@ncukondo/reference-manager 0.24.0 → 0.25.0

package/dist/chunks/{loader-CV71qNY2.js → loader-B-fte1uv.js}

@@ -144,6 +144,7 @@ const attachmentsConfigSchema = z.object({
 const configSchema = z.object({
   library: z.string().min(1),
   logLevel: logLevelSchema,
+  email: z.string().optional(),
   backup: backupConfigSchema,
   watch: watchConfigSchema,
   server: serverConfigSchema,
@@ -159,6 +160,7 @@ const partialConfigSchema = z.object({
   logLevel: logLevelSchema.optional(),
   log_level: logLevelSchema.optional(),
   // snake_case support
+  email: z.string().optional(),
   backup: z.object({
     maxGenerations: z.number().int().positive().optional(),
     max_generations: z.number().int().positive().optional(),
@@ -398,6 +400,9 @@ function normalizePartialConfig(partial) {
   if (logLevel !== void 0) {
     normalized.logLevel = logLevel;
   }
+  if (partial.email !== void 0) {
+    normalized.email = partial.email;
+  }
   for (const key of Object.keys(sectionNormalizers)) {
     applyNormalizer(normalized, partial, key, sectionNormalizers[key]);
   }
@@ -549,6 +554,7 @@ function getDefaultAttachmentsDirectory() {
 const defaultConfig = {
   library: getDefaultLibraryPath(),
   logLevel: "info",
+  email: void 0,
   backup: {
     maxGenerations: 50,
     maxAgeDays: 365,
@@ -657,6 +663,9 @@ function applyOverride(result, override) {
   if (override.logLevel !== void 0) {
     result.logLevel = override.logLevel;
   }
+  if (override.email !== void 0) {
+    result.email = override.email;
+  }
   for (const key of flatSectionKeys) {
     if (override[key] !== void 0) {
       result[key] = {
@@ -683,9 +692,11 @@ function mergeConfigs(base, ...overrides) {
 function fillDefaults(partial) {
   const envLibrary = process.env.REFERENCE_MANAGER_LIBRARY;
   const library = envLibrary ?? partial.library ?? defaultConfig.library;
+  const email = process.env.EMAIL ?? partial.email ?? defaultConfig.email;
   return {
     library: expandTilde(library),
     logLevel: partial.logLevel ?? defaultConfig.logLevel,
+    email,
     backup: {
       maxGenerations: partial.backup?.maxGenerations ?? defaultConfig.backup.maxGenerations,
       maxAgeDays: partial.backup?.maxAgeDays ?? defaultConfig.backup.maxAgeDays,
@@ -702,8 +713,8 @@ function fillDefaults(partial) {
       autoStopMinutes: partial.server?.autoStopMinutes ?? defaultConfig.server.autoStopMinutes
     },
     citation: fillCitationDefaults(partial.citation),
-    pubmed: fillPubmedDefaults(partial.pubmed),
-    fulltext: fillFulltextDefaults(partial.fulltext),
+    pubmed: fillPubmedDefaults(partial.pubmed, email),
+    fulltext: fillFulltextDefaults(partial.fulltext, email),
     attachments: fillAttachmentsDefaults(partial.attachments),
     cli: fillCliDefaults(partial.cli),
     mcp: fillMcpDefaults(partial.mcp)
@@ -718,18 +729,18 @@ function fillCitationDefaults(partial) {
     defaultKeyFormat: partial?.defaultKeyFormat ?? defaultConfig.citation.defaultKeyFormat
   };
 }
-function fillPubmedDefaults(partial) {
-  const email = process.env.PUBMED_EMAIL ?? partial?.email ?? defaultConfig.pubmed.email;
+function fillPubmedDefaults(partial, fallbackEmail) {
+  const email = process.env.PUBMED_EMAIL ?? partial?.email ?? fallbackEmail ?? defaultConfig.pubmed.email;
   const apiKey = process.env.PUBMED_API_KEY ?? partial?.apiKey ?? defaultConfig.pubmed.apiKey;
   return {
     email,
     apiKey
   };
 }
-function fillFulltextDefaults(partial) {
-  const unpaywallEmail = process.env.UNPAYWALL_EMAIL ?? partial?.sources?.unpaywallEmail ?? defaultConfig.fulltext.sources.unpaywallEmail;
+function fillFulltextDefaults(partial, fallbackEmail) {
+  const unpaywallEmail = process.env.UNPAYWALL_EMAIL ?? partial?.sources?.unpaywallEmail ?? fallbackEmail ?? defaultConfig.fulltext.sources.unpaywallEmail;
   const coreApiKey = process.env.CORE_API_KEY ?? partial?.sources?.coreApiKey ?? defaultConfig.fulltext.sources.coreApiKey;
-  const ncbiEmail = process.env.NCBI_EMAIL ?? partial?.sources?.ncbiEmail ?? defaultConfig.fulltext.sources.ncbiEmail;
+  const ncbiEmail = process.env.NCBI_EMAIL ?? partial?.sources?.ncbiEmail ?? fallbackEmail ?? defaultConfig.fulltext.sources.ncbiEmail;
   const ncbiTool = process.env.NCBI_TOOL ?? partial?.sources?.ncbiTool ?? defaultConfig.fulltext.sources.ncbiTool;
   const envPreferredType = process.env.REFERENCE_MANAGER_FULLTEXT_PREFERRED_TYPE;
   if (envPreferredType !== void 0 && envPreferredType !== "pdf" && envPreferredType !== "markdown") {
@@ -839,4 +850,4 @@ export {
   partialConfigSchema as p,
   watchConfigSchema as w
 };
-//# sourceMappingURL=loader-CV71qNY2.js.map
+//# sourceMappingURL=loader-B-fte1uv.js.map

package/dist/chunks/loader-B-fte1uv.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"loader-B-fte1uv.js","sources":["../../src/utils/opener.ts","../../src/config/schema.ts","../../node_modules/env-paths/index.js","../../src/config/paths.ts","../../src/config/defaults.ts","../../src/config/loader.ts"],"sourcesContent":["import { type ChildProcess, spawn } from \"node:child_process\";\nimport fs from \"node:fs\";\n\n/**\n * Detect if running in Windows Subsystem for Linux (WSL)\n */\nexport function isWSL(): boolean {\n  // Check for WSL_DISTRO_NAME environment variable\n  if (process.env.WSL_DISTRO_NAME !== undefined) {\n    return true;\n  }\n\n  // Check for WSLInterop file\n  try {\n    return fs.existsSync(\"/proc/sys/fs/binfmt_misc/WSLInterop\");\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Get the system opener command for the specified platform.\n * @param platform - The platform (darwin, linux, win32)\n * @param wsl - Whether running in WSL (defaults to isWSL())\n * @returns The command array to execute\n */\nexport function getOpenerCommand(platform: string, wsl: boolean = isWSL()): string[] {\n  switch (platform) {\n    case \"darwin\":\n      return [\"open\"];\n    case \"linux\":\n      if (wsl) {\n        return [\"wslview\"];\n      }\n      return [\"xdg-open\"];\n    case \"win32\":\n      return [\"cmd\", \"/c\", \"start\", \"\"];\n    default:\n      throw new Error(`Unsupported platform: ${platform}`);\n  }\n}\n\n/**\n * Open a file with the system's default application.\n * @param filePath - The path to the file to open\n * @param platform - The platform (defaults to process.platform)\n */\nexport async function openWithSystemApp(\n  filePath: string,\n  platform: string = process.platform\n): Promise<void> {\n  const wsl = isWSL();\n  const commandParts = getOpenerCommand(platform, wsl);\n  const [command, ...baseArgs] = commandParts;\n  const args = [...baseArgs, filePath];\n\n  // Use a timer to keep the event loop alive while waiting for the close event.\n  // In Node.js 22+, after enquirer prompts complete, the event loop may have no\n  // active handles. Combined with proc.unref(), this can cause Node.js to exit\n  // before the close event fires.\n  const keepAliveTimer = setInterval(() => {\n    // No-op: timer exists solely to keep event loop active\n  }, 60000);\n\n  return new Promise<void>((resolve, reject) => {\n    const proc: ChildProcess = spawn(command as string, args, {\n      detached: true,\n      stdio: \"ignore\",\n    });\n\n    const cleanup = (): void => {\n      clearInterval(keepAliveTimer);\n    };\n\n    proc.on(\"error\", (err: NodeJS.ErrnoException) => {\n      cleanup();\n      // Check if the command was not found (ENOENT)\n      if (err.code === \"ENOENT\") {\n        if (wsl && command === \"wslview\") {\n          reject(new Error(\"wslview not found. Install with: sudo apt install wslu\"));\n        } else if (command === \"xdg-open\") {\n          reject(new Error(\"xdg-open not found. Install a desktop environment or xdg-utils.\"));\n        } else {\n          reject(new Error(`Opener command '${command}' not found`));\n        }\n      } else {\n        reject(new Error(`Failed to open: ${filePath}`));\n      }\n    });\n\n    proc.on(\"close\", (code: number | null) => {\n      cleanup();\n      // wslview may return non-zero exit codes even on success\n      // We treat the operation as successful if the process exited without error\n      if (code === 0 || (wsl && command === \"wslview\")) {\n        resolve();\n      } else {\n        reject(new Error(`Failed to open: ${filePath}`));\n      }\n    });\n\n    proc.unref();\n  });\n}\n","/**\n * Configuration schema using Zod\n */\n\nimport { z } from \"zod\";\nimport { sortFieldSchema, sortOrderSchema } from \"../features/pagination/types.js\";\n\n/**\n * Log level schema\n */\nexport const logLevelSchema = z.enum([\"silent\", \"info\", \"debug\"]);\n\n/**\n * TUI (interactive) search configuration schema\n */\nexport const tuiConfigSchema = z.object({\n  limit: z.number().int().nonnegative(),\n  debounceMs: z.number().int().nonnegative(),\n  clipboardAutoCopy: z.boolean(),\n});\n\n/**\n * Edit format schema\n */\nexport const editFormatSchema = z.enum([\"yaml\", \"json\"]);\n\n/**\n * Edit command configuration schema\n */\nexport const editConfigSchema = z.object({\n  defaultFormat: editFormatSchema,\n});\n\n/**\n * CLI configuration schema\n */\nexport const cliConfigSchema = z.object({\n  defaultLimit: z.number().int().nonnegative(),\n  defaultSort: sortFieldSchema,\n  defaultOrder: sortOrderSchema,\n  tui: tuiConfigSchema,\n  edit: editConfigSchema,\n});\n\n/**\n * MCP configuration schema\n */\nexport const mcpConfigSchema = z.object({\n  defaultLimit: z.number().int().nonnegative(),\n});\n\n/**\n * Backup configuration schema\n */\nexport const backupConfigSchema = z.object({\n  maxGenerations: z.number().int().positive(),\n  maxAgeDays: z.number().int().positive(),\n  directory: z.string().min(1),\n});\n\n/**\n * File watching configuration schema\n * Note: File watching is always enabled in server mode (HTTP/MCP).\n * CLI mode does not use file watching.\n */\nexport const watchConfigSchema = z.object({\n  debounceMs: z.number().int().nonnegative(),\n  pollIntervalMs: z.number().int().positive(),\n  retryIntervalMs: z.number().int().positive(),\n  maxRetries: z.number().int().nonnegative(),\n});\n\n/**\n * Server configuration schema\n */\nexport const serverConfigSchema = z.object({\n  autoStart: z.boolean(),\n  autoStopMinutes: z.number().int().nonnegative(),\n});\n\n/**\n * Citation format schema\n */\nexport const citationFormatSchema = z.enum([\"text\", \"html\", \"rtf\"]);\n\n/**\n * Citation key format schema\n */\nexport const citationKeyFormatSchema = z.enum([\"pandoc\", \"latex\"]);\n\n/**\n * Citation configuration schema\n */\nexport const citationConfigSchema = z.object({\n  defaultStyle: z.string(),\n  cslDirectory: z.array(z.string()),\n  defaultLocale: z.string(),\n  defaultFormat: citationFormatSchema,\n  defaultKeyFormat: citationKeyFormatSchema,\n});\n\n/**\n * PubMed API configuration schema\n */\nexport const pubmedConfigSchema = z.object({\n  email: z.string().optional(),\n  apiKey: z.string().optional(),\n});\n\n/**\n * Fulltext source enum schema\n */\nexport const fulltextSourceSchema = z.enum([\"pmc\", \"arxiv\", \"unpaywall\", \"core\"]);\nconst fulltextPreferredTypeSchema = z.enum([\"pdf\", \"markdown\"]);\n\n/**\n * Fulltext retrieval configuration schema\n */\nexport const fulltextConfigSchema = z.object({\n  preferSources: z.array(fulltextSourceSchema),\n  preferredType: fulltextPreferredTypeSchema.optional(),\n  autoFetchOnAdd: z.boolean(),\n  sources: z.object({\n    unpaywallEmail: z.string().optional(),\n    coreApiKey: z.string().optional(),\n    ncbiEmail: z.string().optional(),\n    ncbiTool: z.string().optional(),\n  }),\n});\n\n/**\n * Attachments storage configuration schema\n */\nexport const attachmentsConfigSchema = z.object({\n  directory: z.string().min(1),\n});\n\n/**\n * Complete configuration schema\n */\nexport const configSchema = z.object({\n  library: z.string().min(1),\n  logLevel: logLevelSchema,\n  email: z.string().optional(),\n  backup: backupConfigSchema,\n  watch: watchConfigSchema,\n  server: serverConfigSchema,\n  citation: citationConfigSchema,\n  pubmed: pubmedConfigSchema,\n  fulltext: fulltextConfigSchema,\n  attachments: attachmentsConfigSchema,\n  cli: cliConfigSchema,\n  mcp: mcpConfigSchema,\n});\n\n/**\n * Partial configuration schema (for TOML files)\n * Supports both camelCase and snake_case field names\n */\nexport const partialConfigSchema = z\n  .object({\n    library: z.string().min(1).optional(),\n    logLevel: logLevelSchema.optional(),\n    log_level: logLevelSchema.optional(), // snake_case support\n    email: z.string().optional(),\n    backup: z\n      .object({\n        maxGenerations: z.number().int().positive().optional(),\n        max_generations: z.number().int().positive().optional(),\n        maxAgeDays: z.number().int().positive().optional(),\n        max_age_days: z.number().int().positive().optional(),\n        directory: z.string().min(1).optional(),\n      })\n      .optional(),\n    watch: z\n      .object({\n        debounceMs: z.number().int().nonnegative().optional(),\n        debounce_ms: z.number().int().nonnegative().optional(),\n        pollIntervalMs: z.number().int().positive().optional(),\n        poll_interval_ms: z.number().int().positive().optional(),\n        retryIntervalMs: z.number().int().positive().optional(),\n        retry_interval_ms: z.number().int().positive().optional(),\n        maxRetries: z.number().int().nonnegative().optional(),\n        max_retries: z.number().int().nonnegative().optional(),\n      })\n      .optional(),\n    server: z\n      .object({\n        autoStart: z.boolean().optional(),\n        auto_start: z.boolean().optional(),\n        autoStopMinutes: z.number().int().nonnegative().optional(),\n        auto_stop_minutes: z.number().int().nonnegative().optional(),\n      })\n      .optional(),\n    citation: z\n      .object({\n        defaultStyle: z.string().optional(),\n        default_style: z.string().optional(),\n        cslDirectory: z.union([z.string(), z.array(z.string())]).optional(),\n        csl_directory: z.union([z.string(), z.array(z.string())]).optional(),\n        defaultLocale: z.string().optional(),\n        default_locale: z.string().optional(),\n        defaultFormat: citationFormatSchema.optional(),\n        default_format: citationFormatSchema.optional(),\n        defaultKeyFormat: citationKeyFormatSchema.optional(),\n        default_key_format: citationKeyFormatSchema.optional(),\n      })\n      .optional(),\n    pubmed: z\n      .object({\n        email: z.string().optional(),\n        apiKey: z.string().optional(),\n        api_key: z.string().optional(),\n      })\n      .optional(),\n    fulltext: z\n      .object({\n        preferSources: z.array(fulltextSourceSchema).optional(),\n        prefer_sources: z.array(fulltextSourceSchema).optional(),\n        preferredType: fulltextPreferredTypeSchema.optional(),\n        preferred_type: fulltextPreferredTypeSchema.optional(),\n        autoFetchOnAdd: z.boolean().optional(),\n        auto_fetch_on_add: z.boolean().optional(),\n        sources: z\n          .object({\n            unpaywallEmail: z.string().optional(),\n            unpaywall_email: z.string().optional(),\n            coreApiKey: z.string().optional(),\n            core_api_key: z.string().optional(),\n            ncbiEmail: z.string().optional(),\n            ncbi_email: z.string().optional(),\n            ncbiTool: z.string().optional(),\n            ncbi_tool: z.string().optional(),\n          })\n          .optional(),\n      })\n      .optional(),\n    attachments: z\n      .object({\n        directory: z.string().min(1).optional(),\n      })\n      .optional(),\n    cli: z\n      .object({\n        defaultLimit: z.number().int().nonnegative().optional(),\n        default_limit: z.number().int().nonnegative().optional(),\n        defaultSort: sortFieldSchema.optional(),\n        default_sort: sortFieldSchema.optional(),\n        defaultOrder: sortOrderSchema.optional(),\n        default_order: sortOrderSchema.optional(),\n        tui: z\n          .object({\n            limit: z.number().int().nonnegative().optional(),\n            debounceMs: z.number().int().nonnegative().optional(),\n            debounce_ms: z.number().int().nonnegative().optional(),\n            clipboardAutoCopy: z.boolean().optional(),\n            clipboard_auto_copy: z.boolean().optional(),\n          })\n          .optional(),\n        edit: z\n          .object({\n            defaultFormat: editFormatSchema.optional(),\n            default_format: editFormatSchema.optional(),\n          })\n          .optional(),\n      })\n      .optional(),\n    mcp: z\n      .object({\n        defaultLimit: z.number().int().nonnegative().optional(),\n        default_limit: z.number().int().nonnegative().optional(),\n      })\n      .optional(),\n  })\n  .passthrough(); // Allow unknown fields in TOML files\n\n/**\n * Inferred types from schemas\n */\nexport type LogLevel = z.infer<typeof logLevelSchema>;\nexport type BackupConfig = z.infer<typeof backupConfigSchema>;\nexport type WatchConfig = z.infer<typeof watchConfigSchema>;\nexport type ServerConfig = z.infer<typeof serverConfigSchema>;\nexport type CitationFormat = z.infer<typeof citationFormatSchema>;\nexport type CitationKeyFormat = z.infer<typeof citationKeyFormatSchema>;\nexport type CitationConfig = z.infer<typeof citationConfigSchema>;\nexport type PubmedConfig = z.infer<typeof pubmedConfigSchema>;\nexport type FulltextSource = z.infer<typeof fulltextSourceSchema>;\nexport type FulltextPreferredType = z.infer<typeof fulltextPreferredTypeSchema>;\nexport type FulltextConfig = z.infer<typeof fulltextConfigSchema>;\nexport type AttachmentsConfig = z.infer<typeof attachmentsConfigSchema>;\nexport type TuiConfig = z.infer<typeof tuiConfigSchema>;\nexport type EditConfigFormat = z.infer<typeof editFormatSchema>;\nexport type EditConfig = z.infer<typeof editConfigSchema>;\nexport type CliConfig = z.infer<typeof cliConfigSchema>;\nexport type McpConfig = z.infer<typeof mcpConfigSchema>;\nexport type Config = z.infer<typeof configSchema>;\nexport type PartialConfig = z.infer<typeof partialConfigSchema>;\n\n/**\n * Deep partial type for Config\n */\nexport type DeepPartialConfig = {\n  library?: string;\n  logLevel?: LogLevel;\n  email?: string;\n  backup?: Partial<BackupConfig>;\n  watch?: Partial<WatchConfig>;\n  server?: Partial<ServerConfig>;\n  citation?: Partial<CitationConfig>;\n  pubmed?: Partial<PubmedConfig>;\n  fulltext?: Partial<Omit<FulltextConfig, \"sources\">> & {\n    sources?: Partial<FulltextConfig[\"sources\"]>;\n  };\n  attachments?: Partial<AttachmentsConfig>;\n  cli?: Partial<Omit<CliConfig, \"tui\" | \"edit\">> & {\n    tui?: Partial<TuiConfig>;\n    edit?: Partial<EditConfig>;\n  };\n  mcp?: Partial<McpConfig>;\n};\n\n/**\n * Normalize backup configuration from snake_case to camelCase\n */\nfunction normalizeBackupConfig(\n  backup: Partial<{\n    maxGenerations?: number;\n    max_generations?: number;\n    maxAgeDays?: number;\n    max_age_days?: number;\n    directory?: string;\n  }>\n): Partial<BackupConfig> | undefined {\n  const normalized: Partial<BackupConfig> = {};\n\n  const maxGenerations = backup.maxGenerations ?? backup.max_generations;\n  if (maxGenerations !== undefined) {\n    normalized.maxGenerations = maxGenerations;\n  }\n\n  const maxAgeDays = backup.maxAgeDays ?? backup.max_age_days;\n  if (maxAgeDays !== undefined) {\n    normalized.maxAgeDays = maxAgeDays;\n  }\n\n  if (backup.directory !== undefined) {\n    normalized.directory = backup.directory;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize watch configuration from snake_case to camelCase\n */\nfunction normalizeWatchConfig(\n  watch: Partial<{\n    debounceMs?: number;\n    debounce_ms?: number;\n    pollIntervalMs?: number;\n    poll_interval_ms?: number;\n    retryIntervalMs?: number;\n    retry_interval_ms?: number;\n    maxRetries?: number;\n    max_retries?: number;\n  }>\n): Partial<WatchConfig> | undefined {\n  const normalized: Partial<WatchConfig> = {};\n\n  const debounceMs = watch.debounceMs ?? watch.debounce_ms;\n  if (debounceMs !== undefined) {\n    normalized.debounceMs = debounceMs;\n  }\n\n  const pollIntervalMs = watch.pollIntervalMs ?? watch.poll_interval_ms;\n  if (pollIntervalMs !== undefined) {\n    normalized.pollIntervalMs = pollIntervalMs;\n  }\n\n  const retryIntervalMs = watch.retryIntervalMs ?? watch.retry_interval_ms;\n  if (retryIntervalMs !== undefined) {\n    normalized.retryIntervalMs = retryIntervalMs;\n  }\n\n  const maxRetries = watch.maxRetries ?? watch.max_retries;\n  if (maxRetries !== undefined) {\n    normalized.maxRetries = maxRetries;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize server configuration from snake_case to camelCase\n */\nfunction normalizeServerConfig(\n  server: Partial<{\n    autoStart?: boolean;\n    auto_start?: boolean;\n    autoStopMinutes?: number;\n    auto_stop_minutes?: number;\n  }>\n): Partial<ServerConfig> | undefined {\n  const normalized: Partial<ServerConfig> = {};\n\n  const autoStart = server.autoStart ?? server.auto_start;\n  if (autoStart !== undefined) {\n    normalized.autoStart = autoStart;\n  }\n\n  const autoStopMinutes = server.autoStopMinutes ?? server.auto_stop_minutes;\n  if (autoStopMinutes !== undefined) {\n    normalized.autoStopMinutes = autoStopMinutes;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize citation configuration from snake_case to camelCase\n */\nfunction normalizeCitationConfig(\n  citation: Partial<{\n    defaultStyle?: string;\n    default_style?: string;\n    cslDirectory?: string | string[];\n    csl_directory?: string | string[];\n    defaultLocale?: string;\n    default_locale?: string;\n    defaultFormat?: CitationFormat;\n    default_format?: CitationFormat;\n    defaultKeyFormat?: CitationKeyFormat;\n    default_key_format?: CitationKeyFormat;\n  }>\n): Partial<CitationConfig> | undefined {\n  const normalized: Partial<CitationConfig> = {};\n\n  const defaultStyle = citation.defaultStyle ?? citation.default_style;\n  if (defaultStyle !== undefined) {\n    normalized.defaultStyle = defaultStyle;\n  }\n\n  const cslDirectory = citation.cslDirectory ?? citation.csl_directory;\n  if (cslDirectory !== undefined) {\n    // Normalize to array: string -> [string]\n    normalized.cslDirectory = Array.isArray(cslDirectory) ? cslDirectory : [cslDirectory];\n  }\n\n  const defaultLocale = citation.defaultLocale ?? citation.default_locale;\n  if (defaultLocale !== undefined) {\n    normalized.defaultLocale = defaultLocale;\n  }\n\n  const defaultFormat = citation.defaultFormat ?? citation.default_format;\n  if (defaultFormat !== undefined) {\n    normalized.defaultFormat = defaultFormat;\n  }\n\n  const defaultKeyFormat =\n    (citation as Record<string, unknown>).defaultKeyFormat ??\n    (citation as Record<string, unknown>).default_key_format;\n  if (defaultKeyFormat !== undefined) {\n    normalized.defaultKeyFormat = defaultKeyFormat as CitationKeyFormat;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize pubmed configuration from snake_case to camelCase\n */\nfunction normalizePubmedConfig(\n  pubmed: Partial<{\n    email?: string;\n    apiKey?: string;\n    api_key?: string;\n  }>\n): Partial<PubmedConfig> | undefined {\n  const normalized: Partial<PubmedConfig> = {};\n\n  if (pubmed.email !== undefined) {\n    normalized.email = pubmed.email;\n  }\n\n  const apiKey = pubmed.apiKey ?? pubmed.api_key;\n  if (apiKey !== undefined) {\n    normalized.apiKey = apiKey;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize fulltext configuration from snake_case to camelCase\n */\nfunction normalizeFulltextConfig(\n  fulltext: Partial<{\n    preferSources?: FulltextSource[];\n    prefer_sources?: FulltextSource[];\n    preferredType?: FulltextPreferredType;\n    preferred_type?: FulltextPreferredType;\n    autoFetchOnAdd?: boolean;\n    auto_fetch_on_add?: boolean;\n    sources?: Partial<{\n      unpaywallEmail?: string;\n      unpaywall_email?: string;\n      coreApiKey?: string;\n      core_api_key?: string;\n    }>;\n  }>\n): DeepPartialConfig[\"fulltext\"] | undefined {\n  const normalized: NonNullable<DeepPartialConfig[\"fulltext\"]> = {};\n\n  const preferSources = fulltext.preferSources ?? fulltext.prefer_sources;\n  if (preferSources !== undefined) {\n    normalized.preferSources = preferSources;\n  }\n\n  const preferredType = fulltext.preferredType ?? fulltext.preferred_type;\n  if (preferredType !== undefined) {\n    normalized.preferredType = preferredType;\n  }\n\n  const autoFetchOnAdd = fulltext.autoFetchOnAdd ?? fulltext.auto_fetch_on_add;\n  if (autoFetchOnAdd !== undefined) {\n    normalized.autoFetchOnAdd = autoFetchOnAdd;\n  }\n\n  const sources = normalizeFulltextSources(fulltext.sources);\n  if (sources !== undefined) {\n    normalized.sources = sources;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\nfunction normalizeFulltextSources(\n  sources?: Partial<{\n    unpaywallEmail?: string;\n    unpaywall_email?: string;\n    coreApiKey?: string;\n    core_api_key?: string;\n    ncbiEmail?: string;\n    ncbi_email?: string;\n    ncbiTool?: string;\n    ncbi_tool?: string;\n  }>\n): Partial<FulltextConfig[\"sources\"]> | undefined {\n  if (sources === undefined) {\n    return undefined;\n  }\n\n  const normalized: Partial<FulltextConfig[\"sources\"]> = {};\n\n  const unpaywallEmail = sources.unpaywallEmail ?? sources.unpaywall_email;\n  if (unpaywallEmail !== undefined) {\n    normalized.unpaywallEmail = unpaywallEmail;\n  }\n\n  const coreApiKey = sources.coreApiKey ?? sources.core_api_key;\n  if (coreApiKey !== undefined) {\n    normalized.coreApiKey = coreApiKey;\n  }\n\n  const ncbiEmail = sources.ncbiEmail ?? sources.ncbi_email;\n  if (ncbiEmail !== undefined) {\n    normalized.ncbiEmail = ncbiEmail;\n  }\n\n  const ncbiTool = sources.ncbiTool ?? sources.ncbi_tool;\n  if (ncbiTool !== undefined) {\n    normalized.ncbiTool = ncbiTool;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Section normalizers mapping\n */\nconst sectionNormalizers = {\n  backup: normalizeBackupConfig,\n  watch: normalizeWatchConfig,\n  server: normalizeServerConfig,\n  citation: normalizeCitationConfig,\n  pubmed: normalizePubmedConfig,\n  fulltext: normalizeFulltextConfig,\n  attachments: normalizeAttachmentsConfig,\n  cli: normalizeCliConfig,\n  mcp: normalizeMcpConfig,\n} as const;\n\ntype SectionKey = keyof typeof sectionNormalizers;\n\n/**\n * Helper to apply a normalizer function to a config section\n */\nfunction applyNormalizer<K extends SectionKey>(\n  normalized: DeepPartialConfig,\n  partial: PartialConfig,\n  key: K,\n  normalizer: (typeof sectionNormalizers)[K]\n): void {\n  const value = partial[key];\n  if (value !== undefined) {\n    const result = (normalizer as (input: unknown) => DeepPartialConfig[K] | undefined)(value);\n    if (result) {\n      normalized[key] = result;\n    }\n  }\n}\n\n/**\n * Normalize snake_case fields to camelCase\n */\nexport function normalizePartialConfig(partial: PartialConfig): DeepPartialConfig {\n  const normalized: DeepPartialConfig = {};\n\n  // Simple fields\n  if (partial.library !== undefined) {\n    normalized.library = partial.library;\n  }\n  const logLevel = partial.logLevel ?? partial.log_level;\n  if (logLevel !== undefined) {\n    normalized.logLevel = logLevel;\n  }\n  if (partial.email !== undefined) {\n    normalized.email = partial.email;\n  }\n\n  // Section fields\n  for (const key of Object.keys(sectionNormalizers) as SectionKey[]) {\n    applyNormalizer(normalized, partial, key, sectionNormalizers[key]);\n  }\n\n  return normalized;\n}\n\n/**\n * Normalize attachments configuration\n */\nfunction normalizeAttachmentsConfig(attachments: {\n  directory?: string | undefined;\n}): Partial<AttachmentsConfig> | undefined {\n  const normalized: Partial<AttachmentsConfig> = {};\n\n  if (attachments.directory !== undefined) {\n    normalized.directory = attachments.directory;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize TUI config subsection\n */\nfunction normalizeTuiSection(\n  tui: Partial<{\n    limit?: number;\n    debounceMs?: number;\n    debounce_ms?: number;\n    clipboardAutoCopy?: boolean;\n    clipboard_auto_copy?: boolean;\n  }>\n): Partial<TuiConfig> | undefined {\n  const normalized: Partial<TuiConfig> = {};\n  if (tui.limit !== undefined) {\n    normalized.limit = tui.limit;\n  }\n  const debounceMs = tui.debounceMs ?? tui.debounce_ms;\n  if (debounceMs !== undefined) {\n    normalized.debounceMs = debounceMs;\n  }\n  const clipboardAutoCopy = tui.clipboardAutoCopy ?? tui.clipboard_auto_copy;\n  if (clipboardAutoCopy !== undefined) {\n    normalized.clipboardAutoCopy = clipboardAutoCopy;\n  }\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize edit config subsection\n */\nfunction normalizeEditSection(\n  edit: Partial<{\n    defaultFormat?: EditConfigFormat;\n    default_format?: EditConfigFormat;\n  }>\n): Partial<EditConfig> | undefined {\n  const normalized: Partial<EditConfig> = {};\n  const defaultFormat = edit.defaultFormat ?? edit.default_format;\n  if (defaultFormat !== undefined) {\n    normalized.defaultFormat = defaultFormat;\n  }\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize CLI configuration from snake_case to camelCase\n */\nfunction normalizeCliConfig(\n  cli: Partial<{\n    defaultLimit?: number;\n    default_limit?: number;\n    defaultSort?: CliConfig[\"defaultSort\"];\n    default_sort?: CliConfig[\"defaultSort\"];\n    defaultOrder?: CliConfig[\"defaultOrder\"];\n    default_order?: CliConfig[\"defaultOrder\"];\n    tui?: Partial<{\n      limit?: number;\n      debounceMs?: number;\n      debounce_ms?: number;\n    }>;\n    edit?: Partial<{\n      defaultFormat?: EditConfigFormat;\n      default_format?: EditConfigFormat;\n    }>;\n  }>\n): Partial<CliConfig> | undefined {\n  const normalized: Partial<CliConfig> = {};\n\n  const defaultLimit = cli.defaultLimit ?? cli.default_limit;\n  if (defaultLimit !== undefined) {\n    normalized.defaultLimit = defaultLimit;\n  }\n\n  const defaultSort = cli.defaultSort ?? cli.default_sort;\n  if (defaultSort !== undefined) {\n    normalized.defaultSort = defaultSort;\n  }\n\n  const defaultOrder = cli.defaultOrder ?? cli.default_order;\n  if (defaultOrder !== undefined) {\n    normalized.defaultOrder = defaultOrder;\n  }\n\n  if (cli.tui !== undefined) {\n    const tui = normalizeTuiSection(cli.tui);\n    if (tui) {\n      normalized.tui = tui as TuiConfig;\n    }\n  }\n\n  if (cli.edit !== undefined) {\n    const edit = normalizeEditSection(cli.edit);\n    if (edit) {\n      normalized.edit = edit as EditConfig;\n    }\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n\n/**\n * Normalize MCP configuration from snake_case to camelCase\n */\nfunction normalizeMcpConfig(\n  mcp: Partial<{\n    defaultLimit?: number;\n    default_limit?: number;\n  }>\n): Partial<McpConfig> | undefined {\n  const normalized: Partial<McpConfig> = {};\n\n  const defaultLimit = mcp.defaultLimit ?? mcp.default_limit;\n  if (defaultLimit !== undefined) {\n    normalized.defaultLimit = defaultLimit;\n  }\n\n  return Object.keys(normalized).length > 0 ? normalized : undefined;\n}\n","import path from 'node:path';\nimport os from 'node:os';\nimport process from 'node:process';\n\nconst homedir = os.homedir();\nconst tmpdir = os.tmpdir();\nconst {env} = process;\n\nconst macos = name => {\n\tconst library = path.join(homedir, 'Library');\n\n\treturn {\n\t\tdata: path.join(library, 'Application Support', name),\n\t\tconfig: path.join(library, 'Preferences', name),\n\t\tcache: path.join(library, 'Caches', name),\n\t\tlog: path.join(library, 'Logs', name),\n\t\ttemp: path.join(tmpdir, name),\n\t};\n};\n\nconst windows = name => {\n\tconst appData = env.APPDATA || path.join(homedir, 'AppData', 'Roaming');\n\tconst localAppData = env.LOCALAPPDATA || path.join(homedir, 'AppData', 'Local');\n\n\treturn {\n\t\t// Data/config/cache/log are invented by me as Windows isn't opinionated about this\n\t\tdata: path.join(localAppData, name, 'Data'),\n\t\tconfig: path.join(appData, name, 'Config'),\n\t\tcache: path.join(localAppData, name, 'Cache'),\n\t\tlog: path.join(localAppData, name, 'Log'),\n\t\ttemp: path.join(tmpdir, name),\n\t};\n};\n\n// https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html\nconst linux = name => {\n\tconst username = path.basename(homedir);\n\n\treturn {\n\t\tdata: path.join(env.XDG_DATA_HOME || path.join(homedir, '.local', 'share'), name),\n\t\tconfig: path.join(env.XDG_CONFIG_HOME || path.join(homedir, '.config'), name),\n\t\tcache: path.join(env.XDG_CACHE_HOME || path.join(homedir, '.cache'), name),\n\t\t// https://wiki.debian.org/XDGBaseDirectorySpecification#state\n\t\tlog: path.join(env.XDG_STATE_HOME || path.join(homedir, '.local', 'state'), name),\n\t\ttemp: path.join(tmpdir, username, name),\n\t};\n};\n\nexport default function envPaths(name, {suffix = 'nodejs'} = {}) {\n\tif (typeof name !== 'string') {\n\t\tthrow new TypeError(`Expected a string, got ${typeof name}`);\n\t}\n\n\tif (suffix) {\n\t\t// Add suffix to prevent possible conflict with native apps\n\t\tname += `-${suffix}`;\n\t}\n\n\tif (process.platform === 'darwin') {\n\t\treturn macos(name);\n\t}\n\n\tif (process.platform === 'win32') {\n\t\treturn windows(name);\n\t}\n\n\treturn linux(name);\n}\n","/**\n * Platform-specific paths using env-paths\n *\n * Returns XDG-compliant paths on Linux, standard paths on macOS/Windows\n */\n\nimport envPaths from \"env-paths\";\n\nconst paths = envPaths(\"reference-manager\", { suffix: \"\" });\n\nexport interface Paths {\n  config: string;\n  data: string;\n  cache: string;\n}\n\n/**\n * Get platform-specific paths for config, data, and cache directories\n *\n * - Linux: XDG Base Directory Specification (~/.config, ~/.local/share, ~/.cache)\n * - macOS: ~/Library/Preferences, ~/Library/Application Support, ~/Library/Caches\n * - Windows: %APPDATA%, %LOCALAPPDATA%\n */\nexport function getPaths(): Paths {\n  return {\n    config: paths.config,\n    data: paths.data,\n    cache: paths.cache,\n  };\n}\n","/**\n * Default configuration values\n */\n\nimport { join } from \"node:path\";\nimport { getPaths } from \"./paths.js\";\nimport type { Config } from \"./schema.js\";\n\n/**\n * Get the default backup directory\n * Uses platform-specific cache path + backups/\n */\nexport function getDefaultBackupDirectory(): string {\n  return join(getPaths().cache, \"backups\");\n}\n\n/**\n * Get the default library path\n * Uses platform-specific data path + library.json\n */\nexport function getDefaultLibraryPath(): string {\n  return join(getPaths().data, \"library.json\");\n}\n\n/**\n * Get the default user config path\n * Uses platform-specific config path + config.toml\n */\nexport function getDefaultUserConfigPath(): string {\n  return join(getPaths().config, \"config.toml\");\n}\n\n/**\n * Get the default current directory config filename\n * Uses .reference-manager.config.toml\n */\nexport function getDefaultCurrentDirConfigFilename(): string {\n  return \".reference-manager.config.toml\";\n}\n\n/**\n * Get the default CSL directory\n * Uses platform-specific data path + csl/\n */\nexport function getDefaultCslDirectory(): string {\n  return join(getPaths().data, \"csl\");\n}\n\n/**\n * Get the default attachments directory\n * Uses platform-specific data path + attachments/\n */\nexport function getDefaultAttachmentsDirectory(): string {\n  return join(getPaths().data, \"attachments\");\n}\n\n/**\n * Default configuration\n */\nexport const defaultConfig: Config = {\n  library: getDefaultLibraryPath(),\n  logLevel: \"info\",\n  email: undefined,\n  backup: {\n    maxGenerations: 50,\n    maxAgeDays: 365,\n    directory: getDefaultBackupDirectory(),\n  },\n  watch: {\n    debounceMs: 500,\n    pollIntervalMs: 5000,\n    retryIntervalMs: 200,\n    maxRetries: 10,\n  },\n  server: {\n    autoStart: false,\n    autoStopMinutes: 0,\n  },\n  citation: {\n    defaultStyle: \"apa\",\n    cslDirectory: [getDefaultCslDirectory()],\n    defaultLocale: \"en-US\",\n    defaultFormat: \"text\",\n    defaultKeyFormat: \"pandoc\",\n  },\n  pubmed: {\n    email: undefined,\n    apiKey: undefined,\n  },\n  fulltext: {\n    preferSources: [\"pmc\", \"arxiv\", \"unpaywall\", \"core\"],\n    preferredType: undefined,\n    autoFetchOnAdd: false,\n    sources: {\n      unpaywallEmail: undefined,\n      coreApiKey: undefined,\n      ncbiEmail: undefined,\n      ncbiTool: undefined,\n    },\n  },\n  attachments: {\n    directory: getDefaultAttachmentsDirectory(),\n  },\n  cli: {\n    defaultLimit: 0,\n    defaultSort: \"updated\",\n    defaultOrder: \"desc\",\n    tui: {\n      limit: 20,\n      debounceMs: 200,\n      clipboardAutoCopy: false,\n    },\n    edit: {\n      defaultFormat: \"yaml\",\n    },\n  },\n  mcp: {\n    defaultLimit: 20,\n  },\n};\n","/**\n * Configuration loader\n */\n\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { homedir } from \"node:os\";\nimport { join } from \"node:path\";\nimport { parse as parseTOML } from \"@iarna/toml\";\nimport {\n  defaultConfig,\n  getDefaultCurrentDirConfigFilename,\n  getDefaultUserConfigPath,\n} from \"./defaults.js\";\nimport {\n  type Config,\n  type DeepPartialConfig,\n  type PartialConfig,\n  configSchema,\n  normalizePartialConfig,\n  partialConfigSchema,\n} from \"./schema.js\";\n\n/**\n * Options for loading configuration\n */\nexport interface LoadConfigOptions {\n  /** Current working directory (default: process.cwd()) */\n  cwd?: string;\n  /** User config path (default: ~/.reference-manager/config.toml) */\n  userConfigPath?: string;\n  /** CLI --config flag: explicit config file path (highest file priority) */\n  configPath?: string;\n  /** CLI argument overrides */\n  overrides?: Partial<Config>;\n}\n\n/**\n * Load and parse a TOML config file\n */\nfunction loadTOMLFile(path: string): PartialConfig | null {\n  if (!existsSync(path)) {\n    return null;\n  }\n\n  try {\n    const content = readFileSync(path, \"utf-8\");\n    const parsed = parseTOML(content);\n\n    // Validate with partial schema\n    const validated = partialConfigSchema.parse(parsed);\n    return validated;\n  } catch (error) {\n    throw new Error(\n      `Failed to load config from ${path}: ${error instanceof Error ? error.message : String(error)}`\n    );\n  }\n}\n\n/**\n * Merge CLI config with nested interactive section\n */\nfunction mergeCliConfig(\n  base: DeepPartialConfig[\"cli\"],\n  override: NonNullable<DeepPartialConfig[\"cli\"]>\n): NonNullable<DeepPartialConfig[\"cli\"]> {\n  const { tui: overrideTui, ...overrideCliRest } = override;\n  const { tui: baseTui, ...baseCliRest } = base ?? {};\n  const mergedTui = overrideTui !== undefined ? { ...baseTui, ...overrideTui } : baseTui;\n  return {\n    ...baseCliRest,\n    ...overrideCliRest,\n    ...(mergedTui !== undefined ? { tui: mergedTui } : {}),\n  };\n}\n\n/**\n * Merge fulltext config with nested sources section\n */\nfunction mergeFulltextConfig(\n  base: DeepPartialConfig[\"fulltext\"],\n  override: NonNullable<DeepPartialConfig[\"fulltext\"]>\n): NonNullable<DeepPartialConfig[\"fulltext\"]> {\n  const { sources: overrideSources, ...overrideRest } = override;\n  const { sources: baseSources, ...baseRest } = base ?? {};\n  const mergedSources =\n    overrideSources !== undefined ? { ...baseSources, ...overrideSources } : baseSources;\n  return {\n    ...baseRest,\n    ...overrideRest,\n    ...(mergedSources !== undefined ? { sources: mergedSources } : {}),\n  };\n}\n\nconst flatSectionKeys = [\n  \"backup\",\n  \"watch\",\n  \"server\",\n  \"citation\",\n  \"pubmed\",\n  \"attachments\",\n  \"mcp\",\n] as const;\n\n/**\n * Apply a single override to the result config\n */\nfunction applyOverride(result: DeepPartialConfig, override: DeepPartialConfig): void {\n  // Merge top-level primitive fields\n  if (override.library !== undefined) {\n    result.library = override.library;\n  }\n  if (override.logLevel !== undefined) {\n    result.logLevel = override.logLevel;\n  }\n  if (override.email !== undefined) {\n    result.email = override.email;\n  }\n\n  // Merge flat section configs\n  for (const key of flatSectionKeys) {\n    if (override[key] !== undefined) {\n      result[key] = {\n        ...result[key],\n        ...override[key],\n      };\n    }\n  }\n\n  // Merge nested section configs\n  if (override.fulltext !== undefined) {\n    result.fulltext = mergeFulltextConfig(result.fulltext, override.fulltext);\n  }\n  if (override.cli !== undefined) {\n    result.cli = mergeCliConfig(result.cli, override.cli);\n  }\n}\n\n/**\n * Merge partial configurations\n * Later configs override earlier ones\n */\nfunction mergeConfigs(\n  base: DeepPartialConfig,\n  ...overrides: (DeepPartialConfig | null | undefined)[]\n): DeepPartialConfig {\n  const result: DeepPartialConfig = { ...base };\n\n  for (const override of overrides) {\n    if (!override) continue;\n    applyOverride(result, override);\n  }\n\n  return result;\n}\n\n/**\n * Fill missing fields with defaults\n */\nfunction fillDefaults(partial: DeepPartialConfig): Config {\n  const envLibrary = process.env.REFERENCE_MANAGER_LIBRARY;\n  const library = envLibrary ?? partial.library ?? defaultConfig.library;\n  const email = process.env.EMAIL ?? partial.email ?? defaultConfig.email;\n  return {\n    library: expandTilde(library),\n    logLevel: partial.logLevel ?? defaultConfig.logLevel,\n    email,\n    backup: {\n      maxGenerations: partial.backup?.maxGenerations ?? defaultConfig.backup.maxGenerations,\n      maxAgeDays: partial.backup?.maxAgeDays ?? defaultConfig.backup.maxAgeDays,\n      directory: partial.backup?.directory ?? defaultConfig.backup.directory,\n    },\n    watch: {\n      debounceMs: partial.watch?.debounceMs ?? defaultConfig.watch.debounceMs,\n      pollIntervalMs: partial.watch?.pollIntervalMs ?? defaultConfig.watch.pollIntervalMs,\n      retryIntervalMs: partial.watch?.retryIntervalMs ?? defaultConfig.watch.retryIntervalMs,\n      maxRetries: partial.watch?.maxRetries ?? defaultConfig.watch.maxRetries,\n    },\n    server: {\n      autoStart: partial.server?.autoStart ?? defaultConfig.server.autoStart,\n      autoStopMinutes: partial.server?.autoStopMinutes ?? defaultConfig.server.autoStopMinutes,\n    },\n    citation: fillCitationDefaults(partial.citation),\n    pubmed: fillPubmedDefaults(partial.pubmed, email),\n    fulltext: fillFulltextDefaults(partial.fulltext, email),\n    attachments: fillAttachmentsDefaults(partial.attachments),\n    cli: fillCliDefaults(partial.cli),\n    mcp: fillMcpDefaults(partial.mcp),\n  };\n}\n\n/**\n * Fill citation config with defaults\n */\nfunction fillCitationDefaults(partial: DeepPartialConfig[\"citation\"]): Config[\"citation\"] {\n  return {\n    defaultStyle: partial?.defaultStyle ?? defaultConfig.citation.defaultStyle,\n    cslDirectory: partial?.cslDirectory ?? defaultConfig.citation.cslDirectory,\n    defaultLocale: partial?.defaultLocale ?? defaultConfig.citation.defaultLocale,\n    defaultFormat: partial?.defaultFormat ?? defaultConfig.citation.defaultFormat,\n    defaultKeyFormat: partial?.defaultKeyFormat ?? defaultConfig.citation.defaultKeyFormat,\n  };\n}\n\n/**\n * Fill pubmed config with defaults\n * Environment variables take priority over config file values\n */\nfunction fillPubmedDefaults(\n  partial: DeepPartialConfig[\"pubmed\"],\n  fallbackEmail?: string\n): Config[\"pubmed\"] {\n  // Priority: PUBMED_EMAIL env > pubmed.email config > EMAIL env / top-level email > undefined\n  const email =\n    process.env.PUBMED_EMAIL ?? partial?.email ?? fallbackEmail ?? defaultConfig.pubmed.email;\n  const apiKey = process.env.PUBMED_API_KEY ?? partial?.apiKey ?? defaultConfig.pubmed.apiKey;\n\n  return {\n    email,\n    apiKey,\n  };\n}\n\n/**\n * Fill fulltext config with defaults\n * Environment variables take priority over config file values\n */\nfunction fillFulltextDefaults(\n  partial: DeepPartialConfig[\"fulltext\"],\n  fallbackEmail?: string\n): Config[\"fulltext\"] {\n  // Priority: service-specific env > service-specific config > EMAIL env / top-level email > undefined\n  const unpaywallEmail =\n    process.env.UNPAYWALL_EMAIL ??\n    partial?.sources?.unpaywallEmail ??\n    fallbackEmail ??\n    defaultConfig.fulltext.sources.unpaywallEmail;\n  const coreApiKey =\n    process.env.CORE_API_KEY ??\n    partial?.sources?.coreApiKey ??\n    defaultConfig.fulltext.sources.coreApiKey;\n  const ncbiEmail =\n    process.env.NCBI_EMAIL ??\n    partial?.sources?.ncbiEmail ??\n    fallbackEmail ??\n    defaultConfig.fulltext.sources.ncbiEmail;\n  const ncbiTool =\n    process.env.NCBI_TOOL ?? partial?.sources?.ncbiTool ?? defaultConfig.fulltext.sources.ncbiTool;\n\n  const envPreferredType = process.env.REFERENCE_MANAGER_FULLTEXT_PREFERRED_TYPE;\n  if (\n    envPreferredType !== undefined &&\n    envPreferredType !== \"pdf\" &&\n    envPreferredType !== \"markdown\"\n  ) {\n    throw new Error(\n      `Invalid value for REFERENCE_MANAGER_FULLTEXT_PREFERRED_TYPE: \"${envPreferredType}\". Must be \"pdf\" or \"markdown\".`\n    );\n  }\n  const preferredType =\n    envPreferredType ?? partial?.preferredType ?? defaultConfig.fulltext.preferredType;\n\n  return {\n    preferSources: partial?.preferSources ?? defaultConfig.fulltext.preferSources,\n    preferredType,\n    autoFetchOnAdd: partial?.autoFetchOnAdd ?? defaultConfig.fulltext.autoFetchOnAdd,\n    sources: {\n      unpaywallEmail,\n      coreApiKey,\n      ncbiEmail,\n      ncbiTool,\n    },\n  };\n}\n\n/**\n * Expand ~ to home directory\n */\nfunction expandTilde(path: string): string {\n  if (path.startsWith(\"~/\")) {\n    return join(homedir(), path.slice(2));\n  }\n  return path;\n}\n\n/**\n * Fill attachments config with defaults\n *\n * Priority:\n * 1. Environment variable REFERENCE_MANAGER_ATTACHMENTS_DIR\n * 2. Config file setting\n * 3. Default value\n */\nfunction fillAttachmentsDefaults(partial: DeepPartialConfig[\"attachments\"]): Config[\"attachments\"] {\n  const envDir = process.env.REFERENCE_MANAGER_ATTACHMENTS_DIR;\n  const directory = envDir ?? partial?.directory ?? defaultConfig.attachments.directory;\n  return {\n    directory: expandTilde(directory),\n  };\n}\n\n/**\n * Fill CLI config with defaults\n *\n * Priority:\n * 1. Environment variable REFERENCE_MANAGER_CLI_DEFAULT_LIMIT\n * 2. Config file setting\n * 3. Default value\n */\nfunction fillCliDefaults(partial: DeepPartialConfig[\"cli\"]): Config[\"cli\"] {\n  const envLimit = process.env.REFERENCE_MANAGER_CLI_DEFAULT_LIMIT;\n  const defaultLimit =\n    envLimit !== undefined\n      ? Number(envLimit)\n      : (partial?.defaultLimit ?? defaultConfig.cli.defaultLimit);\n  const envClipboard = process.env.REFERENCE_MANAGER_CLIPBOARD_AUTO_COPY;\n  const clipboardAutoCopy =\n    envClipboard !== undefined\n      ? envClipboard === \"1\" || envClipboard === \"true\"\n      : (partial?.tui?.clipboardAutoCopy ?? defaultConfig.cli.tui.clipboardAutoCopy);\n  return {\n    defaultLimit,\n    defaultSort: partial?.defaultSort ?? defaultConfig.cli.defaultSort,\n    defaultOrder: partial?.defaultOrder ?? defaultConfig.cli.defaultOrder,\n    tui: {\n      limit: partial?.tui?.limit ?? defaultConfig.cli.tui.limit,\n      debounceMs: partial?.tui?.debounceMs ?? defaultConfig.cli.tui.debounceMs,\n      clipboardAutoCopy,\n    },\n    edit: {\n      defaultFormat: partial?.edit?.defaultFormat ?? defaultConfig.cli.edit.defaultFormat,\n    },\n  };\n}\n\n/**\n * Fill MCP config with defaults\n *\n * Priority:\n * 1. Environment variable REFERENCE_MANAGER_MCP_DEFAULT_LIMIT\n * 2. Config file setting\n * 3. Default value\n */\nfunction fillMcpDefaults(partial: DeepPartialConfig[\"mcp\"]): Config[\"mcp\"] {\n  const envLimit = process.env.REFERENCE_MANAGER_MCP_DEFAULT_LIMIT;\n  const defaultLimit =\n    envLimit !== undefined\n      ? Number(envLimit)\n      : (partial?.defaultLimit ?? defaultConfig.mcp.defaultLimit);\n  return {\n    defaultLimit,\n  };\n}\n\n/**\n * Load configuration from multiple sources\n *\n * Priority (highest to lowest):\n * 1. CLI argument overrides\n * 2. CLI --config file (configPath)\n * 3. Current directory config (.reference-manager.config.toml)\n * 4. Environment variable (REFERENCE_MANAGER_CONFIG)\n * 5. User config (~/.reference-manager/config.toml)\n * 6. Default values\n */\nexport function loadConfig(options: LoadConfigOptions = {}): Config {\n  const cwd = options.cwd ?? process.cwd();\n  const userConfigPath = options.userConfigPath ?? getDefaultUserConfigPath();\n\n  // If configPath is specified, it must exist (explicit user intent)\n  if (options.configPath && !existsSync(options.configPath)) {\n    throw new Error(`Config file not found: ${options.configPath}`);\n  }\n\n  // 1. Load user config (lowest priority)\n  const userConfig = loadTOMLFile(userConfigPath);\n\n  // 2. Load environment variable config\n  const envConfigPath = process.env.REFERENCE_MANAGER_CONFIG;\n  const envConfig = envConfigPath ? loadTOMLFile(envConfigPath) : null;\n\n  // 3. Load current directory config\n  const currentConfigPath = join(cwd, getDefaultCurrentDirConfigFilename());\n  const currentConfig = loadTOMLFile(currentConfigPath);\n\n  // 4. Load CLI --config file (highest file priority)\n  const cliConfig = options.configPath ? loadTOMLFile(options.configPath) : null;\n\n  // Normalize snake_case to camelCase\n  const normalizedUser = userConfig ? normalizePartialConfig(userConfig) : null;\n  const normalizedEnv = envConfig ? normalizePartialConfig(envConfig) : null;\n  const normalizedCurrent = currentConfig ? normalizePartialConfig(currentConfig) : null;\n  const normalizedCli = cliConfig ? normalizePartialConfig(cliConfig) : null;\n\n  // Merge configs (priority: cli > current > env > user > defaults)\n  const merged = mergeConfigs(\n    {},\n    normalizedUser,\n    normalizedEnv,\n    normalizedCurrent,\n    normalizedCli,\n    options.overrides as DeepPartialConfig\n  );\n\n  // Fill missing fields with defaults\n  const config = fillDefaults(merged);\n\n  // Validate final config\n  try {\n    return configSchema.parse(config);\n  } catch (error) {\n    throw new Error(\n      `Invalid configuration: ${error instanceof Error ? error.message : String(error)}`\n    );\n  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package/dist/chunks/pubmed-client-J18fg3fG.js

@@ -0,0 +1,51 @@
+import { g as getRateLimiter } from "./index-D2HsxXnK.js";
+const PUBMED_ESUMMARY_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi";
+function buildEsummaryUrl(pmid, config) {
+  const url = new URL(PUBMED_ESUMMARY_BASE);
+  url.searchParams.set("db", "pubmed");
+  url.searchParams.set("id", pmid);
+  url.searchParams.set("retmode", "json");
+  if (config?.email) {
+    url.searchParams.set("email", config.email);
+  }
+  if (config?.apiKey) {
+    url.searchParams.set("api_key", config.apiKey);
+  }
+  return url.toString();
+}
+async function queryPubmed(pmid, config) {
+  const rateLimiterConfig = config?.apiKey ? { pubmedApiKey: config.apiKey } : {};
+  const rateLimiter = getRateLimiter("pubmed", rateLimiterConfig);
+  await rateLimiter.acquire();
+  try {
+    const url = buildEsummaryUrl(pmid, config);
+    const response = await fetch(url);
+    if (!response.ok) {
+      return {
+        success: false,
+        error: `PubMed API returned ${response.status} ${response.statusText}`
+      };
+    }
+    const data = await response.json();
+    const resultObj = data.result;
+    const articleData = resultObj?.[pmid];
+    if (!articleData) {
+      return { success: true, isRetracted: false, hasConcern: false };
+    }
+    const pubTypes = articleData.pubtype ?? [];
+    const isRetracted = pubTypes.some(
+      (t) => t === "Retracted Publication" || t === "Retraction of Publication"
+    );
+    const hasConcern = pubTypes.some((t) => t === "Expression of Concern");
+    return { success: true, isRetracted, hasConcern };
+  } catch (error) {
+    return {
+      success: false,
+      error: error instanceof Error ? error.message : String(error)
+    };
+  }
+}
+export {
+  queryPubmed
+};
+//# sourceMappingURL=pubmed-client-J18fg3fG.js.map

package/dist/chunks/pubmed-client-J18fg3fG.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pubmed-client-J18fg3fG.js","sources":["../../src/features/check/pubmed-client.ts"],"sourcesContent":["import { getRateLimiter } from \"../import/rate-limiter.js\";\n\nconst PUBMED_ESUMMARY_BASE = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi\";\n\nexport type PubmedResult =\n  | { success: true; isRetracted: boolean; hasConcern: boolean }\n  | { success: false; error: string };\n\n/**\n * Build PubMed E-utilities esummary URL.\n */\nfunction buildEsummaryUrl(pmid: string, config?: { email?: string; apiKey?: string }): string {\n  const url = new URL(PUBMED_ESUMMARY_BASE);\n  url.searchParams.set(\"db\", \"pubmed\");\n  url.searchParams.set(\"id\", pmid);\n  url.searchParams.set(\"retmode\", \"json\");\n  if (config?.email) {\n    url.searchParams.set(\"email\", config.email);\n  }\n  if (config?.apiKey) {\n    url.searchParams.set(\"api_key\", config.apiKey);\n  }\n  return url.toString();\n}\n\n/**\n * Query PubMed E-utilities for publication status of a PMID.\n *\n * @param pmid - The PubMed ID to query\n * @param config - Optional PubMed config (email, apiKey)\n * @returns PubMed result with retraction status\n */\nexport async function queryPubmed(\n  pmid: string,\n  config?: { email?: string; apiKey?: string }\n): Promise<PubmedResult> {\n  const rateLimiterConfig = config?.apiKey ? { pubmedApiKey: config.apiKey } : {};\n  const rateLimiter = getRateLimiter(\"pubmed\", rateLimiterConfig);\n  await rateLimiter.acquire();\n\n  try {\n    const url = buildEsummaryUrl(pmid, config);\n    const response = await fetch(url);\n\n    if (!response.ok) {\n      return {\n        success: false,\n        error: `PubMed API returned ${response.status} ${response.statusText}`,\n      };\n    }\n\n    const data = (await response.json()) as Record<string, unknown>;\n    const resultObj = data.result as Record<string, unknown> | undefined;\n    const articleData = resultObj?.[pmid] as Record<string, unknown> | undefined;\n\n    if (!articleData) {\n      return { success: true, isRetracted: false, hasConcern: false };\n    }\n\n    const pubTypes = (articleData.pubtype ?? []) as string[];\n    const isRetracted = pubTypes.some(\n      (t) => t === \"Retracted Publication\" || t === \"Retraction of Publication\"\n    );\n    const hasConcern = pubTypes.some((t) => t === \"Expression of Concern\");\n\n    return { success: true, isRetracted, hasConcern };\n  } catch (error) {\n    return {\n      success: false,\n      error: error instanceof Error ? error.message : String(error),\n    };\n  }\n}\n"],"names":[],"mappings":";AAEA,MAAM,uBAAuB;AAS7B,SAAS,iBAAiB,MAAc,QAAsD;AAC5F,QAAM,MAAM,IAAI,IAAI,oBAAoB;AACxC,MAAI,aAAa,IAAI,MAAM,QAAQ;AACnC,MAAI,aAAa,IAAI,MAAM,IAAI;AAC/B,MAAI,aAAa,IAAI,WAAW,MAAM;AACtC,MAAI,QAAQ,OAAO;AACjB,QAAI,aAAa,IAAI,SAAS,OAAO,KAAK;AAAA,EAC5C;AACA,MAAI,QAAQ,QAAQ;AAClB,QAAI,aAAa,IAAI,WAAW,OAAO,MAAM;AAAA,EAC/C;AACA,SAAO,IAAI,SAAA;AACb;AASA,eAAsB,YACpB,MACA,QACuB;AACvB,QAAM,oBAAoB,QAAQ,SAAS,EAAE,cAAc,OAAO,OAAA,IAAW,CAAA;AAC7E,QAAM,cAAc,eAAe,UAAU,iBAAiB;AAC9D,QAAM,YAAY,QAAA;AAElB,MAAI;AACF,UAAM,MAAM,iBAAiB,MAAM,MAAM;AACzC,UAAM,WAAW,MAAM,MAAM,GAAG;AAEhC,QAAI,CAAC,SAAS,IAAI;AAChB,aAAO;AAAA,QACL,SAAS;AAAA,QACT,OAAO,uBAAuB,SAAS,MAAM,IAAI,SAAS,UAAU;AAAA,MAAA;AAAA,IAExE;AAEA,UAAM,OAAQ,MAAM,SAAS,KAAA;AAC7B,UAAM,YAAY,KAAK;AACvB,UAAM,cAAc,YAAY,IAAI;AAEpC,QAAI,CAAC,aAAa;AAChB,aAAO,EAAE,SAAS,MAAM,aAAa,OAAO,YAAY,MAAA;AAAA,IAC1D;AAEA,UAAM,WAAY,YAAY,WAAW,CAAA;AACzC,UAAM,cAAc,SAAS;AAAA,MAC3B,CAAC,MAAM,MAAM,2BAA2B,MAAM;AAAA,IAAA;AAEhD,UAAM,aAAa,SAAS,KAAK,CAAC,MAAM,MAAM,uBAAuB;AAErE,WAAO,EAAE,SAAS,MAAM,aAAa,WAAA;AAAA,EACvC,SAAS,OAAO;AACd,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO,iBAAiB,QAAQ,MAAM,UAAU,OAAO,KAAK;AAAA,IAAA;AAAA,EAEhE;AACF;"}

package/dist/chunks/{reference-select-CrOVXP7v.js → reference-select-Qpgt9cbN.js}

@@ -1,8 +1,8 @@
 import { t as tokenize, s as search } from "./file-watcher-Dlx0PolG.js";
 import { render, useApp } from "ink";
 import { createElement } from "react";
-import { r as restoreStdinAfterInk } from "./index-ChvsE9WF.js";
-import { t as toChoice, c as calculateEffectiveLimit, S as SearchableMultiSelect } from "./SearchableMultiSelect-BigM9xv_.js";
+import { r as restoreStdinAfterInk } from "./index-QTYx5RaF.js";
+import { t as toChoice, c as calculateEffectiveLimit, S as SearchableMultiSelect } from "./SearchableMultiSelect-B7qEWPDT.js";
 import { checkTTY } from "./tty-BMyaEOhX.js";
 function SearchPromptApp({
   choices,
@@ -126,4 +126,4 @@ export {
   selectReferenceItemsOrExit,
   selectReferencesOrExit
 };
-//# sourceMappingURL=reference-select-CrOVXP7v.js.map
+//# sourceMappingURL=reference-select-Qpgt9cbN.js.map

package/dist/chunks/{reference-select-CrOVXP7v.js.map → reference-select-Qpgt9cbN.js.map}

@@ -1 +1 @@
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wraps SearchableMultiSelect for search prompt\n */\nfunction SearchPromptApp({\n  choices,\n  filterFn,\n  visibleCount,\n  defaultSort,\n  onSubmit,\n  onCancel,\n}: SearchPromptAppProps): React.ReactElement {\n  const { exit } = useApp();\n\n  const handleSubmit = (selected: Choice<CslItem>[]): void => {\n    onSubmit(selected);\n    exit();\n  };\n\n  const handleCancel = (): void => {\n    onCancel();\n    exit();\n  };\n\n  return createElement(SearchableMultiSelect<CslItem>, {\n    choices,\n    filterFn,\n    visibleCount,\n    onSubmit: handleSubmit,\n    onCancel: handleCancel,\n    header: \"Search references\",\n    placeholder: \"Type to search...\",\n    defaultSort,\n  });\n}\n\n/**\n * Creates and runs an interactive search prompt\n */\nexport async function runSearchPrompt(\n  allReferences: CslItem[],\n  searchFn: SearchFunction,\n  config: SearchPromptConfig,\n  _initialQuery = \"\" // kept for API compatibility, not used in Ink version\n): Promise<SearchPromptResult> {\n  // Convert references to choices\n  const choices = allReferences.map(toChoice);\n\n  // Calculate effective visible count\n  const effectiveLimit = calculateEffectiveLimit(config.limit);\n\n  // Create filter function using the provided search function\n  const filterFn = (query: string, choices: Choice<CslItem>[]): Choice<CslItem>[] => {\n    if (!query.trim()) return choices;\n\n    const results = searchFn(query);\n    return results.map((r) => toChoice(r.reference));\n  };\n\n  // Create a promise to capture the result\n  return new Promise<SearchPromptResult>((resolve) => {\n    let result: SearchPromptResult = { selected: [], cancelled: true };\n\n    const handleSubmit = (selected: Choice<CslItem>[]): void => {\n      result = {\n        selected: selected.map((c) => c.value),\n        cancelled: false,\n      };\n    };\n\n    const handleCancel = (): void => {\n      result = {\n        selected: [],\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app\n    const { waitUntilExit, clear } = render(\n      createElement(SearchPromptApp, {\n        choices,\n        filterFn,\n        visibleCount: effectiveLimit,\n        defaultSort: \"updated-desc\",\n        onSubmit: handleSubmit,\n        onCancel: handleCancel,\n      })\n    );\n\n    // Wait for the app to exit, clear the screen, then resolve\n    waitUntilExit()\n      .then(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve(result);\n      })\n      .catch(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve({\n          selected: [],\n          cancelled: true,\n        });\n      });\n  });\n}\n","/**\n * Shared reference selection utility for interactive ID selection.\n *\n * This module provides a reusable function to select references interactively\n * using the existing search prompt infrastructure.\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { search } from \"../search/matcher.js\";\nimport { tokenize } from \"../search/tokenizer.js\";\nimport { type SearchPromptConfig, runSearchPrompt } from \"./search-prompt.js\";\nimport { checkTTY } from \"./tty.js\";\n\n/**\n * Options for reference selection\n */\nexport interface ReferenceSelectOptions {\n  /** Whether to allow multiple selection (default: true) */\n  multiSelect: boolean;\n  /** Custom prompt message */\n  prompt?: string;\n  /** Initial search query */\n  initialQuery?: string;\n}\n\n/**\n * Result from reference selection\n */\nexport interface ReferenceSelectResult {\n  /** Selected references */\n  selected: CslItem[];\n  /** Whether the selection was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Run interactive reference selection.\n *\n * Launches an interactive search prompt to select references from the library.\n * Supports both single and multiple selection modes.\n *\n * @param allReferences - 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+{"version":3,"file":"reference-select-Qpgt9cbN.js","sources":["../../src/features/interactive/search-prompt.ts","../../src/features/interactive/reference-select.ts"],"sourcesContent":["/**\n * Interactive search prompt using React Ink\n *\n * Provides real-time incremental search with multiple selection support.\n */\n\nimport { render, useApp } from \"ink\";\nimport type React from \"react\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { SearchResult } from \"../search/types.js\";\nimport { restoreStdinAfterInk } from \"./alternate-screen.js\";\nimport { toChoice } from \"./choice-builder.js\";\nimport {\n  type Choice,\n  SearchableMultiSelect,\n  type SortOption,\n  calculateEffectiveLimit,\n  getTerminalHeight,\n  getTerminalWidth,\n} from \"./components/index.js\";\n\n/**\n * Configuration for the search prompt\n */\nexport interface SearchPromptConfig {\n  /** Maximum number of results to display */\n  limit: number;\n  /** Debounce delay in milliseconds (not used in Ink version, kept for API compatibility) */\n  debounceMs: number;\n}\n\n/**\n * Search function type for filtering references\n */\nexport type SearchFunction = (query: string) => SearchResult[];\n\n/**\n * Result from the search prompt\n */\nexport interface SearchPromptResult {\n  /** Selected references */\n  selected: CslItem[];\n  /** Whether the prompt was cancelled */\n  cancelled: boolean;\n}\n\nexport { calculateEffectiveLimit, getTerminalHeight, getTerminalWidth };\n\n/**\n * Props for the SearchPromptApp component\n */\ninterface SearchPromptAppProps {\n  choices: Choice<CslItem>[];\n  filterFn: (query: string, choices: Choice<CslItem>[]) => Choice<CslItem>[];\n  visibleCount: number;\n  defaultSort: SortOption;\n  onSubmit: (selected: Choice<CslItem>[]) => void;\n  onCancel: () => void;\n}\n\n/**\n * SearchPromptApp component - wraps SearchableMultiSelect for search prompt\n */\nfunction SearchPromptApp({\n  choices,\n  filterFn,\n  visibleCount,\n  defaultSort,\n  onSubmit,\n  onCancel,\n}: SearchPromptAppProps): React.ReactElement {\n  const { exit } = useApp();\n\n  const handleSubmit = (selected: Choice<CslItem>[]): void => {\n    onSubmit(selected);\n    exit();\n  };\n\n  const handleCancel = (): void => {\n    onCancel();\n    exit();\n  };\n\n  return createElement(SearchableMultiSelect<CslItem>, {\n    choices,\n    filterFn,\n    visibleCount,\n    onSubmit: handleSubmit,\n    onCancel: handleCancel,\n    header: \"Search references\",\n    placeholder: \"Type to search...\",\n    defaultSort,\n  });\n}\n\n/**\n * Creates and runs an interactive search prompt\n */\nexport async function runSearchPrompt(\n  allReferences: CslItem[],\n  searchFn: SearchFunction,\n  config: SearchPromptConfig,\n  _initialQuery = \"\" // kept for API compatibility, not used in Ink version\n): Promise<SearchPromptResult> {\n  // Convert references to choices\n  const choices = allReferences.map(toChoice);\n\n  // Calculate effective visible count\n  const effectiveLimit = calculateEffectiveLimit(config.limit);\n\n  // Create filter function using the provided search function\n  const filterFn = (query: string, choices: Choice<CslItem>[]): Choice<CslItem>[] => {\n    if (!query.trim()) return choices;\n\n    const results = searchFn(query);\n    return results.map((r) => toChoice(r.reference));\n  };\n\n  // Create a promise to capture the result\n  return new Promise<SearchPromptResult>((resolve) => {\n    let result: SearchPromptResult = { selected: [], cancelled: true };\n\n    const handleSubmit = (selected: Choice<CslItem>[]): void => {\n      result = {\n        selected: selected.map((c) => c.value),\n        cancelled: false,\n      };\n    };\n\n    const handleCancel = (): void => {\n      result = {\n        selected: [],\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app\n    const { waitUntilExit, clear } = render(\n      createElement(SearchPromptApp, {\n        choices,\n        filterFn,\n        visibleCount: effectiveLimit,\n        defaultSort: \"updated-desc\",\n        onSubmit: handleSubmit,\n        onCancel: handleCancel,\n      })\n    );\n\n    // Wait for the app to exit, clear the screen, then resolve\n    waitUntilExit()\n      .then(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve(result);\n      })\n      .catch(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve({\n          selected: [],\n          cancelled: true,\n        });\n      });\n  });\n}\n","/**\n * Shared reference selection utility for interactive ID selection.\n *\n * This module provides a reusable function to select references interactively\n * using the existing search prompt infrastructure.\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { search } from \"../search/matcher.js\";\nimport { tokenize } from \"../search/tokenizer.js\";\nimport { type SearchPromptConfig, runSearchPrompt } from \"./search-prompt.js\";\nimport { checkTTY } from \"./tty.js\";\n\n/**\n * Options for reference selection\n */\nexport interface ReferenceSelectOptions {\n  /** Whether to allow multiple selection (default: true) */\n  multiSelect: boolean;\n  /** Custom prompt message */\n  prompt?: string;\n  /** Initial search query */\n  initialQuery?: string;\n}\n\n/**\n * Result from reference selection\n */\nexport interface ReferenceSelectResult {\n  /** Selected references */\n  selected: CslItem[];\n  /** Whether the selection was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Run interactive reference selection.\n *\n * Launches an interactive search prompt to select references from the library.\n * Supports both single and multiple selection modes.\n *\n * @param allReferences - All references available for selection\n * @param options - Selection options\n * @param config - Interactive prompt configuration\n * @returns Selection result with selected references\n * @throws TTYError if not running in a TTY environment\n */\nexport async function runReferenceSelect(\n  allReferences: CslItem[],\n  options: ReferenceSelectOptions,\n  config: SearchPromptConfig\n): Promise<ReferenceSelectResult> {\n  // Check TTY requirement\n  checkTTY();\n\n  // Create search function for runSearchPrompt\n  const searchFn = (query: string) => {\n    const { tokens } = tokenize(query);\n    return search(allReferences, tokens);\n  };\n\n  // Run search prompt\n  const searchResult = await runSearchPrompt(\n    allReferences,\n    searchFn,\n    config,\n    options.initialQuery ?? \"\"\n  );\n\n  if (searchResult.cancelled) {\n    return { selected: [], cancelled: true };\n  }\n\n  // For single-select mode, return only the first selected item\n  const selected = options.multiSelect ? searchResult.selected : searchResult.selected.slice(0, 1);\n\n  return {\n    selected,\n    cancelled: false,\n  };\n}\n\n/**\n * Options for selectReferencesOrExit helper\n */\nexport interface SelectReferencesOrExitOptions {\n  /** Whether to allow multiple selection */\n  multiSelect: boolean;\n  /** Initial search query */\n  initialQuery?: string;\n}\n\n/**\n * Select references interactively or exit if cancelled/empty.\n *\n * This is a convenience wrapper around runReferenceSelect that handles\n * common patterns:\n * - Exits with code 0 if library is empty\n * - Exits with code 0 if selection is cancelled\n * - Returns selected identifiers\n *\n * @param allReferences - All references available for selection\n * @param options - Selection options\n * @param config - Interactive prompt configuration\n * @returns Array of selected reference IDs (never empty)\n */\nexport async function selectReferencesOrExit(\n  allReferences: CslItem[],\n  options: SelectReferencesOrExitOptions,\n  config: SearchPromptConfig\n): Promise<string[]> {\n  if (allReferences.length === 0) {\n    process.stderr.write(\"No references in library.\\n\");\n    process.exit(0);\n  }\n\n  const selectResult = await runReferenceSelect(allReferences, options, config);\n\n  if (selectResult.cancelled || selectResult.selected.length === 0) {\n    process.exit(0);\n  }\n\n  return selectResult.selected.map((item) => item.id);\n}\n\n/**\n * Select reference items interactively or exit if cancelled/empty.\n *\n * Similar to selectReferencesOrExit but returns full CslItem objects\n * instead of just identifiers. 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package/dist/chunks/{style-select-BVP0KQz4.js → style-select-mEMoWbM2.js}

@@ -2,8 +2,8 @@ import * as fs from "node:fs";
 import * as path from "node:path";
 import "ink";
 import "react";
-import { B as BUILTIN_STYLES } from "./index-DWAtvFtp.js";
-import "./index-ChvsE9WF.js";
+import { B as BUILTIN_STYLES } from "./index-D2HsxXnK.js";
+import "./index-QTYx5RaF.js";
 function expandTilde(filePath) {
   if (filePath.startsWith("~/")) {
     const home = process.env.HOME || process.env.USERPROFILE || "";
@@ -58,4 +58,4 @@ export {
   buildStyleChoices,
   listCustomStyles
 };
-//# sourceMappingURL=style-select-BVP0KQz4.js.map
+//# sourceMappingURL=style-select-mEMoWbM2.js.map

package/dist/chunks/{style-select-BVP0KQz4.js.map → style-select-mEMoWbM2.js.map}

@@ -1 +1 @@
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cslDirectory : [cslDirectory];\n  const styles = new Set<string>();\n\n  for (const dir of directories) {\n    const expandedDir = expandTilde(dir);\n\n    if (!fs.existsSync(expandedDir)) {\n      continue;\n    }\n\n    try {\n      const files = fs.readdirSync(expandedDir);\n      for (const file of files) {\n        if (file.endsWith(\".csl\")) {\n          styles.add(file.slice(0, -4)); // Remove .csl extension\n        }\n      }\n    } catch {\n      // Ignore read errors\n    }\n  }\n\n  return Array.from(styles).sort();\n}\n\n/**\n * Build style choices for the selection prompt.\n *\n * @param customStyles - Custom style names from csl_directory\n * @param defaultStyle - Default style to show first\n * @returns Array of SelectOption for Ink Select prompt\n */\nexport function buildStyleChoices(\n  customStyles: string[],\n  defaultStyle = \"apa\"\n): SelectOption<string>[] {\n  const choices: SelectOption<string>[] = [];\n  const addedStyles = new Set<string>();\n\n  // Helper to add a style choice\n  const addChoice = (styleName: string, isDefault: boolean): void => {\n    if (addedStyles.has(styleName)) return;\n    addedStyles.add(styleName);\n\n    choices.push({\n      label: isDefault ? `${styleName} (default)` : styleName,\n      value: styleName,\n    });\n  };\n\n  // Add default style first\n  addChoice(defaultStyle, true);\n\n  // Add built-in styles\n  for (const style of BUILTIN_STYLES) {\n    addChoice(style, false);\n  }\n\n  // Add custom styles (excluding any that match built-in names)\n  for (const style of customStyles) {\n    addChoice(style, false);\n  }\n\n  return choices;\n}\n\n/**\n * Props for the StyleSelectApp component\n */\ninterface StyleSelectAppProps {\n  options: SelectOption<string>[];\n  onSelect: (value: string) => void;\n  onCancel: () => void;\n}\n\n/**\n * StyleSelectApp component - wraps Select for style selection\n */\nfunction StyleSelectApp({ options, onSelect, onCancel }: StyleSelectAppProps): React.ReactElement {\n  const { exit } = useApp();\n\n  const handleSelect = (value: string): void => {\n    onSelect(value);\n    exit();\n  };\n\n  const handleCancel = (): void => {\n    onCancel();\n    exit();\n  };\n\n  return createElement(Select<string>, {\n    options,\n    message: \"Select citation style:\",\n    onSelect: handleSelect,\n    onCancel: handleCancel,\n  });\n}\n\n/**\n * Run the style selection prompt.\n *\n * @param options - Style selection options\n * @returns Selection result with style name\n */\nexport async function runStyleSelect(options: StyleSelectOptions): Promise<StyleSelectResult> {\n  // List custom styles from csl_directory\n  const customStyles = listCustomStyles(options.cslDirectory);\n\n  // Build choices with default first\n  const choices = buildStyleChoices(customStyles, options.defaultStyle);\n\n  // Create a promise to capture the result\n  return new Promise<StyleSelectResult>((resolve) => {\n    let result: StyleSelectResult = { cancelled: true };\n\n    const handleSelect = (value: string): void => {\n      result = {\n        style: value,\n        cancelled: false,\n      };\n    };\n\n    const handleCancel = (): void => {\n      result = {\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app\n    const { waitUntilExit, clear } = render(\n      createElement(StyleSelectApp, {\n        options: choices,\n        onSelect: handleSelect,\n        onCancel: handleCancel,\n      })\n    );\n\n    // Wait for the app to exit, clear the screen, then resolve\n    waitUntilExit()\n      .then(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve(result);\n      })\n      .catch(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve({\n          cancelled: true,\n        });\n      });\n  });\n}\n"],"names":[],"mappings":";;;;;;AAuCA,SAAS,YAAY,UAA0B;AAC7C,MAAI,SAAS,WAAW,IAAI,GAAG;AAC7B,UAAM,OAAO,QAAQ,IAAI,QAAQ,QAAQ,IAAI,eAAe;AAC5D,WAAO,KAAK,KAAK,MAAM,SAAS,MAAM,CAAC,CAAC;AAAA,EAC1C;AACA,SAAO;AACT;AAQO,SAAS,iBAAiB,cAAuD;AACtF,MAAI,CAAC,cAAc;AACjB,WAAO,CAAA;AAAA,EACT;AAEA,QAAM,cAAc,MAAM,QAAQ,YAAY,IAAI,eAAe,CAAC,YAAY;AAC9E,QAAM,6BAAa,IAAA;AAEnB,aAAW,OAAO,aAAa;AAC7B,UAAM,cAAc,YAAY,GAAG;AAEnC,QAAI,CAAC,GAAG,WAAW,WAAW,GAAG;AAC/B;AAAA,IACF;AAEA,QAAI;AACF,YAAM,QAAQ,GAAG,YAAY,WAAW;AACxC,iBAAW,QAAQ,OAAO;AACxB,YAAI,KAAK,SAAS,MAAM,GAAG;AACzB,iBAAO,IAAI,KAAK,MAAM,GAAG,EAAE,CAAC;AAAA,QAC9B;AAAA,MACF;AAAA,IACF,QAAQ;AAAA,IAER;AAAA,EACF;AAEA,SAAO,MAAM,KAAK,MAAM,EAAE,KAAA;AAC5B;AASO,SAAS,kBACd,cACA,eAAe,OACS;AACxB,QAAM,UAAkC,CAAA;AACxC,QAAM,kCAAkB,IAAA;AAGxB,QAAM,YAAY,CAAC,WAAmB,cAA6B;AACjE,QAAI,YAAY,IAAI,SAAS,EAAG;AAChC,gBAAY,IAAI,SAAS;AAEzB,YAAQ,KAAK;AAAA,MACX,OAAO,YAAY,GAAG,SAAS,eAAe;AAAA,MAC9C,OAAO;AAAA,IAAA,CACR;AAAA,EACH;AAGA,YAAU,cAAc,IAAI;AAG5B,aAAW,SAAS,gBAAgB;AAClC,cAAU,OAAO,KAAK;AAAA,EACxB;AAGA,aAAW,SAAS,cAAc;AAChC,cAAU,OAAO,KAAK;AAAA,EACxB;AAEA,SAAO;AACT;"}
+{"version":3,"file":"style-select-mEMoWbM2.js","sources":["../../src/features/interactive/style-select.ts"],"sourcesContent":["/**\n * Style selection prompt for citation style selection.\n *\n * Lists built-in styles and custom styles from csl_directory,\n * with the default style shown first.\n */\n\nimport * as fs from \"node:fs\";\nimport * as path from \"node:path\";\nimport { render, useApp } from \"ink\";\nimport { createElement } from \"react\";\nimport type React from \"react\";\nimport { BUILTIN_STYLES } from \"../../config/csl-styles.js\";\nimport { restoreStdinAfterInk } from \"./alternate-screen.js\";\nimport { Select, type SelectOption } from \"./components/index.js\";\n\n/**\n * Options for style selection\n */\nexport interface StyleSelectOptions {\n  /** Directory or directories containing custom CSL files */\n  cslDirectory?: string | string[];\n  /** Default style to show first */\n  defaultStyle?: string;\n}\n\n/**\n * Result from style selection\n */\nexport interface StyleSelectResult {\n  /** Selected style name */\n  style?: string;\n  /** Whether the selection was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Expand tilde (~) in path to home directory\n */\nfunction expandTilde(filePath: string): string {\n  if (filePath.startsWith(\"~/\")) {\n    const home = process.env.HOME || process.env.USERPROFILE || \"\";\n    return path.join(home, filePath.slice(2));\n  }\n  return filePath;\n}\n\n/**\n * List custom CSL style names from the specified directory/directories.\n *\n * @param cslDirectory - Directory or directories to search for CSL files\n * @returns Array of style names (without .csl extension)\n */\nexport function listCustomStyles(cslDirectory: string | string[] | undefined): string[] {\n  if (!cslDirectory) {\n    return [];\n  }\n\n  const directories = Array.isArray(cslDirectory) ? cslDirectory : [cslDirectory];\n  const styles = new Set<string>();\n\n  for (const dir of directories) {\n    const expandedDir = expandTilde(dir);\n\n    if (!fs.existsSync(expandedDir)) {\n      continue;\n    }\n\n    try {\n      const files = fs.readdirSync(expandedDir);\n      for (const file of files) {\n        if (file.endsWith(\".csl\")) {\n          styles.add(file.slice(0, -4)); // Remove .csl extension\n        }\n      }\n    } catch {\n      // Ignore read errors\n    }\n  }\n\n  return Array.from(styles).sort();\n}\n\n/**\n * Build style choices for the selection prompt.\n *\n * @param customStyles - Custom style names from csl_directory\n * @param defaultStyle - Default style to show first\n * @returns Array of SelectOption for Ink Select prompt\n */\nexport function buildStyleChoices(\n  customStyles: string[],\n  defaultStyle = \"apa\"\n): SelectOption<string>[] {\n  const choices: SelectOption<string>[] = [];\n  const addedStyles = new Set<string>();\n\n  // Helper to add a style choice\n  const addChoice = (styleName: string, isDefault: boolean): void => {\n    if (addedStyles.has(styleName)) return;\n    addedStyles.add(styleName);\n\n    choices.push({\n      label: isDefault ? `${styleName} (default)` : styleName,\n      value: styleName,\n    });\n  };\n\n  // Add default style first\n  addChoice(defaultStyle, true);\n\n  // Add built-in styles\n  for (const style of BUILTIN_STYLES) {\n    addChoice(style, false);\n  }\n\n  // Add custom styles (excluding any that match built-in names)\n  for (const style of customStyles) {\n    addChoice(style, false);\n  }\n\n  return choices;\n}\n\n/**\n * Props for the StyleSelectApp component\n */\ninterface StyleSelectAppProps {\n  options: SelectOption<string>[];\n  onSelect: (value: string) => void;\n  onCancel: () => void;\n}\n\n/**\n * StyleSelectApp component - wraps Select for style selection\n */\nfunction StyleSelectApp({ options, onSelect, onCancel }: StyleSelectAppProps): React.ReactElement {\n  const { exit } = useApp();\n\n  const handleSelect = (value: string): void => {\n    onSelect(value);\n    exit();\n  };\n\n  const handleCancel = (): void => {\n    onCancel();\n    exit();\n  };\n\n  return createElement(Select<string>, {\n    options,\n    message: \"Select citation style:\",\n    onSelect: handleSelect,\n    onCancel: handleCancel,\n  });\n}\n\n/**\n * Run the style selection prompt.\n *\n * @param options - Style selection options\n * @returns Selection result with style name\n */\nexport async function runStyleSelect(options: StyleSelectOptions): Promise<StyleSelectResult> {\n  // List custom styles from csl_directory\n  const customStyles = listCustomStyles(options.cslDirectory);\n\n  // Build choices with default first\n  const choices = buildStyleChoices(customStyles, options.defaultStyle);\n\n  // Create a promise to capture the result\n  return new Promise<StyleSelectResult>((resolve) => {\n    let result: StyleSelectResult = { cancelled: true };\n\n    const handleSelect = (value: string): void => {\n      result = {\n        style: value,\n        cancelled: false,\n      };\n    };\n\n    const handleCancel = (): void => {\n      result = {\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app\n    const { waitUntilExit, clear } = render(\n      createElement(StyleSelectApp, {\n        options: choices,\n        onSelect: handleSelect,\n        onCancel: handleCancel,\n      })\n    );\n\n    // Wait for the app to exit, clear the screen, then resolve\n    waitUntilExit()\n      .then(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve(result);\n      })\n      .catch(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve({\n          cancelled: true,\n        });\n      });\n  });\n}\n"],"names":[],"mappings":";;;;;;AAuCA,SAAS,YAAY,UAA0B;AAC7C,MAAI,SAAS,WAAW,IAAI,GAAG;AAC7B,UAAM,OAAO,QAAQ,IAAI,QAAQ,QAAQ,IAAI,eAAe;AAC5D,WAAO,KAAK,KAAK,MAAM,SAAS,MAAM,CAAC,CAAC;AAAA,EAC1C;AACA,SAAO;AACT;AAQO,SAAS,iBAAiB,cAAuD;AACtF,MAAI,CAAC,cAAc;AACjB,WAAO,CAAA;AAAA,EACT;AAEA,QAAM,cAAc,MAAM,QAAQ,YAAY,IAAI,eAAe,CAAC,YAAY;AAC9E,QAAM,6BAAa,IAAA;AAEnB,aAAW,OAAO,aAAa;AAC7B,UAAM,cAAc,YAAY,GAAG;AAEnC,QAAI,CAAC,GAAG,WAAW,WAAW,GAAG;AAC/B;AAAA,IACF;AAEA,QAAI;AACF,YAAM,QAAQ,GAAG,YAAY,WAAW;AACxC,iBAAW,QAAQ,OAAO;AACxB,YAAI,KAAK,SAAS,MAAM,GAAG;AACzB,iBAAO,IAAI,KAAK,MAAM,GAAG,EAAE,CAAC;AAAA,QAC9B;AAAA,MACF;AAAA,IACF,QAAQ;AAAA,IAER;AAAA,EACF;AAEA,SAAO,MAAM,KAAK,MAAM,EAAE,KAAA;AAC5B;AASO,SAAS,kBACd,cACA,eAAe,OACS;AACxB,QAAM,UAAkC,CAAA;AACxC,QAAM,kCAAkB,IAAA;AAGxB,QAAM,YAAY,CAAC,WAAmB,cAA6B;AACjE,QAAI,YAAY,IAAI,SAAS,EAAG;AAChC,gBAAY,IAAI,SAAS;AAEzB,YAAQ,KAAK;AAAA,MACX,OAAO,YAAY,GAAG,SAAS,eAAe;AAAA,MAC9C,OAAO;AAAA,IAAA,CACR;AAAA,EACH;AAGA,YAAU,cAAc,IAAI;AAG5B,aAAW,SAAS,gBAAgB;AAClC,cAAU,OAAO,KAAK;AAAA,EACxB;AAGA,aAAW,SAAS,cAAc;AAChC,cAAU,OAAO,KAAK;AAAA,EACxB;AAEA,SAAO;AACT;"}

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

@@ -0,0 +1,42 @@
+import type { Config } from "../../config/schema.js";
+import type { CslItem } from "../../core/csl-json/types.js";
+import type { CheckResult } from "../../features/check/types.js";
+import type { CheckOperationResult } from "../../features/operations/check.js";
+import { type ExecutionContext } from "../execution-context.js";
+export interface CheckCommandOptions {
+    identifiers: string[];
+    uuid?: boolean;
+    all?: boolean;
+    search?: string;
+    output?: "text" | "json";
+    full?: boolean;
+    noSave?: boolean;
+    days?: number;
+    fix?: boolean;
+}
+export type CheckCommandResult = CheckOperationResult;
+/**
+ * Execute check command.
+ */
+export declare function executeCheck(options: CheckCommandOptions, context: ExecutionContext, appConfig?: Config): Promise<CheckCommandResult>;
+/**
+ * Format check result as text output.
+ */
+export declare function formatCheckTextOutput(result: CheckOperationResult): string;
+export interface FormatCheckJsonOptions {
+    full?: boolean;
+    items?: Map<string, CslItem>;
+}
+/**
+ * Format check result as JSON output.
+ */
+export declare function formatCheckJsonOutput(result: CheckOperationResult, options?: FormatCheckJsonOptions): CheckOperationResult & {
+    results: (CheckResult & {
+        item?: CslItem;
+    })[];
+};
+/**
+ * Handle 'check' command action.
+ */
+export declare function handleCheckAction(identifiers: string[], options: Omit<CheckCommandOptions, "identifiers">, globalOpts: Record<string, unknown>): Promise<void>;
+//# sourceMappingURL=check.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/cli/commands/index.d.ts

@@ -13,6 +13,8 @@ export { executeUpdate, formatUpdateOutput } from "./update.js";
 export type { UpdateCommandOptions, UpdateCommandResult } from "./update.js";
 export { serverStart, serverStop, serverStatus } from "./server.js";
 export type { ServerStartOptions, ServerInfo } from "./server.js";
+export { executeCheck, formatCheckTextOutput, formatCheckJsonOutput, } from "./check.js";
+export type { CheckCommandOptions, CheckCommandResult } from "./check.js";
 export { executeCite, formatCiteOutput, formatCiteErrors, getCiteExitCode } from "./cite.js";
 export type { CiteCommandOptions, CiteCommandResult } from "./cite.js";
 export { executeFulltextAttach, executeFulltextGet, executeFulltextDetach, formatFulltextAttachOutput, formatFulltextGetOutput, formatFulltextDetachOutput, getFulltextExitCode, } from "./fulltext.js";

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

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package/dist/cli/help/search-help.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Builds the additional help text for the search command.
+ * Includes query syntax, field list, case sensitivity rules, and examples.
+ */
+export declare function buildSearchHelpText(): string;
+//# sourceMappingURL=search-help.d.ts.map

package/dist/cli/help/search-help.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/index.d.ts.map

@@ -1 +1 @@
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package/dist/cli/server-client.d.ts

@@ -1,6 +1,6 @@
 import type { CslItem } from "../core/csl-json/types.js";
 import type { FindOptions, RemoveResult as ILibraryRemoveResult, RemoveOptions, UpdateOptions, UpdateResult } from "../core/library-interface.js";
-import type { AddAttachmentOptions, AddAttachmentResult, AddReferencesResult, CiteResult, DetachAttachmentOptions, DetachAttachmentResult, GetAttachmentOptions, GetAttachmentResult, ILibraryOperations, ImportOptions, ListAttachmentsOptions, ListAttachmentsResult, ListOptions, ListResult, OpenAttachmentOptions, OpenAttachmentResult, SearchOperationOptions, SearchResult, SyncAttachmentOptions, SyncAttachmentResult } from "../features/operations/index.js";
+import type { AddAttachmentOptions, AddAttachmentResult, AddReferencesResult, CheckOperationOptions, CheckOperationResult, CiteResult, DetachAttachmentOptions, DetachAttachmentResult, GetAttachmentOptions, GetAttachmentResult, ILibraryOperations, ImportOptions, ListAttachmentsOptions, ListAttachmentsResult, ListOptions, ListResult, OpenAttachmentOptions, OpenAttachmentResult, SearchOperationOptions, SearchResult, SyncAttachmentOptions, SyncAttachmentResult } from "../features/operations/index.js";
 import type { IdentifierType } from "../core/library-interface.js";
 /**
  * Options for cite method.
@@ -64,6 +64,7 @@ export declare class ServerClient implements ILibraryOperations {
      * @returns Result containing added, failed, and skipped items
      */
     import(inputs: string[], options?: ImportOptions): Promise<AddReferencesResult>;
+    check(options: CheckOperationOptions): Promise<CheckOperationResult>;
     /**
      * Generate citations for references.
      * @param options - Cite options including identifiers and formatting

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

@@ -1 +1 @@
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package/dist/cli.js

@@ -1,5 +1,5 @@
 import "commander";
-import { c, m } from "./chunks/index-ChvsE9WF.js";
+import { c, m } from "./chunks/index-QTYx5RaF.js";
 import "./chunks/file-watcher-Dlx0PolG.js";
 export {
   c as createProgram,

package/dist/config/defaults.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"defaults.d.ts","sourceRoot":"","sources":["../../src/config/defaults.ts"],"names":[],"mappings":"AAAA;;GAEG;AAIH,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,aAAa,CAAC;AAE1C;;;GAGG;AACH,wBAAgB,yBAAyB,IAAI,MAAM,CAElD;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,IAAI,MAAM,CAE9C;AAED;;;GAGG;AACH,wBAAgB,wBAAwB,IAAI,MAAM,CAEjD;AAED;;;GAGG;AACH,wBAAgB,kCAAkC,IAAI,MAAM,CAE3D;AAED;;;GAGG;AACH,wBAAgB,sBAAsB,IAAI,MAAM,CAE/C;AAED;;;GAGG;AACH,wBAAgB,8BAA8B,IAAI,MAAM,CAEvD;AAED;;GAEG;AACH,eAAO,MAAM,aAAa,EAAE,MA4D3B,CAAC"}

package/dist/config/env-override.d.ts.map

@@ -1 +1 @@
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package/dist/config/key-parser.d.ts.map

@@ -1 +1 @@
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package/dist/config/loader.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"loader.d.ts","sourceRoot":"","sources":["../../src/config/loader.ts"],"names":[],"mappings":"AAAA;;GAEG;AAWH,OAAO,EACL,KAAK,MAAM,EAMZ,MAAM,aAAa,CAAC;AAErB;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,yDAAyD;IACzD,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,mEAAmE;IACnE,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,2EAA2E;IAC3E,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,6BAA6B;IAC7B,SAAS,CAAC,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;CAC7B;AA+TD;;;;;;;;;;GAUG;AACH,wBAAgB,UAAU,CAAC,OAAO,GAAE,iBAAsB,GAAG,MAAM,CAkDlE"}