@ncukondo/reference-manager 0.27.2 → 0.28.0

package/dist/chunks/{fix-interaction-BCtx4Q9F.js.map → fix-interaction-BR3VVyHq.js.map}

@@ -1 +1 @@
-{"version":3,"file":"fix-interaction-BCtx4Q9F.js","sources":["../../src/features/check/fix-actions.ts","../../src/features/check/fix-interaction.ts"],"sourcesContent":["import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport type { CheckFinding } from \"./types.js\";\n\nexport type FixActionType =\n  | \"add_retracted_tag\"\n  | \"add_retraction_note\"\n  | \"remove_from_library\"\n  | \"update_from_published\"\n  | \"add_version_tag\"\n  | \"add_concern_tag\"\n  | \"add_concern_note\"\n  | \"update_all_fields\"\n  | \"update_selected_fields\"\n  | \"skip\";\n\nexport interface FixAction {\n  type: FixActionType;\n  label: string;\n}\n\nexport interface FixActionResult {\n  applied: boolean;\n  message: string;\n  removed?: boolean;\n}\n\nexport function getFixActionsForFinding(finding: CheckFinding): FixAction[] {\n  switch (finding.type) {\n    case \"retracted\":\n      return [\n        { type: \"add_retracted_tag\", label: 'Add tag \"retracted\"' },\n        { type: \"add_retraction_note\", label: \"Add note with retraction details\" },\n        { type: \"remove_from_library\", label: \"Remove from library\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"version_changed\":\n      return [\n        { type: \"update_from_published\", label: \"Update metadata from published version\" },\n        { type: \"add_version_tag\", label: 'Add tag \"has-published-version\"' },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"concern\":\n      return [\n        { type: \"add_concern_tag\", label: 'Add tag \"expression-of-concern\"' },\n        { type: \"add_concern_note\", label: \"Add note with concern details\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"metadata_mismatch\":\n    case \"metadata_outdated\":\n      return [\n        { type: \"update_all_fields\", label: \"Update all changed fields from remote\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    default:\n      return [];\n  }\n}\n\nfunction addTag(item: CslItem, tag: string): string[] {\n  const existing = (item.custom?.tags as string[] | undefined) ?? [];\n  if (existing.includes(tag)) {\n    return existing;\n  }\n  return [...existing, tag];\n}\n\nfunction buildNoteText(prefix: string, finding: CheckFinding): string {\n  const parts = [prefix];\n  if (finding.details?.retractionDate) {\n    parts.push(`Date: ${finding.details.retractionDate}`);\n  }\n  if (finding.details?.retractionDoi) {\n    parts.push(`DOI: ${finding.details.retractionDoi}`);\n  }\n  return parts.join(\". \");\n}\n\nfunction appendNote(existingNote: string | undefined, newNote: string): string {\n  if (existingNote) {\n    return `${existingNote}\\n\\n${newNote}`;\n  }\n  return newNote;\n}\n\nasync function applyTagAction(\n  library: ILibrary,\n  item: CslItem,\n  tag: string\n): Promise<FixActionResult> {\n  const tags = addTag(item, tag);\n  await library.update(item.id, { custom: { ...item.custom, tags } } as Partial<CslItem>, {\n    idType: \"id\",\n  });\n  await library.save();\n  return { applied: true, message: `Added tag \"${tag}\"` };\n}\n\nasync function applyNoteAction(\n  library: ILibrary,\n  item: CslItem,\n  prefix: string,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const noteText = buildNoteText(prefix, finding);\n  const note = appendNote(item.note, noteText);\n  await library.update(item.id, { note } as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Added note: ${noteText}` };\n}\n\nasync function applyUpdateFromPublished(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const newDoi = finding.details?.newDoi;\n  if (!newDoi) {\n    return { applied: false, message: \"No published DOI available in finding details\" };\n  }\n  const { fetchDoi } = await import(\"../import/fetcher.js\");\n  const fetchResult = await fetchDoi(newDoi);\n  if (!fetchResult.success) {\n    return {\n      applied: false,\n      message: `Failed to fetch metadata for ${newDoi}: ${fetchResult.error}`,\n    };\n  }\n  const { id: _id, custom: _custom, ...metadata } = fetchResult.item;\n  await library.update(item.id, metadata as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Updated metadata from ${newDoi}` };\n}\n\nasync function applyUpdateAllFields(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  let fetchedItem: CslItem;\n\n  if (item.DOI) {\n    const { fetchDoi } = await import(\"../import/fetcher.js\");\n    const fetchResult = await fetchDoi(item.DOI);\n    if (!fetchResult.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for DOI ${item.DOI}: ${fetchResult.error}`,\n      };\n    }\n    fetchedItem = fetchResult.item;\n  } else if (item.PMID) {\n    const { fetchPmids } = await import(\"../import/fetcher.js\");\n    const results = await fetchPmids([item.PMID], {});\n    const result = results[0];\n    if (!result || !result.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for PMID ${item.PMID}: ${result?.error ?? \"unknown error\"}`,\n      };\n    }\n    fetchedItem = result.item;\n  } else {\n    return { applied: false, message: \"No DOI or PMID available for metadata update\" };\n  }\n\n  const updatedFields = finding.details?.updatedFields ?? 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API.\n    case \"update_selected_fields\":\n      return { applied: false, message: \"Field selection not available in CLI mode\" };\n\n    case \"skip\":\n      return { applied: true, message: \"Skipped\" };\n\n    default:\n      return { applied: false, message: `Unknown action: ${actionType}` };\n  }\n}\n","import { render } from \"ink\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { restoreStdinAfterInk } from \"../interactive/alternate-screen.js\";\nimport { Select } from \"../interactive/components/index.js\";\nimport type { SelectOption } from \"../interactive/components/index.js\";\nimport { type FixActionType, applyFixAction, getFixActionsForFinding } from \"./fix-actions.js\";\nimport type { CheckFinding, CheckResult } from \"./types.js\";\n\nexport interface FixInteractionResult {\n  totalFindings: number;\n  applied: number;\n  skipped: number;\n  removed: string[];\n}\n\nfunction selectFixAction(\n  message: string,\n  options: SelectOption<FixActionType>[]\n): Promise<FixActionType | null> {\n  return new Promise<FixActionType | null>((resolve) => {\n    let selected: FixActionType | null = null;\n\n    const { waitUntilExit } = render(\n      createElement(Select<FixActionType>, {\n        options,\n        message,\n        onSelect: (value: FixActionType) => {\n          selected = value;\n        },\n        onCancel: () => {\n          selected = null;\n        },\n      })\n    );\n\n    waitUntilExit()\n      .then(() => {\n        restoreStdinAfterInk();\n        resolve(selected);\n      })\n      .catch(() => {\n        restoreStdinAfterInk();\n        resolve(null);\n      });\n  });\n}\n\nfunction getStatusLabel(type: string): string {\n  switch (type) {\n    case \"retracted\":\n      return \"RETRACTED\";\n    case \"concern\":\n      return \"CONCERN\";\n    case \"version_changed\":\n      return 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selectedAction);\n\n  if (!actionResult.applied) {\n    process.stderr.write(`  Error: ${actionResult.message}\\n`);\n    return;\n  }\n\n  process.stderr.write(`  ${actionResult.message}\\n`);\n  if (selectedAction === \"skip\") {\n    result.skipped++;\n  } else {\n    result.applied++;\n    if (actionResult.removed) {\n      result.removed.push(resultId);\n    }\n  }\n}\n\nexport async function runFixInteraction(\n  results: CheckResult[],\n  library: ILibrary,\n  findItem: (id: string) => CslItem | undefined\n): Promise<FixInteractionResult> {\n  const interactionResult: FixInteractionResult = {\n    totalFindings: 0,\n    applied: 0,\n    skipped: 0,\n    removed: [],\n  };\n\n  const warningResults = results.filter((r) => r.status === \"warning\");\n\n  for (const checkResult of warningResults) {\n    const item = findItem(checkResult.id);\n    if (!item) continue;\n\n    for (const finding of checkResult.findings) {\n      await processFinding(interactionResult, library, item, 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API.\n    case \"update_selected_fields\":\n      return { applied: false, message: \"Field selection not available in CLI mode\" };\n\n    case \"skip\":\n      return { applied: true, message: \"Skipped\" };\n\n    default:\n      return { applied: false, message: `Unknown action: ${actionType}` };\n  }\n}\n","import { render } from \"ink\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { restoreStdinAfterInk } from \"../interactive/alternate-screen.js\";\nimport { Select } from \"../interactive/components/index.js\";\nimport type { SelectOption } from \"../interactive/components/index.js\";\nimport { type FixActionType, applyFixAction, getFixActionsForFinding } from \"./fix-actions.js\";\nimport type { CheckFinding, CheckResult } from \"./types.js\";\n\nexport interface FixInteractionResult {\n  totalFindings: number;\n  applied: number;\n  skipped: 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package/dist/chunks/{index-Cf5bYLrr.js → index-BP_TPa_d.js}

@@ -1,8 +1,8 @@
 import { useApp, Box, render } from "ink";
 import { useState, useEffect, createElement } from "react";
-import { getActionChoices, OUTPUT_FORMAT_CHOICES, STYLE_CHOICES, isSideEffectAction, generateOutput } from "./action-menu-Crcd5X1-.js";
-import { S as SearchableMultiSelect, t as toChoice$1, c as calculateEffectiveLimit, f as formatAuthors, a as formatIdentifiers } from "./SearchableMultiSelect-0cyizees.js";
-import { S as Select, r as restoreStdinAfterInk } from "./index-DkJT7s7N.js";
+import { getActionChoices, OUTPUT_FORMAT_CHOICES, STYLE_CHOICES, isSideEffectAction, generateOutput } from "./action-menu-CdJjcmdk.js";
+import { S as SearchableMultiSelect, t as toChoice$1, c as calculateEffectiveLimit, f as formatAuthors, a as formatIdentifiers } from "./SearchableMultiSelect-LIMpJm8A.js";
+import { S as Select, r as restoreStdinAfterInk } from "./index-C9Gc8dcm.js";
 function SearchFlowApp({
   choices,
   filterFn,
@@ -392,4 +392,4 @@ export {
   runCiteFlow,
   runSearchFlow
 };
-//# sourceMappingURL=index-Cf5bYLrr.js.map
+//# sourceMappingURL=index-BP_TPa_d.js.map

package/dist/chunks/{index-Cf5bYLrr.js.map → index-BP_TPa_d.js.map}

@@ -1 +1 @@
-{"version":3,"file":"index-Cf5bYLrr.js","sources":["../../src/features/interactive/apps/SearchFlowApp.tsx","../../src/features/interactive/apps/runSearchFlow.ts","../../src/features/interactive/apps/CiteFlowApp.tsx","../../src/features/interactive/apps/runCiteFlow.ts"],"sourcesContent":["/**\n * SearchFlowApp - Single App for search -t flow\n *\n * Manages state transitions: search → action → (style/output-format if needed)\n * Following React Ink Single App Pattern (ADR-015)\n */\n\nimport { Box, useApp } from \"ink\";\nimport type React from \"react\";\nimport { createElement, useEffect, useState } from \"react\";\nimport type { CitationKeyFormat } from \"../../../config/schema.js\";\nimport type { CslItem } from \"../../../core/csl-json/types.js\";\nimport {\n  type ActionMenuResult,\n  type ActionType,\n  OUTPUT_FORMAT_CHOICES,\n  type OutputFormatType,\n  STYLE_CHOICES,\n  generateOutput,\n  getActionChoices,\n  isSideEffectAction,\n} from \"../action-menu.js\";\nimport {\n  type 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Reference selection (SearchableMultiSelect)\n * 2. Style selection (Select) - optional\n * 3. Exit\n */\nexport function CiteFlowApp({\n  choices,\n  filterFn,\n  visibleCount,\n  defaultSort,\n  styleOptions,\n  showStyleSelect,\n  onComplete,\n  onCancel,\n}: CiteFlowAppProps): React.ReactElement {\n  const { exit } = useApp();\n  const [state, setState] = useState<FlowState>(\"search\");\n  const [selectedItems, setSelectedItems] = useState<CslItem[]>([]);\n  const [pendingResult, setPendingResult] = useState<CiteFlowResult | null>(null);\n\n  // Exit when entering \"exiting\" state\n  useEffect(() => {\n    if (state === \"exiting\" && pendingResult) {\n      exit();\n      if (pendingResult.cancelled) {\n        onCancel();\n      } else {\n        onComplete(pendingResult);\n      }\n    }\n  }, [state, pendingResult, exit, onCancel, onComplete]);\n\n  // Transition to exiting state with result\n  const exitWith = (result: CiteFlowResult) => {\n    setPendingResult(result);\n    setState(\"exiting\");\n  };\n\n  // Handle search submission\n  const handleSearchSubmit = (selected: Choice<CslItem>[]) => {\n    if (selected.length === 0) {\n      exitWith({ identifiers: [], cancelled: true });\n      return;\n    }\n    const items = selected.map((c) => c.value);\n    setSelectedItems(items);\n\n    if (showStyleSelect) {\n      setState(\"style\");\n    } else {\n      // No style selection needed, complete immediately\n      exitWith({\n        identifiers: items.map((item) => item.id),\n        cancelled: false,\n      });\n    }\n  };\n\n  // Handle search cancel\n  const handleSearchCancel = () => {\n    exitWith({ identifiers: [], cancelled: true });\n  };\n\n  // Handle style selection\n  const handleStyleSelect = (style: string) => {\n    exitWith({\n      identifiers: selectedItems.map((item) => item.id),\n      style,\n      cancelled: false,\n    });\n  };\n\n  // Handle style cancel (go back to search)\n  const handleStyleCancel = () => {\n    setState(\"search\");\n  };\n\n  // Render based on current state\n  if (state === \"exiting\") {\n 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\"../../search/types.js\";\nimport { restoreStdinAfterInk } from \"../alternate-screen.js\";\nimport { formatIdentifiers } from \"../choice-builder.js\";\nimport {\n  type Choice,\n  type SelectOption,\n  type SortOption,\n  calculateEffectiveLimit,\n} from \"../components/index.js\";\nimport { formatAuthors } from \"../format.js\";\nimport { CiteFlowApp, type CiteFlowResult } from \"./CiteFlowApp.js\";\n\n/**\n * Configuration for the cite flow\n */\nexport interface CiteFlowConfig {\n  /** Maximum number of results to display */\n  limit: number;\n}\n\n/**\n * Search function type for filtering references\n */\nexport type SearchFunction = (query: string) => SearchResult[];\n\n/**\n * Extract year from CSL item\n */\nfunction extractYear(item: CslItem): number | undefined {\n  const dateParts = item.issued?.[\"date-parts\"];\n  if (!dateParts || dateParts.length === 0) return undefined;\n  const firstDatePart = dateParts[0];\n  if (!firstDatePart || firstDatePart.length === 0) return 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Date | undefined {\n  const dateStr = item.custom?.created_at;\n  if (!dateStr || typeof dateStr !== \"string\") return undefined;\n  const date = new Date(dateStr);\n  return Number.isNaN(date.getTime()) ? undefined : date;\n}\n\n/**\n * Format item type for display\n */\nfunction formatType(type: string): string {\n  const typeMap: Record<string, string> = {\n    \"article-journal\": \"Journal article\",\n    \"article-magazine\": \"Magazine article\",\n    \"article-newspaper\": \"Newspaper article\",\n    book: \"Book\",\n    chapter: \"Book chapter\",\n    \"paper-conference\": \"Conference paper\",\n    thesis: \"Thesis\",\n    report: \"Report\",\n    webpage: \"Web page\",\n  };\n  return typeMap[type] ?? type;\n}\n\n/**\n * Convert CslItem to Choice for SearchableMultiSelect\n */\nfunction toChoice(item: CslItem): Choice<CslItem> {\n  const authors = formatAuthors(item.author);\n  const year = extractYear(item);\n  const identifiers = formatIdentifiers(item);\n  const itemType = formatType(item.type);\n\n  // Build meta line: Year · Type · Identifiers\n  const metaParts: string[] = [];\n  if (year) metaParts.push(String(year));\n  metaParts.push(itemType);\n  if (identifiers) metaParts.push(identifiers);\n\n  const updatedDate = extractUpdatedDate(item);\n  const createdDate = extractCreatedDate(item);\n  const publishedDate = extractPublishedDate(item);\n\n  return {\n    id: item.id,\n    title: item.title ?? \"(No title)\",\n    subtitle: authors || \"(No authors)\",\n    meta: metaParts.join(\" · \"),\n    value: item,\n    ...(updatedDate && { updatedDate }),\n    ...(createdDate && { createdDate }),\n    ...(publishedDate && { publishedDate }),\n  };\n}\n\n/**\n * Options for running the cite flow\n */\nexport interface RunCiteFlowOptions {\n  /** All references available for selection */\n  allReferences: CslItem[];\n  /** Search function for filtering */\n  searchFn: SearchFunction;\n  /** Flow configuration */\n  config: CiteFlowConfig;\n  /** Style options for style selection */\n  styleOptions: SelectOption<string>[];\n  /** Whether to show style selection */\n  showStyleSelect: boolean;\n}\n\n/**\n * Run the cite flow (reference selection → style selection if needed)\n *\n * This is the main entry point for interactive cite command.\n */\nexport async function runCiteFlow(options: RunCiteFlowOptions): Promise<CiteFlowResult> {\n  const { allReferences, searchFn, config, styleOptions, showStyleSelect } = options;\n\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  // Default sort option\n  const defaultSort: SortOption = \"updated-desc\";\n\n  // Create a promise to capture the result\n  return new Promise<CiteFlowResult>((resolve) => {\n    let flowResult: CiteFlowResult = {\n      identifiers: [],\n      cancelled: true,\n    };\n\n    const handleComplete = (result: CiteFlowResult): void => {\n      flowResult = result;\n    };\n\n    const handleCancel = (): void => {\n      flowResult = {\n        identifiers: [],\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app (single render for entire flow)\n    const { waitUntilExit } = render(\n      createElement(CiteFlowApp, {\n        choices,\n        filterFn,\n        visibleCount: effectiveLimit,\n        defaultSort,\n        styleOptions,\n        showStyleSelect,\n        onComplete: handleComplete,\n        onCancel: handleCancel,\n      })\n    );\n\n    // Wait for the app to exit, then resolve\n    waitUntilExit()\n      .then(() => {\n        restoreStdinAfterInk();\n        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Reference selection (SearchableMultiSelect)\n * 2. Style selection (Select) - optional\n * 3. Exit\n */\nexport function CiteFlowApp({\n  choices,\n  filterFn,\n  visibleCount,\n  defaultSort,\n  styleOptions,\n  showStyleSelect,\n  onComplete,\n  onCancel,\n}: CiteFlowAppProps): React.ReactElement {\n  const { exit } = useApp();\n  const [state, setState] = useState<FlowState>(\"search\");\n  const [selectedItems, setSelectedItems] = useState<CslItem[]>([]);\n  const [pendingResult, setPendingResult] = useState<CiteFlowResult | null>(null);\n\n  // Exit when entering \"exiting\" state\n  useEffect(() => {\n    if (state === \"exiting\" && pendingResult) {\n      exit();\n      if (pendingResult.cancelled) {\n        onCancel();\n      } else {\n        onComplete(pendingResult);\n      }\n    }\n  }, [state, pendingResult, exit, onCancel, onComplete]);\n\n  // Transition to exiting state with result\n  const exitWith = (result: CiteFlowResult) => {\n    setPendingResult(result);\n    setState(\"exiting\");\n  };\n\n  // Handle search submission\n  const handleSearchSubmit = (selected: Choice<CslItem>[]) => {\n    if (selected.length === 0) {\n      exitWith({ identifiers: [], cancelled: true });\n      return;\n    }\n    const items = selected.map((c) => c.value);\n    setSelectedItems(items);\n\n    if (showStyleSelect) {\n      setState(\"style\");\n    } else {\n      // No style selection needed, complete immediately\n      exitWith({\n        identifiers: items.map((item) => item.id),\n        cancelled: false,\n      });\n    }\n  };\n\n  // Handle search cancel\n  const handleSearchCancel = () => {\n    exitWith({ identifiers: [], cancelled: true });\n  };\n\n  // Handle style selection\n  const handleStyleSelect = (style: string) => {\n    exitWith({\n      identifiers: selectedItems.map((item) => item.id),\n      style,\n      cancelled: false,\n    });\n  };\n\n  // Handle style cancel (go back to search)\n  const handleStyleCancel = () => {\n    setState(\"search\");\n  };\n\n  // Render based on current state\n  if (state === \"exiting\") {\n 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\"../../search/types.js\";\nimport { restoreStdinAfterInk } from \"../alternate-screen.js\";\nimport { formatIdentifiers } from \"../choice-builder.js\";\nimport {\n  type Choice,\n  type SelectOption,\n  type SortOption,\n  calculateEffectiveLimit,\n} from \"../components/index.js\";\nimport { formatAuthors } from \"../format.js\";\nimport { CiteFlowApp, type CiteFlowResult } from \"./CiteFlowApp.js\";\n\n/**\n * Configuration for the cite flow\n */\nexport interface CiteFlowConfig {\n  /** Maximum number of results to display */\n  limit: number;\n}\n\n/**\n * Search function type for filtering references\n */\nexport type SearchFunction = (query: string) => SearchResult[];\n\n/**\n * Extract year from CSL item\n */\nfunction extractYear(item: CslItem): number | undefined {\n  const dateParts = item.issued?.[\"date-parts\"];\n  if (!dateParts || dateParts.length === 0) return undefined;\n  const firstDatePart = dateParts[0];\n  if (!firstDatePart || firstDatePart.length === 0) return 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Date | undefined {\n  const dateStr = item.custom?.created_at;\n  if (!dateStr || typeof dateStr !== \"string\") return undefined;\n  const date = new Date(dateStr);\n  return Number.isNaN(date.getTime()) ? undefined : date;\n}\n\n/**\n * Format item type for display\n */\nfunction formatType(type: string): string {\n  const typeMap: Record<string, string> = {\n    \"article-journal\": \"Journal article\",\n    \"article-magazine\": \"Magazine article\",\n    \"article-newspaper\": \"Newspaper article\",\n    book: \"Book\",\n    chapter: \"Book chapter\",\n    \"paper-conference\": \"Conference paper\",\n    thesis: \"Thesis\",\n    report: \"Report\",\n    webpage: \"Web page\",\n  };\n  return typeMap[type] ?? type;\n}\n\n/**\n * Convert CslItem to Choice for SearchableMultiSelect\n */\nfunction toChoice(item: CslItem): Choice<CslItem> {\n  const authors = formatAuthors(item.author);\n  const year = extractYear(item);\n  const identifiers = formatIdentifiers(item);\n  const itemType = formatType(item.type);\n\n  // Build meta line: Year · Type · Identifiers\n  const metaParts: string[] = [];\n  if (year) metaParts.push(String(year));\n  metaParts.push(itemType);\n  if (identifiers) metaParts.push(identifiers);\n\n  const updatedDate = extractUpdatedDate(item);\n  const createdDate = extractCreatedDate(item);\n  const publishedDate = extractPublishedDate(item);\n\n  return {\n    id: item.id,\n    title: item.title ?? \"(No title)\",\n    subtitle: authors || \"(No authors)\",\n    meta: metaParts.join(\" · \"),\n    value: item,\n    ...(updatedDate && { updatedDate }),\n    ...(createdDate && { createdDate }),\n    ...(publishedDate && { publishedDate }),\n  };\n}\n\n/**\n * Options for running the cite flow\n */\nexport interface RunCiteFlowOptions {\n  /** All references available for selection */\n  allReferences: CslItem[];\n  /** Search function for filtering */\n  searchFn: SearchFunction;\n  /** Flow configuration */\n  config: CiteFlowConfig;\n  /** Style options for style selection */\n  styleOptions: SelectOption<string>[];\n  /** Whether to show style selection */\n  showStyleSelect: boolean;\n}\n\n/**\n * Run the cite flow (reference selection → style selection if needed)\n *\n * This is the main entry point for interactive cite command.\n */\nexport async function runCiteFlow(options: RunCiteFlowOptions): Promise<CiteFlowResult> {\n  const { allReferences, searchFn, config, styleOptions, showStyleSelect } = options;\n\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  // Default sort option\n  const defaultSort: SortOption = \"updated-desc\";\n\n  // Create a promise to capture the result\n  return new Promise<CiteFlowResult>((resolve) => {\n    let flowResult: CiteFlowResult = {\n      identifiers: [],\n      cancelled: true,\n    };\n\n    const handleComplete = (result: CiteFlowResult): void => {\n      flowResult = result;\n    };\n\n    const handleCancel = (): void => {\n      flowResult = {\n        identifiers: [],\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app (single render for entire flow)\n    const { waitUntilExit } = render(\n      createElement(CiteFlowApp, {\n        choices,\n        filterFn,\n        visibleCount: effectiveLimit,\n        defaultSort,\n        styleOptions,\n        showStyleSelect,\n        onComplete: handleComplete,\n        onCancel: handleCancel,\n      })\n    );\n\n    // Wait for the app to exit, then resolve\n    waitUntilExit()\n      .then(() => {\n        restoreStdinAfterInk();\n        resolve(flowResult);\n      })\n      .catch(() => {\n        restoreStdinAfterInk();\n        resolve({\n          identifiers: [],\n          cancelled: true,\n        });\n      });\n  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package/dist/chunks/{index-DkJT7s7N.js → index-C9Gc8dcm.js}

@@ -1,13 +1,13 @@
 import { Command, Option } from "commander";
-import { i as isEqual, M as MANAGED_CUSTOM_FIELDS, w as writeFileAtomic, L as Library, h as CslItemSchema, p as pickDefined, a as sortOrderSchema, z as paginationOptionsSchema, F as FileWatcher, b as sortFieldSchema, y as searchSortFieldSchema } from "./file-watcher-Dlx0PolG.js";
+import { i as isEqual, M as MANAGED_CUSTOM_FIELDS, w as writeFileAtomic, L as Library, h as CslItemSchema, p as pickDefined, a as sortOrderSchema, z as paginationOptionsSchema, F as FileWatcher, b as sortFieldSchema, y as searchSortFieldSchema } from "./file-watcher-CWHg1yol.js";
 import * as fs from "node:fs";
 import { promises, readFileSync, existsSync, mkdirSync, writeFileSync } from "node:fs";
 import * as os from "node:os";
 import * as path from "node:path";
 import path__default, { join, basename, dirname } from "node:path";
-import { n as normalizePathForOutput, d as deleteDirectoryIfEmpty, p as parseFilename, i as isReservedRole, e as ensureDirectory, a as addAttachment, R as RESERVED_ROLES, b as generateFilename, c as findFulltextFiles, h as findFulltextFile, j as extensionToFormat, k as fulltextAttach, l as fulltextDiscover, m as fulltextFetch, o as fulltextConvert, q as fulltextGet, r as getExtension, s as getDefaultExportFromCjs, B as BUILTIN_STYLES, t as getFulltextAttachmentTypes, u as startServerWithFileWatcher } from "./index-BdLVfbj0.js";
+import { n as normalizePathForOutput, d as deleteDirectoryIfEmpty, p as parseFilename, i as isReservedRole, e as ensureDirectory, a as addAttachment, R as RESERVED_ROLES, b as generateFilename, c as findFulltextFiles, h as findFulltextFile, j as extensionToFormat, k as fulltextAttach, l as fulltextDiscover, m as fulltextFetch, o as fulltextConvert, q as fulltextGet, r as getExtension, s as getDefaultExportFromCjs, B as BUILTIN_STYLES, t as getFulltextAttachmentTypes, u as startServerWithFileWatcher } from "./index-T-edKSzd.js";
 import { readFile, unlink, stat, readdir, rename } from "node:fs/promises";
-import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-B-fte1uv.js";
+import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-B6sytmQd.js";
 import { spawn, spawnSync } from "node:child_process";
 import process$1, { stdin, stdout } from "node:process";
 import * as readline from "node:readline";
@@ -19,7 +19,7 @@ import "@citation-js/plugin-csl";
 import { ZodOptional as ZodOptional$2, z } from "zod";
 import { serve } from "@hono/node-server";
 const name = "@ncukondo/reference-manager";
-const version$1 = "0.27.2";
+const version$1 = "0.28.0";
 const description$1 = "A local reference management tool using CSL-JSON as the single source of truth";
 const packageJson = {
   name,
@@ -802,10 +802,9 @@ async function resolveDirectory(ref2, attachmentsDirectory) {
   }
   return { dirPath, directoryCreated };
 }
-async function updateDirectoryMetadata(library, ref2, dirPath) {
+async function updateDirectoryMetadata(library, item, dirPath) {
   const dirName = basename(dirPath);
-  const item = ref2;
-  await library.update(ref2.id, {
+  await library.update(item.id, {
     custom: {
       ...item.custom,
       attachments: {
@@ -860,7 +859,7 @@ async function openAttachment(library, options) {
   const attachments = ref2.custom?.attachments;
   const { dirPath, directoryCreated } = await resolveDirectory(ref2, attachmentsDirectory);
   if (directoryCreated && !attachments?.directory) {
-    await updateDirectoryMetadata(library, ref2, dirPath);
+    await updateDirectoryMetadata(library, item, dirPath);
   }
   const targetResult = await resolveTargetPath(dirPath, filename, role, attachments);
   if ("error" in targetResult) {
@@ -902,15 +901,15 @@ class OperationsLibrary {
   }
   // High-level operations
   async search(options) {
-    const { searchReferences } = await import("./index-BdLVfbj0.js").then((n) => n.E);
+    const { searchReferences } = await import("./index-T-edKSzd.js").then((n) => n.E);
     return searchReferences(this.library, options);
   }
   async list(options) {
-    const { listReferences } = await import("./index-BdLVfbj0.js").then((n) => n.D);
+    const { listReferences } = await import("./index-T-edKSzd.js").then((n) => n.D);
     return listReferences(this.library, options ?? {});
   }
   async cite(options) {
-    const { citeReferences } = await import("./index-BdLVfbj0.js").then((n) => n.C);
+    const { citeReferences } = await import("./index-T-edKSzd.js").then((n) => n.C);
     const defaultStyle = options.defaultStyle ?? this.citationConfig?.defaultStyle;
     const cslDirectory = options.cslDirectory ?? this.citationConfig?.cslDirectory;
     const mergedOptions = {
@@ -921,36 +920,36 @@ class OperationsLibrary {
     return citeReferences(this.library, mergedOptions);
   }
   async import(inputs, options) {
-    const { addReferences } = await import("./index-BdLVfbj0.js").then((n) => n.z);
+    const { addReferences } = await import("./index-T-edKSzd.js").then((n) => n.z);
     return addReferences(inputs, this.library, options ?? {});
   }
   async check(options) {
-    const { checkReferences } = await import("./index-BdLVfbj0.js").then((n) => n.A);
+    const { checkReferences } = await import("./index-T-edKSzd.js").then((n) => n.A);
     return checkReferences(this.library, options);
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-SwsAKyQr.js");
+    const { addAttachment: addAttachment2 } = await import("./index-CHe855EM.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-SwsAKyQr.js");
+    const { listAttachments: listAttachments2 } = await import("./index-CHe855EM.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-SwsAKyQr.js");
+    const { getAttachment: getAttachment2 } = await import("./index-CHe855EM.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-SwsAKyQr.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-CHe855EM.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-SwsAKyQr.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-CHe855EM.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-SwsAKyQr.js");
+    const { openAttachment: openAttachment2 } = await import("./index-CHe855EM.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1806,7 +1805,7 @@ function getAttachExitCode(result) {
 }
 async function executeInteractiveSelect$2(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B54Upu7p.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2471,7 +2470,7 @@ async function handleCheckAction(identifiers, options, globalOpts) {
     const jsonOptions = buildJsonOptionsFromRefs(options, outputFormat, result, allRefs);
     outputCheckResult(result, outputFormat, jsonOptions);
     if (options.fix && result.summary.warnings > 0 && allRefs) {
-      const { runFixInteraction } = await import("./fix-interaction-BCtx4Q9F.js");
+      const { runFixInteraction } = await import("./fix-interaction-BR3VVyHq.js");
       const findItem = (id2) => allRefs.find((item) => item.id === id2);
       const fixResult = await runFixInteraction(result.results, context.library, findItem);
       const removedSuffix = fixResult.removed.length > 0 ? `, ${fixResult.removed.length} removed` : "";
@@ -2539,7 +2538,7 @@ function outputCheckError(error, format2) {
 }
 async function selectReferencesInteractively(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-B54Upu7p.js");
   const allReferences = await context.library.getAll();
   if (allReferences.length === 0) {
     process.stderr.write("No references in library.\n");
@@ -2607,10 +2606,10 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-Cf5bYLrr.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-AvDsSnlB.js");
-  const { search } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.B);
-  const { tokenize } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.A);
+  const { runCiteFlow } = await import("./index-BP_TPa_d.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-BUwM-Azt.js");
+  const { search } = await import("./file-watcher-CWHg1yol.js").then((n) => n.B);
+  const { tokenize } = await import("./file-watcher-CWHg1yol.js").then((n) => n.A);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
   checkTTY();
   const allReferences = await context.library.getAll();
@@ -7209,7 +7208,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B54Upu7p.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10771,7 +10770,7 @@ function getFulltextExitCode(result) {
 }
 async function executeInteractiveSelect$1(context, config2, multiSelect = false) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B54Upu7p.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect }, config2.cli.tui)
@@ -11211,6 +11210,7 @@ function buildResourceIndicators(item) {
   return labels.join(" ");
 }
 function formatAuthor(author) {
+  if (author.literal) return author.literal;
   const family = author.family || "";
   const givenInitial = author.given ? `${author.given.charAt(0)}.` : "";
   return givenInitial ? `${family}, ${givenInitial}` : family;
@@ -32225,7 +32225,7 @@ async function mcpStart(options) {
 async function executeRemove(options, context) {
   const { identifier, idType = "id", fulltextDirectory, deleteFulltext = false } = options;
   if (context.mode === "local" && deleteFulltext && fulltextDirectory) {
-    const { removeReference } = await import("./index-BdLVfbj0.js").then((n) => n.x);
+    const { removeReference } = await import("./index-T-edKSzd.js").then((n) => n.x);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -32280,7 +32280,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-B54Upu7p.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32505,9 +32505,9 @@ async function executeInteractiveSearch(options, context, config2) {
   validateInteractiveOptions(options);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runSearchFlow } = await import("./index-Cf5bYLrr.js");
-  const { search } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.B);
-  const { tokenize } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.A);
+  const { runSearchFlow } = await import("./index-BP_TPa_d.js");
+  const { search } = await import("./file-watcher-CWHg1yol.js").then((n) => n.B);
+  const { tokenize } = await import("./file-watcher-CWHg1yol.js").then((n) => n.A);
   checkTTY();
   const allReferences = await context.library.getAll();
   const searchFn = (query) => {
@@ -32524,7 +32524,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-Crcd5X1-.js");
+    const { isSideEffectAction } = await import("./action-menu-CdJjcmdk.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32540,7 +32540,7 @@ async function executeSideEffectAction(action, items2, context, config2) {
   switch (action) {
     case "open-url": {
       const { resolveDefaultUrl: resolveDefaultUrl2 } = await Promise.resolve().then(() => url);
-      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-B-fte1uv.js").then((n) => n.j);
+      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-B6sytmQd.js").then((n) => n.j);
       const item = items2[0];
       if (!item) return;
       const url$1 = resolveDefaultUrl2(item);
@@ -32927,7 +32927,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B54Upu7p.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33222,7 +33222,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B54Upu7p.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33275,7 +33275,16 @@ const LIST_OUTPUT_FORMATS = ["pretty", "json", "bibtex", "ids", "uuid"];
 const MUTATION_OUTPUT_FORMATS = ["json", "text"];
 const CONFIG_OUTPUT_FORMATS = ["text", "json"];
 const LOG_LEVELS = ["silent", "info", "debug"];
-const ADD_INPUT_FORMATS = ["json", "bibtex", "ris", "pmid", "doi", "isbn", "auto"];
+const ADD_INPUT_FORMATS = [
+  "json",
+  "bibtex",
+  "ris",
+  "pmid",
+  "doi",
+  "isbn",
+  "arxiv",
+  "auto"
+];
 const CONFIG_SECTIONS = [
   "backup",
   "citation",
@@ -33770,7 +33779,7 @@ function shouldAutoFetch(cliFlag, configEnabled) {
   return configEnabled;
 }
 async function performAutoFetch(addedItems, context, config2) {
-  const { fulltextFetch: fulltextFetch2 } = await import("./index-BdLVfbj0.js").then((n) => n.w);
+  const { fulltextFetch: fulltextFetch2 } = await import("./index-T-edKSzd.js").then((n) => n.w);
   const fetchResults = await autoFetchFulltext(addedItems, context, {
     fulltextConfig: config2.fulltext,
     fulltextDirectory: config2.attachments.directory,
@@ -33828,7 +33837,11 @@ async function handleAddAction(inputs, options, program) {
   }
 }
 function registerAddCommand(program) {
-  program.command("add").description("Add new reference(s) to the library").argument("[input...]", "File paths or identifiers (PMID/DOI/ISBN), or use stdin").option("-f, --force", "Skip duplicate detection").option("-i, --input <format>", "Input format: json|bibtex|ris|pmid|doi|isbn|auto", "auto").option("--verbose", "Show detailed error information").option("-o, --output <format>", "Output format: json|text", "text").option("--full", "Include full CSL-JSON data in JSON output").option("--fetch-fulltext", "Auto-fetch OA fulltext after adding").option("--no-fetch-fulltext", "Disable auto-fetch fulltext (overrides config)").action(async (inputs, options) => {
+  program.command("add").description("Add new reference(s) to the library").argument("[input...]", "File paths or identifiers (PMID/DOI/ISBN/arXiv), or use stdin").option("-f, --force", "Skip duplicate detection").option(
+    "-i, --input <format>",
+    "Input format: json|bibtex|ris|pmid|doi|isbn|arxiv|auto",
+    "auto"
+  ).option("--verbose", "Show detailed error information").option("-o, --output <format>", "Output format: json|text", "text").option("--full", "Include full CSL-JSON data in JSON output").option("--fetch-fulltext", "Auto-fetch OA fulltext after adding").option("--no-fetch-fulltext", "Disable auto-fetch fulltext (overrides config)").action(async (inputs, options) => {
     await handleAddAction(inputs, options, program);
   });
 }
@@ -34058,4 +34071,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-DkJT7s7N.js.map
+//# sourceMappingURL=index-C9Gc8dcm.js.map