);\n      } catch (error) {\n        const message = error instanceof Error ? error.message : String(error);\n        if (message.includes(\"not running\")) {\n          process.stderr.write(`Error: ${message}\\n`);\n          process.exit(1);\n        }\n        process.stderr.write(`Error: ${message}\\n`);\n        process.exit(4);\n      }\n    });\n\n  serverCmd\n    .command(\"status\")\n    .description(\"Check server status\")\n    .action(async () => {\n      try {\n        const portfilePath = getPortfilePath();\n        const status = await serverStatus(portfilePath);\n\n        if (status) {\n          process.stdout.write(\n            `Server is running\\nPort: ${status.port}\\nPID: ${status.pid}\\nLibrary: ${status.library}\\n`\n          );\n          process.exit(0);\n        } else {\n          process.stdout.write(\"Server not running\\n\");\n          process.exit(1);\n        }\n      } catch (error) {\n        process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}\\n`);\n        process.exit(4);\n      }\n    });\n}\n\n/**\n * Check if an option value is a valid file path (not a boolean flag)\n */\nfunction isValidFilePath(value: string | boolean | undefined): value is string {\n  return typeof value === \"string\" && value !== \"\" && value !== \"true\";\n}\n\n/**\n * Parse fulltext attach options to determine file type and path\n */\nfunction parseFulltextAttachTypeAndPath(\n  filePathArg: string | undefined,\n  options: { pdf?: string | boolean; markdown?: string | boolean }\n): { type: \"pdf\" | \"markdown\" | undefined; filePath: string | undefined } {\n  if (options.pdf) {\n    return { type: \"pdf\", filePath: isValidFilePath(options.pdf) ? options.pdf : filePathArg };\n  }\n  if (options.markdown) {\n    return {\n      type: \"markdown\",\n      filePath: isValidFilePath(options.markdown) ? options.markdown : filePathArg,\n    };\n  }\n  return { type: undefined, filePath: filePathArg };\n}\n\n/**\n * Handle 'fulltext attach' command action\n */\nasync function handleFulltextAttachAction(\n  identifier: string,\n  filePathArg: string | undefined,\n  options: {\n    pdf?: string;\n    markdown?: string;\n    move?: boolean;\n    force?: boolean;\n    uuid?: boolean;\n  },\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n    const context = await createExecutionContext(config, Library.load);\n\n    const { type, filePath } = parseFulltextAttachTypeAndPath(filePathArg, options);\n\n    // If no file path and type is specified, read from stdin\n    const stdinContent = !filePath && type ? await readStdinBuffer() : undefined;\n\n    const attachOptions: FulltextAttachOptions = {\n      identifier,\n      fulltextDirectory: config.fulltext.directory,\n      ...(filePath && { filePath }),\n      ...(type && { type }),\n      ...(options.move && { move: options.move }),\n      ...(options.force && { force: options.force }),\n      ...(options.uuid && { byUuid: options.uuid }),\n      ...(stdinContent && { stdinContent }),\n    };\n\n    const result = await executeFulltextAttach(attachOptions, context);\n    const output = formatFulltextAttachOutput(result);\n    process.stderr.write(`${output}\\n`);\n    process.exit(getFulltextExitCode(result));\n  } catch (error) {\n    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}\\n`);\n    process.exit(4);\n  }\n}\n\n/**\n * Handle 'fulltext get' command action\n */\nasync function handleFulltextGetAction(\n  identifier: string,\n  options: {\n    pdf?: boolean;\n    markdown?: boolean;\n    stdout?: boolean;\n    uuid?: boolean;\n  },\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n    const context = await createExecutionContext(config, Library.load);\n\n    const getOptions: FulltextGetOptions = {\n      identifier,\n      fulltextDirectory: config.fulltext.directory,\n      ...(options.pdf && { type: \"pdf\" as const }),\n      ...(options.markdown && { type: \"markdown\" as const }),\n      ...(options.stdout && { stdout: options.stdout }),\n      ...(options.uuid && { byUuid: options.uuid }),\n    };\n\n    const result = await executeFulltextGet(getOptions, context);\n\n    if (result.success && result.content && options.stdout) {\n      // Write raw content to stdout\n      process.stdout.write(result.content);\n    } else {\n      const output = formatFulltextGetOutput(result);\n      if (result.success) {\n        process.stdout.write(`${output}\\n`);\n      } else {\n        process.stderr.write(`${output}\\n`);\n      }\n    }\n\n    process.exit(getFulltextExitCode(result));\n  } catch (error) {\n    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}\\n`);\n    process.exit(4);\n  }\n}\n\n/**\n * Handle 'fulltext detach' command action\n */\nasync function handleFulltextDetachAction(\n  identifier: string,\n  options: {\n    pdf?: boolean;\n    markdown?: boolean;\n    delete?: boolean;\n    force?: boolean;\n    uuid?: boolean;\n  },\n  program: Command\n): Promise<void> {\n  try {\n    const globalOpts = program.opts();\n    const config = await loadConfigWithOverrides({ ...globalOpts, ...options });\n\n    const context = await createExecutionContext(config, Library.load);\n\n    const detachOptions: FulltextDetachOptions = {\n      identifier,\n      fulltextDirectory: config.fulltext.directory,\n      ...(options.pdf && { type: \"pdf\" as const }),\n      ...(options.markdown && { type: \"markdown\" as const }),\n      ...(options.delete && { delete: options.delete }),\n      ...(options.force && { force: options.force }),\n      ...(options.uuid && { byUuid: options.uuid }),\n    };\n\n    const result = await executeFulltextDetach(detachOptions, context);\n    const output = formatFulltextDetachOutput(result);\n    process.stderr.write(`${output}\\n`);\n\n    process.exit(getFulltextExitCode(result));\n  } catch (error) {\n    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}\\n`);\n    process.exit(4);\n  }\n}\n\n/**\n * Register 'fulltext' command with subcommands\n */\nfunction registerFulltextCommand(program: Command): void {\n  const fulltextCmd = program\n    .command(\"fulltext\")\n    .description(\"Manage full-text files attached to references\");\n\n  fulltextCmd\n    .command(\"attach\")\n    .description(\"Attach a full-text file to a reference\")\n    .argument(\"<identifier>\", \"Citation key or UUID\")\n    .argument(\"[file-path]\", \"Path to the file to attach\")\n    .option(\"--pdf [path]\", \"Attach as PDF (path optional if provided as argument)\")\n    .option(\"--markdown [path]\", \"Attach as Markdown (path optional if provided as argument)\")\n    .option(\"--move\", \"Move file instead of copy\")\n    .option(\"-f, --force\", \"Overwrite existing attachment\")\n    .option(\"--uuid\", \"Interpret identifier as UUID\")\n    .action(async (identifier: string, filePath: string | undefined, options) => {\n      await handleFulltextAttachAction(identifier, filePath, options, program);\n    });\n\n  fulltextCmd\n    .command(\"get\")\n    .description(\"Get full-text file path or content\")\n    .argument(\"<identifier>\", \"Citation key or UUID\")\n    .option(\"--pdf\", \"Get PDF file only\")\n    .option(\"--markdown\", \"Get Markdown file only\")\n    .option(\"--stdout\", \"Output file content to stdout\")\n    .option(\"--uuid\", \"Interpret identifier as UUID\")\n    .action(async (identifier: string, options) => {\n      await handleFulltextGetAction(identifier, options, program);\n    });\n\n  fulltextCmd\n    .command(\"detach\")\n    .description(\"Detach full-text file from a reference\")\n    .argument(\"<identifier>\", \"Citation key or UUID\")\n    .option(\"--pdf\", \"Detach PDF only\")\n    .option(\"--markdown\", \"Detach Markdown only\")\n    .option(\"--delete\", \"Also delete the file from disk\")\n    .option(\"-f, --force\", \"Skip confirmation for delete\")\n    .option(\"--uuid\", \"Interpret identifier as UUID\")\n    .action(async (identifier: string, options) => {\n      await handleFulltextDetachAction(identifier, options, program);\n    });\n}\n\n/**\n * Main CLI entry point\n */\nexport async function main(argv: string[]): Promise<void> {\n  const program = createProgram();\n\n  // Setup signal handlers\n  process.on(\"SIGINT\", () => {\n    process.exit(130);\n  });\n\n  process.on(\"SIGTERM\", () => {\n    process.exit(0);\n  });\n\n  await 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package/dist/config/csl-styles.d.ts

@@ -0,0 +1,83 @@
+/**
+ * CSL Style Management
+ *
+ * Handles resolution and loading of CSL (Citation Style Language) style files.
+ *
+ * Style Resolution Order:
+ * 1. --csl-file <path> (exact file path)
+ * 2. Built-in style matching --style <name>
+ * 3. Search in csl_directory paths (in array order)
+ * 4. Default style from config (default_style)
+ * 5. "apa" (hardcoded default)
+ */
+/**
+ * Built-in styles available in @citation-js/plugin-csl
+ * These can be used directly without loading external files
+ */
+export declare const BUILTIN_STYLES: readonly ["apa", "vancouver", "harvard"];
+export type BuiltinStyleName = (typeof BUILTIN_STYLES)[number];
+/**
+ * Check if a style name is a built-in style
+ */
+export declare function isBuiltinStyle(styleName: string): styleName is BuiltinStyleName;
+export interface StyleResolutionOptions {
+    /**
+     * Exact path to CSL file (from --csl-file option)
+     * Takes highest priority
+     */
+    cslFile?: string;
+    /**
+     * Style name to resolve (from --style option)
+     */
+    style?: string;
+    /**
+     * Directory or directories to search for custom CSL files
+     * (from csl_directory config)
+     * Can be a single string or array of strings
+     */
+    cslDirectory?: string | string[];
+    /**
+     * Default style to use if specified style not found
+     * (from default_style config)
+     */
+    defaultStyle?: string;
+}
+export interface StyleResolution {
+    /**
+     * Type of resolution: "builtin" for citation-js built-in styles,
+     * "custom" for external CSL files
+     */
+    type: "builtin" | "custom";
+    /**
+     * The resolved style name (for built-in) or identifier (for custom)
+     */
+    styleName: string;
+    /**
+     * CSL XML content (only for custom styles)
+     */
+    styleXml?: string;
+}
+/**
+ * Load CSL style file content from the given path
+ *
+ * @param stylePath - Path to the CSL style file
+ * @returns Content of the CSL style file (XML string)
+ * @throws Error if file cannot be read
+ */
+export declare function loadCSLStyleFile(stylePath: string): string;
+/**
+ * Resolve the style based on resolution options
+ *
+ * Resolution order:
+ * 1. cslFile (exact path) - throws if doesn't exist
+ * 2. Built-in style matching style name
+ * 3. Search in csl_directory paths (in order)
+ * 4. Default style (defaultStyle) - if built-in
+ * 5. "apa" (hardcoded fallback)
+ *
+ * @param options - Style resolution options
+ * @returns StyleResolution with type, styleName, and optional styleXml
+ * @throws Error if cslFile is specified but doesn't exist
+ */
+export declare function resolveStyle(options: StyleResolutionOptions): StyleResolution;
+//# sourceMappingURL=csl-styles.d.ts.map

package/dist/config/csl-styles.d.ts.map

@@ -0,0 +1 @@
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