@ncukondo/reference-manager 0.31.0 → 0.32.0

package/dist/chunks/{index-Cqss7VR_.js → index-B8iEozpf.js}

@@ -1,5 +1,5 @@
-import { a } from "./index-CS8S6gE4.js";
-import { d, g, l, o, s } from "./index-DCBYzNj-.js";
+import { a } from "./index-B4-i4PrU.js";
+import { d, g, l, o, s } from "./index-CmkN2-2A.js";
 export {
   a as addAttachment,
   d as detachAttachment,
@@ -8,4 +8,4 @@ export {
   o as openAttachment,
   s as syncAttachments
 };
-//# sourceMappingURL=index-Cqss7VR_.js.map
+//# sourceMappingURL=index-B8iEozpf.js.map

package/dist/chunks/index-B8iEozpf.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index-B8iEozpf.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;"}

package/dist/chunks/{index-BG3Ef4Pd.js → index-BuQm8A5F.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-D5s90TfM.js";
-import { S as SearchableMultiSelect, t as toChoice$1, c as calculateEffectiveLimit, f as formatAuthors, a as formatIdentifiers } from "./SearchableMultiSelect-BFgiGVkF.js";
-import { S as Select, r as restoreStdinAfterInk } from "./index-DCBYzNj-.js";
+import { getActionChoices, OUTPUT_FORMAT_CHOICES, STYLE_CHOICES, isSideEffectAction, generateOutput } from "./action-menu-DLEwSKrj.js";
+import { S as SearchableMultiSelect, t as toChoice$1, c as calculateEffectiveLimit, f as formatAuthors, a as formatIdentifiers } from "./SearchableMultiSelect-jAKQd_B0.js";
+import { S as Select, r as restoreStdinAfterInk } from "./index-CmkN2-2A.js";
 function SearchFlowApp({
   choices,
   filterFn,
@@ -392,4 +392,4 @@ export {
   runCiteFlow,
   runSearchFlow
 };
-//# sourceMappingURL=index-BG3Ef4Pd.js.map
+//# sourceMappingURL=index-BuQm8A5F.js.map

package/dist/chunks/{index-BG3Ef4Pd.js.map → index-BuQm8A5F.js.map}

@@ -1 +1 @@
-{"version":3,"file":"index-BG3Ef4Pd.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 Choice,\n  SearchableMultiSelect,\n  Select,\n  type SortOption,\n} from \"../components/index.js\";\n\n/**\n * Flow states for the search flow\n */\ntype FlowState = \"search\" | \"action\" | \"style\" | \"output-format\" | \"exiting\";\n\n/**\n * Props for SearchFlowApp\n */\nexport interface SearchFlowAppProps {\n  /** Choices for the search prompt */\n  choices: Choice<CslItem>[];\n  /** Filter function for search */\n  filterFn: (query: string, choices: Choice<CslItem>[]) => Choice<CslItem>[];\n  /** Number of visible items */\n  visibleCount: number;\n  /** Default sort option */\n  defaultSort: SortOption;\n  /** Default citation key format */\n  defaultKeyFormat: CitationKeyFormat;\n  /** Default citation style */\n  defaultStyle: string;\n  /** Debounce delay in milliseconds for search filtering */\n  debounceMs?: number;\n  /** Callback when flow completes */\n  onComplete: (result: ActionMenuResult) => void;\n  /** Callback when flow is cancelled */\n  onCancel: () => void;\n}\n\n/**\n * SearchFlowApp component\n *\n * Single App that manages search → action → style/output-format flow\n */\nexport function SearchFlowApp({\n  choices,\n  filterFn,\n  visibleCount,\n  defaultSort,\n  defaultKeyFormat,\n  defaultStyle,\n  debounceMs,\n  onComplete,\n  onCancel,\n}: SearchFlowAppProps): React.ReactElement {\n  const { exit } = useApp();\n  const [state, setState] = useState<FlowState>(\"search\");\n  const [selectedItems, setSelectedItems] = useState<CslItem[]>([]);\n  const [pendingResult, setPendingResult] = useState<ActionMenuResult | null>(null);\n\n  // Exit when entering \"exiting\" state (after rendering empty component)\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: ActionMenuResult) => {\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({ action: \"cancel\", output: \"\", cancelled: true });\n      return;\n    }\n    setSelectedItems(selected.map((c) => c.value));\n    setState(\"action\");\n  };\n\n  // Handle search cancel\n  const handleSearchCancel = () => {\n    exitWith({ action: \"cancel\", output: \"\", cancelled: true });\n  };\n\n  // Handle action selection\n  const handleActionSelect = (action: ActionType) => {\n    if (action === \"cancel\") {\n      exitWith({ action: \"cancel\", output: \"\", cancelled: true });\n      return;\n    }\n\n    // If cite-choose, go to style selection\n    if (action === \"cite-choose\") {\n      setState(\"style\");\n      return;\n    }\n\n    // If output-format, go to output format submenu\n    if (action === \"output-format\") {\n      setState(\"output-format\");\n      return;\n    }\n\n    // Handle side-effect actions\n    if (isSideEffectAction(action)) {\n      exitWith({ action, output: \"\", cancelled: false, selectedItems });\n      return;\n    }\n\n    // Generate output and complete\n    const output = generateOutput(action, selectedItems, {\n      defaultKeyFormat,\n      defaultStyle,\n    });\n    exitWith({ action, output, cancelled: false });\n  };\n\n  // Handle action cancel (go back to search)\n  const handleActionCancel = () => {\n    setState(\"search\");\n  };\n\n  // Handle style selection\n  const handleStyleSelect = (style: string) => {\n    const output = generateOutput(\"cite-choose\", selectedItems, {\n      defaultKeyFormat,\n      defaultStyle: style,\n    });\n    exitWith({ action: \"cite-choose\", output, cancelled: false });\n  };\n\n  // Handle style cancel (go back to action)\n  const handleStyleCancel = () => {\n    setState(\"action\");\n  };\n\n  // Handle output format selection\n  const handleOutputFormatSelect = (format: OutputFormatType) => {\n    if (format === \"cancel\") {\n      setState(\"action\");\n      return;\n    }\n\n    const output = generateOutput(format, selectedItems, {\n      defaultKeyFormat,\n      defaultStyle,\n    });\n    exitWith({ action: \"output-format\", output, cancelled: false });\n  };\n\n  // Handle output format cancel (go back to action)\n  const handleOutputFormatCancel = () => {\n    setState(\"action\");\n  };\n\n  // Render based on current state\n  if (state === \"exiting\") {\n    // Empty component - Ink will clear the previous content\n    return createElement(Box);\n  }\n\n  if (state === \"search\") {\n    return createElement(SearchableMultiSelect<CslItem>, {\n      choices,\n      filterFn,\n      visibleCount,\n      onSubmit: handleSearchSubmit,\n      onCancel: handleSearchCancel,\n      header: \"Search references\",\n      placeholder: \"Type to search...\",\n      defaultSort,\n      ...(debounceMs !== undefined && { debounceMs }),\n    });\n  }\n\n  if (state === \"action\") {\n    const count = selectedItems.length;\n    const refWord = count === 1 ? \"reference\" : \"references\";\n    return createElement(Select<ActionType>, {\n      key: \"action\",\n      options: getActionChoices(count, { defaultKeyFormat }),\n      message: `Action for ${count} selected ${refWord}:`,\n      onSelect: handleActionSelect,\n      onCancel: handleActionCancel,\n    });\n  }\n\n  if (state === \"output-format\") {\n    return createElement(Select<OutputFormatType>, {\n      key: \"output-format\",\n      options: OUTPUT_FORMAT_CHOICES,\n      message: \"Select output format:\",\n      onSelect: handleOutputFormatSelect,\n      onCancel: handleOutputFormatCancel,\n    });\n  }\n\n  // state === \"style\"\n  return createElement(Select<string>, {\n    key: \"style\",\n    options: STYLE_CHOICES,\n    message: \"Select citation style:\",\n    onSelect: handleStyleSelect,\n    onCancel: handleStyleCancel,\n  });\n}\n","/**\n * Runner for SearchFlowApp\n *\n * Provides the public API for running the search flow.\n */\n\nimport { render } from \"ink\";\nimport { createElement } from \"react\";\nimport type { CitationKeyFormat } from \"../../../config/schema.js\";\nimport type { CslItem } from \"../../../core/csl-json/types.js\";\nimport type { SearchResult } from \"../../search/types.js\";\nimport type { ActionMenuResult } from \"../action-menu.js\";\nimport { restoreStdinAfterInk } from \"../alternate-screen.js\";\nimport { toChoice } from \"../choice-builder.js\";\nimport { type Choice, type SortOption, calculateEffectiveLimit } from \"../components/index.js\";\nimport { SearchFlowApp } from \"./SearchFlowApp.js\";\n\n/**\n * Configuration for the search flow\n */\nexport interface SearchFlowConfig {\n  /** Maximum number of results to display */\n  limit: number;\n  /** Debounce delay in milliseconds for search filtering */\n  debounceMs: number;\n  /** Default citation key format */\n  defaultKeyFormat?: CitationKeyFormat;\n  /** Default citation style */\n  defaultStyle?: string;\n}\n\n/**\n * Search function type for filtering references\n */\nexport type SearchFunction = (query: string) => SearchResult[];\n\n/**\n * Run the search flow (search → action → style if needed)\n *\n * This is the main entry point for the `search -t` command.\n */\nexport async function runSearchFlow(\n  allReferences: CslItem[],\n  searchFn: SearchFunction,\n  config: SearchFlowConfig\n): Promise<ActionMenuResult> {\n  // Convert references to choices and build lookup map\n  const choices = allReferences.map(toChoice);\n  const choiceMap = new Map(choices.map((c) => [c.id, c]));\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.flatMap((r) => {\n      const choice = choiceMap.get(r.reference.id);\n      return choice ? [choice] : [];\n    });\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<ActionMenuResult>((resolve) => {\n    let flowResult: ActionMenuResult = {\n      action: \"cancel\",\n      output: \"\",\n      cancelled: true,\n    };\n\n    const handleComplete = (result: ActionMenuResult): void => {\n      flowResult = result;\n    };\n\n    const handleCancel = (): void => {\n      flowResult = {\n        action: \"cancel\",\n        output: \"\",\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app (single render for entire flow)\n    const { waitUntilExit } = render(\n      createElement(SearchFlowApp, {\n        choices,\n        filterFn,\n        visibleCount: effectiveLimit,\n        defaultSort,\n        defaultKeyFormat: config.defaultKeyFormat ?? \"pandoc\",\n        defaultStyle: config.defaultStyle ?? \"apa\",\n        debounceMs: config.debounceMs,\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          action: \"cancel\",\n          output: \"\",\n          cancelled: true,\n        });\n      });\n  });\n}\n","/**\n * CiteFlowApp - Single App for cite command flow\n *\n * Implements the Single App Pattern (ADR-015) for the cite command.\n * Manages state transitions: reference selection → style selection → exiting\n */\n\nimport { Box, useApp } from \"ink\";\nimport type React from \"react\";\nimport { createElement, useEffect, useState } from \"react\";\nimport type { CslItem } from \"../../../core/csl-json/types.js\";\nimport { SearchableMultiSelect } from \"../components/SearchableMultiSelect.js\";\nimport { Select, type SelectOption } from \"../components/Select.js\";\nimport type { Choice, SortOption } from \"../components/index.js\";\n\n// Flow states\ntype FlowState = \"search\" | \"style\" | \"exiting\";\n\n/**\n * Result from the cite flow\n */\nexport interface CiteFlowResult {\n  /** Selected reference IDs */\n  identifiers: string[];\n  /** Selected style (if style selection was shown) */\n  style?: string;\n  /** Whether the flow was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Props for CiteFlowApp\n */\nexport interface CiteFlowAppProps {\n  /** All reference choices */\n  choices: Choice<CslItem>[];\n  /** Filter function for search */\n  filterFn: (query: string, choices: Choice<CslItem>[]) => Choice<CslItem>[];\n  /** Number of visible items */\n  visibleCount: number;\n  /** Default sort option */\n  defaultSort: SortOption;\n  /** Style options for style selection */\n  styleOptions: SelectOption<string>[];\n  /** Whether to show style selection (false if style already specified) */\n  showStyleSelect: boolean;\n  /** Callback when flow completes */\n  onComplete: (result: CiteFlowResult) => void;\n  /** Callback when flow is cancelled */\n  onCancel: () => void;\n}\n\n/**\n * CiteFlowApp component\n *\n * Single Ink app that handles the entire cite flow:\n * 1. 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    return createElement(Box);\n  }\n\n  if (state === \"search\") {\n    return createElement(SearchableMultiSelect<CslItem>, {\n      choices,\n      filterFn,\n      visibleCount,\n      onSubmit: handleSearchSubmit,\n      onCancel: handleSearchCancel,\n      header: \"Select references to cite\",\n      placeholder: \"Type to search...\",\n      defaultSort,\n    });\n  }\n\n  // state === \"style\"\n  const count = selectedItems.length;\n  const refWord = count === 1 ? \"reference\" : \"references\";\n  return createElement(Select<string>, {\n    options: styleOptions,\n    message: `Select citation style for ${count} ${refWord}:`,\n    onSelect: handleStyleSelect,\n    onCancel: handleStyleCancel,\n  });\n}\n","/**\n * Runner for CiteFlowApp\n *\n * Provides the public API for running the cite flow.\n */\n\nimport { render } from \"ink\";\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 { 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 undefined;\n  return firstDatePart[0];\n}\n\n/**\n * Extract published date from CSL item\n */\nfunction extractPublishedDate(item: CslItem): Date | 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 undefined;\n  const [year, month = 1, day = 1] = firstDatePart;\n  if (year === undefined) return undefined;\n  return new Date(year, month - 1, day);\n}\n\n/**\n * Extract updated date from CSL item (from custom.timestamp)\n */\nfunction extractUpdatedDate(item: CslItem): Date | undefined {\n  const dateStr = item.custom?.timestamp;\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 * Extract created date from CSL item (from custom.created_at)\n */\nfunction extractCreatedDate(item: CslItem): 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  });\n}\n"],"names":["toChoice","choices"],"mappings":";;;;;AA+DO,SAAS,cAAc;AAAA,EAC5B;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF,GAA2C;AACzC,QAAM,EAAE,KAAA,IAAS,OAAA;AACjB,QAAM,CAAC,OAAO,QAAQ,IAAI,SAAoB,QAAQ;AACtD,QAAM,CAAC,eAAe,gBAAgB,IAAI,SAAoB,CAAA,CAAE;AAChE,QAAM,CAAC,eAAe,gBAAgB,IAAI,SAAkC,IAAI;AAGhF,YAAU,MAAM;AACd,QAAI,UAAU,aAAa,eAAe;AACxC,WAAA;AACA,UAAI,cAAc,WAAW;AAC3B,iBAAA;AAAA,MACF,OAAO;AACL,mBAAW,aAAa;AAAA,MAC1B;AAAA,IACF;AAAA,EACF,GAAG,CAAC,OAAO,eAAe,MAAM,UAAU,UAAU,CAAC;AAGrD,QAAM,WAAW,CAAC,WAA6B;AAC7C,qBAAiB,MAAM;AACvB,aAAS,SAAS;AAAA,EACpB;AAGA,QAAM,qBAAqB,CAAC,aAAgC;AAC1D,QAAI,SAAS,WAAW,GAAG;AACzB,eAAS,EAAE,QAAQ,UAAU,QAAQ,IAAI,WAAW,MAAM;AAC1D;AAAA,IACF;AACA,qBAAiB,SAAS,IAAI,CAAC,MAAM,EAAE,KAAK,CAAC;AAC7C,aAAS,QAAQ;AAAA,EACnB;AAGA,QAAM,qBAAqB,MAAM;AAC/B,aAAS,EAAE,QAAQ,UAAU,QAAQ,IAAI,WAAW,MAAM;AAAA,EAC5D;AAGA,QAAM,qBAAqB,CAAC,WAAuB;AACjD,QAAI,WAAW,UAAU;AACvB,eAAS,EAAE,QAAQ,UAAU,QAAQ,IAAI,WAAW,MAAM;AAC1D;AAAA,IACF;AAGA,QAAI,WAAW,eAAe;AAC5B,eAAS,OAAO;AAChB;AAAA,IACF;AAGA,QAAI,WAAW,iBAAiB;AAC9B,eAAS,eAAe;AACxB;AAAA,IACF;AAGA,QAAI,mBAAmB,MAAM,GAAG;AAC9B,eAAS,EAAE,QAAQ,QAAQ,IAAI,WAAW,OAAO,eAAe;AAChE;AAAA,IACF;AAGA,UAAM,SAAS,eAAe,QAAQ,eAAe;AAAA,MACnD;AAAA,MACA;AAAA,IAAA,CACD;AACD,aAAS,EAAE,QAAQ,QAAQ,WAAW,OAAO;AAAA,EAC/C;AAGA,QAAM,qBAAqB,MAAM;AAC/B,aAAS,QAAQ;AAAA,EACnB;AAGA,QAAM,oBAAoB,CAAC,UAAkB;AAC3C,UAAM,SAAS,eAAe,eAAe,eAAe;AAAA,MAC1D;AAAA,MACA,cAAc;AAAA,IAAA,CACf;AACD,aAAS,EAAE,QAAQ,eAAe,QAAQ,WAAW,OAAO;AAAA,EAC9D;AAGA,QAAM,oBAAoB,MAAM;AAC9B,aAAS,QAAQ;AAAA,EACnB;AAGA,QAAM,2BAA2B,CAAC,WAA6B;AAC7D,QAAI,WAAW,UAAU;AACvB,eAAS,QAAQ;AACjB;AAAA,IACF;AAEA,UAAM,SAAS,eAAe,QAAQ,eAAe;AAAA,MACnD;AAAA,MACA;AAAA,IAAA,CACD;AACD,aAAS,EAAE,QAAQ,iBAAiB,QAAQ,WAAW,OAAO;AAAA,EAChE;AAGA,QAAM,2BAA2B,MAAM;AACrC,aAAS,QAAQ;AAAA,EACnB;AAGA,MAAI,UAAU,WAAW;AAEvB,WAAO,cAAc,GAAG;AAAA,EAC1B;AAEA,MAAI,UAAU,UAAU;AACtB,WAAO,cAAc,uBAAgC;AAAA,MACnD;AAAA,MACA;AAAA,MACA;AAAA,MACA,UAAU;AAAA,MACV,UAAU;AAAA,MACV,QAAQ;AAAA,MACR,aAAa;AAAA,MACb;AAAA,MACA,GAAI,eAAe,UAAa,EAAE,WAAA;AAAA,IAAW,CAC9C;AAAA,EACH;AAEA,MAAI,UAAU,UAAU;AACtB,UAAM,QAAQ,cAAc;AAC5B,UAAM,UAAU,UAAU,IAAI,cAAc;AAC5C,WAAO,cAAc,QAAoB;AAAA,MACvC,KAAK;AAAA,MACL,SAAS,iBAAiB,OAAO,EAAE,kBAAkB;AAAA,MACrD,SAAS,cAAc,KAAK,aAAa,OAAO;AAAA,MAChD,UAAU;AAAA,MACV,UAAU;AAAA,IAAA,CACX;AAAA,EACH;AAEA,MAAI,UAAU,iBAAiB;AAC7B,WAAO,cAAc,QAA0B;AAAA,MAC7C,KAAK;AAAA,MACL,SAAS;AAAA,MACT,SAAS;AAAA,MACT,UAAU;AAAA,MACV,UAAU;AAAA,IAAA,CACX;AAAA,EACH;AAGA,SAAO,cAAc,QAAgB;AAAA,IACnC,KAAK;AAAA,IACL,SAAS;AAAA,IACT,SAAS;AAAA,IACT,UAAU;AAAA,IACV,UAAU;AAAA,EAAA,CACX;AACH;AChMA,eAAsB,cACpB,eACA,UACA,QAC2B;AAE3B,QAAM,UAAU,cAAc,IAAIA,UAAQ;AAC1C,QAAM,YAAY,IAAI,IAAI,QAAQ,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC;AAGvD,QAAM,iBAAiB,wBAAwB,OAAO,KAAK;AAG3D,QAAM,WAAW,CAAC,OAAeC,aAAkD;AACjF,QAAI,CAAC,MAAM,KAAA,EAAQ,QAAOA;AAE1B,UAAM,UAAU,SAAS,KAAK;AAC9B,WAAO,QAAQ,QAAQ,CAAC,MAAM;AAC5B,YAAM,SAAS,UAAU,IAAI,EAAE,UAAU,EAAE;AAC3C,aAAO,SAAS,CAAC,MAAM,IAAI,CAAA;AAAA,IAC7B,CAAC;AAAA,EACH;AAGA,QAAM,cAA0B;AAGhC,SAAO,IAAI,QAA0B,CAAC,YAAY;AAChD,QAAI,aAA+B;AAAA,MACjC,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,WAAW;AAAA,IAAA;AAGb,UAAM,iBAAiB,CAAC,WAAmC;AACzD,mBAAa;AAAA,IACf;AAEA,UAAM,eAAe,MAAY;AAC/B,mBAAa;AAAA,QACX,QAAQ;AAAA,QACR,QAAQ;AAAA,QACR,WAAW;AAAA,MAAA;AAAA,IAEf;AAGA,UAAM,EAAE,kBAAkB;AAAA,MACxB,cAAc,eAAe;AAAA,QAC3B;AAAA,QACA;AAAA,QACA,cAAc;AAAA,QACd;AAAA,QACA,kBAAkB,OAAO,oBAAoB;AAAA,QAC7C,cAAc,OAAO,gBAAgB;AAAA,QACrC,YAAY,OAAO;AAAA,QACnB,YAAY;AAAA,QACZ,UAAU;AAAA,MAAA,CACX;AAAA,IAAA;AAIH,kBAAA,EACG,KAAK,MAAM;AACV,2BAAA;AACA,cAAQ,UAAU;AAAA,IACpB,CAAC,EACA,MAAM,MAAM;AACX,2BAAA;AACA,cAAQ;AAAA,QACN,QAAQ;AAAA,QACR,QAAQ;AAAA,QACR,WAAW;AAAA,MAAA,CACZ;AAAA,IACH,CAAC;AAAA,EACL,CAAC;AACH;ACzDO,SAAS,YAAY;AAAA,EAC1B;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF,GAAyC;AACvC,QAAM,EAAE,KAAA,IAAS,OAAA;AACjB,QAAM,CAAC,OAAO,QAAQ,IAAI,SAAoB,QAAQ;AACtD,QAAM,CAAC,eAAe,gBAAgB,IAAI,SAAoB,CAAA,CAAE;AAChE,QAAM,CAAC,eAAe,gBAAgB,IAAI,SAAgC,IAAI;AAG9E,YAAU,MAAM;AACd,QAAI,UAAU,aAAa,eAAe;AACxC,WAAA;AACA,UAAI,cAAc,WAAW;AAC3B,iBAAA;AAAA,MACF,OAAO;AACL,mBAAW,aAAa;AAAA,MAC1B;AAAA,IACF;AAAA,EACF,GAAG,CAAC,OAAO,eAAe,MAAM,UAAU,UAAU,CAAC;AAGrD,QAAM,WAAW,CAAC,WAA2B;AAC3C,qBAAiB,MAAM;AACvB,aAAS,SAAS;AAAA,EACpB;AAGA,QAAM,qBAAqB,CAAC,aAAgC;AAC1D,QAAI,SAAS,WAAW,GAAG;AACzB,eAAS,EAAE,aAAa,CAAA,GAAI,WAAW,MAAM;AAC7C;AAAA,IACF;AACA,UAAM,QAAQ,SAAS,IAAI,CAAC,MAAM,EAAE,KAAK;AACzC,qBAAiB,KAAK;AAEtB,QAAI,iBAAiB;AACnB,eAAS,OAAO;AAAA,IAClB,OAAO;AAEL,eAAS;AAAA,QACP,aAAa,MAAM,IAAI,CAAC,SAAS,KAAK,EAAE;AAAA,QACxC,WAAW;AAAA,MAAA,CACZ;AAAA,IACH;AAAA,EACF;AAGA,QAAM,qBAAqB,MAAM;AAC/B,aAAS,EAAE,aAAa,CAAA,GAAI,WAAW,MAAM;AAAA,EAC/C;AAGA,QAAM,oBAAoB,CAAC,UAAkB;AAC3C,aAAS;AAAA,MACP,aAAa,cAAc,IAAI,CAAC,SAAS,KAAK,EAAE;AAAA,MAChD;AAAA,MACA,WAAW;AAAA,IAAA,CACZ;AAAA,EACH;AAGA,QAAM,oBAAoB,MAAM;AAC9B,aAAS,QAAQ;AAAA,EACnB;AAGA,MAAI,UAAU,WAAW;AACvB,WAAO,cAAc,GAAG;AAAA,EAC1B;AAEA,MAAI,UAAU,UAAU;AACtB,WAAO,cAAc,uBAAgC;AAAA,MACnD;AAAA,MACA;AAAA,MACA;AAAA,MACA,UAAU;AAAA,MACV,UAAU;AAAA,MACV,QAAQ;AAAA,MACR,aAAa;AAAA,MACb;AAAA,IAAA,CACD;AAAA,EACH;AAGA,QAAM,QAAQ,cAAc;AAC5B,QAAM,UAAU,UAAU,IAAI,cAAc;AAC5C,SAAO,cAAc,QAAgB;AAAA,IACnC,SAAS;AAAA,IACT,SAAS,6BAA6B,KAAK,IAAI,OAAO;AAAA,IACtD,UAAU;AAAA,IACV,UAAU;AAAA,EAAA,CACX;AACH;AC1HA,SAAS,YAAY,MAAmC;AACtD,QAAM,YAAY,KAAK,SAAS,YAAY;AAC5C,MAAI,CAAC,aAAa,UAAU,WAAW,EAAG,QAAO;AACjD,QAAM,gBAAgB,UAAU,CAAC;AACjC,MAAI,CAAC,iBAAiB,cAAc,WAAW,EAAG,QAAO;AACzD,SAAO,cAAc,CAAC;AACxB;AAKA,SAAS,qBAAqB,MAAiC;AAC7D,QAAM,YAAY,KAAK,SAAS,YAAY;AAC5C,MAAI,CAAC,aAAa,UAAU,WAAW,EAAG,QAAO;AACjD,QAAM,gBAAgB,UAAU,CAAC;AACjC,MAAI,CAAC,iBAAiB,cAAc,WAAW,EAAG,QAAO;AACzD,QAAM,CAAC,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI;AACnC,MAAI,SAAS,OAAW,QAAO;AAC/B,SAAO,IAAI,KAAK,MAAM,QAAQ,GAAG,GAAG;AACtC;AAKA,SAAS,mBAAmB,MAAiC;AAC3D,QAAM,UAAU,KAAK,QAAQ;AAC7B,MAAI,CAAC,WAAW,OAAO,YAAY,SAAU,QAAO;AACpD,QAAM,OAAO,IAAI,KAAK,OAAO;AAC7B,SAAO,OAAO,MAAM,KAAK,QAAA,CAAS,IAAI,SAAY;AACpD;AAKA,SAAS,mBAAmB,MAAiC;AAC3D,QAAM,UAAU,KAAK,QAAQ;AAC7B,MAAI,CAAC,WAAW,OAAO,YAAY,SAAU,QAAO;AACpD,QAAM,OAAO,IAAI,KAAK,OAAO;AAC7B,SAAO,OAAO,MAAM,KAAK,QAAA,CAAS,IAAI,SAAY;AACpD;AAKA,SAAS,WAAW,MAAsB;AACxC,QAAM,UAAkC;AAAA,IACtC,mBAAmB;AAAA,IACnB,oBAAoB;AAAA,IACpB,qBAAqB;AAAA,IACrB,MAAM;AAAA,IACN,SAAS;AAAA,IACT,oBAAoB;AAAA,IACpB,QAAQ;AAAA,IACR,QAAQ;AAAA,IACR,SAAS;AAAA,EAAA;AAEX,SAAO,QAAQ,IAAI,KAAK;AAC1B;AAKA,SAAS,SAAS,MAAgC;AAChD,QAAM,UAAU,cAAc,KAAK,MAAM;AACzC,QAAM,OAAO,YAAY,IAAI;AAC7B,QAAM,cAAc,kBAAkB,IAAI;AAC1C,QAAM,WAAW,WAAW,KAAK,IAAI;AAGrC,QAAM,YAAsB,CAAA;AAC5B,MAAI,KAAM,WAAU,KAAK,OAAO,IAAI,CAAC;AACrC,YAAU,KAAK,QAAQ;AACvB,MAAI,YAAa,WAAU,KAAK,WAAW;AAE3C,QAAM,cAAc,mBAAmB,IAAI;AAC3C,QAAM,cAAc,mBAAmB,IAAI;AAC3C,QAAM,gBAAgB,qBAAqB,IAAI;AAE/C,SAAO;AAAA,IACL,IAAI,KAAK;AAAA,IACT,OAAO,KAAK,SAAS;AAAA,IACrB,UAAU,WAAW;AAAA,IACrB,MAAM,UAAU,KAAK,KAAK;AAAA,IAC1B,OAAO;AAAA,IACP,GAAI,eAAe,EAAE,YAAA;AAAA,IACrB,GAAI,eAAe,EAAE,YAAA;AAAA,IACrB,GAAI,iBAAiB,EAAE,cAAA;AAAA,EAAc;AAEzC;AAuBA,eAAsB,YAAY,SAAsD;AACtF,QAAM,EAAE,eAAe,UAAU,QAAQ,cAAc,oBAAoB;AAG3E,QAAM,UAAU,cAAc,IAAI,QAAQ;AAG1C,QAAM,iBAAiB,wBAAwB,OAAO,KAAK;AAG3D,QAAM,WAAW,CAAC,OAAeA,aAAkD;AACjF,QAAI,CAAC,MAAM,KAAA,EAAQ,QAAOA;AAE1B,UAAM,UAAU,SAAS,KAAK;AAC9B,WAAO,QAAQ,IAAI,CAAC,MAAM,SAAS,EAAE,SAAS,CAAC;AAAA,EACjD;AAGA,QAAM,cAA0B;AAGhC,SAAO,IAAI,QAAwB,CAAC,YAAY;AAC9C,QAAI,aAA6B;AAAA,MAC/B,aAAa,CAAA;AAAA,MACb,WAAW;AAAA,IAAA;AAGb,UAAM,iBAAiB,CAAC,WAAiC;AACvD,mBAAa;AAAA,IACf;AAEA,UAAM,eAAe,MAAY;AAC/B,mBAAa;AAAA,QACX,aAAa,CAAA;AAAA,QACb,WAAW;AAAA,MAAA;AAAA,IAEf;AAGA,UAAM,EAAE,kBAAkB;AAAA,MACxB,cAAc,aAAa;AAAA,QACzB;AAAA,QACA;AAAA,QACA,cAAc;AAAA,QACd;AAAA,QACA;AAAA,QACA;AAAA,QACA,YAAY;AAAA,QACZ,UAAU;AAAA,MAAA,CACX;AAAA,IAAA;AAIH,kBAAA,EACG,KAAK,MAAM;AACV,2BAAA;AACA,cAAQ,UAAU;AAAA,IACpB,CAAC,EACA,MAAM,MAAM;AACX,2BAAA;AACA,cAAQ;AAAA,QACN,aAAa,CAAA;AAAA,QACb,WAAW;AAAA,MAAA,CACZ;AAAA,IACH,CAAC;AAAA,EACL,CAAC;AACH;"}
+{"version":3,"file":"index-BuQm8A5F.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 Choice,\n  SearchableMultiSelect,\n  Select,\n  type SortOption,\n} from \"../components/index.js\";\n\n/**\n * Flow states for the search flow\n */\ntype FlowState = \"search\" | \"action\" | \"style\" | \"output-format\" | \"exiting\";\n\n/**\n * Props for SearchFlowApp\n */\nexport interface SearchFlowAppProps {\n  /** Choices for the search prompt */\n  choices: Choice<CslItem>[];\n  /** Filter function for search */\n  filterFn: (query: string, choices: Choice<CslItem>[]) => Choice<CslItem>[];\n  /** Number of visible items */\n  visibleCount: number;\n  /** Default sort option */\n  defaultSort: SortOption;\n  /** Default citation key format */\n  defaultKeyFormat: CitationKeyFormat;\n  /** Default citation style */\n  defaultStyle: string;\n  /** Debounce delay in milliseconds for search filtering */\n  debounceMs?: number;\n  /** Callback when flow completes */\n  onComplete: (result: ActionMenuResult) => void;\n  /** Callback when flow is cancelled */\n  onCancel: () => void;\n}\n\n/**\n * SearchFlowApp component\n *\n * Single App that manages search → action → style/output-format flow\n */\nexport function SearchFlowApp({\n  choices,\n  filterFn,\n  visibleCount,\n  defaultSort,\n  defaultKeyFormat,\n  defaultStyle,\n  debounceMs,\n  onComplete,\n  onCancel,\n}: SearchFlowAppProps): React.ReactElement {\n  const { exit } = useApp();\n  const [state, setState] = useState<FlowState>(\"search\");\n  const [selectedItems, setSelectedItems] = useState<CslItem[]>([]);\n  const [pendingResult, setPendingResult] = useState<ActionMenuResult | null>(null);\n\n  // Exit when entering \"exiting\" state (after rendering empty component)\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: ActionMenuResult) => {\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({ action: \"cancel\", output: \"\", cancelled: true });\n      return;\n    }\n    setSelectedItems(selected.map((c) => c.value));\n    setState(\"action\");\n  };\n\n  // Handle search cancel\n  const handleSearchCancel = () => {\n    exitWith({ action: \"cancel\", output: \"\", cancelled: true });\n  };\n\n  // Handle action selection\n  const handleActionSelect = (action: ActionType) => {\n    if (action === \"cancel\") {\n      exitWith({ action: \"cancel\", output: \"\", cancelled: true });\n      return;\n    }\n\n    // If cite-choose, go to style selection\n    if (action === \"cite-choose\") {\n      setState(\"style\");\n      return;\n    }\n\n    // If output-format, go to output format submenu\n    if (action === \"output-format\") {\n      setState(\"output-format\");\n      return;\n    }\n\n    // Handle side-effect actions\n    if (isSideEffectAction(action)) {\n      exitWith({ action, output: \"\", cancelled: false, selectedItems });\n      return;\n    }\n\n    // Generate output and complete\n    const output = generateOutput(action, selectedItems, {\n      defaultKeyFormat,\n      defaultStyle,\n    });\n    exitWith({ action, output, cancelled: false });\n  };\n\n  // Handle action cancel (go back to search)\n  const handleActionCancel = () => {\n    setState(\"search\");\n  };\n\n  // Handle style selection\n  const handleStyleSelect = (style: string) => {\n    const output = generateOutput(\"cite-choose\", selectedItems, {\n      defaultKeyFormat,\n      defaultStyle: style,\n    });\n    exitWith({ action: \"cite-choose\", output, cancelled: false });\n  };\n\n  // Handle style cancel (go back to action)\n  const handleStyleCancel = () => {\n    setState(\"action\");\n  };\n\n  // Handle output format selection\n  const handleOutputFormatSelect = (format: OutputFormatType) => {\n    if (format === \"cancel\") {\n      setState(\"action\");\n      return;\n    }\n\n    const output = generateOutput(format, selectedItems, {\n      defaultKeyFormat,\n      defaultStyle,\n    });\n    exitWith({ action: \"output-format\", output, cancelled: false });\n  };\n\n  // Handle output format cancel (go back to action)\n  const handleOutputFormatCancel = () => {\n    setState(\"action\");\n  };\n\n  // Render based on current state\n  if (state === \"exiting\") {\n    // Empty component - Ink will clear the previous content\n    return createElement(Box);\n  }\n\n  if (state === \"search\") {\n    return createElement(SearchableMultiSelect<CslItem>, {\n      choices,\n      filterFn,\n      visibleCount,\n      onSubmit: handleSearchSubmit,\n      onCancel: handleSearchCancel,\n      header: \"Search references\",\n      placeholder: \"Type to search...\",\n      defaultSort,\n      ...(debounceMs !== undefined && { debounceMs }),\n    });\n  }\n\n  if (state === \"action\") {\n    const count = selectedItems.length;\n    const refWord = count === 1 ? \"reference\" : \"references\";\n    return createElement(Select<ActionType>, {\n      key: \"action\",\n      options: getActionChoices(count, { defaultKeyFormat }),\n      message: `Action for ${count} selected ${refWord}:`,\n      onSelect: handleActionSelect,\n      onCancel: handleActionCancel,\n    });\n  }\n\n  if (state === \"output-format\") {\n    return createElement(Select<OutputFormatType>, {\n      key: \"output-format\",\n      options: OUTPUT_FORMAT_CHOICES,\n      message: \"Select output format:\",\n      onSelect: handleOutputFormatSelect,\n      onCancel: handleOutputFormatCancel,\n    });\n  }\n\n  // state === \"style\"\n  return createElement(Select<string>, {\n    key: \"style\",\n    options: STYLE_CHOICES,\n    message: \"Select citation style:\",\n    onSelect: handleStyleSelect,\n    onCancel: handleStyleCancel,\n  });\n}\n","/**\n * Runner for SearchFlowApp\n *\n * Provides the public API for running the search flow.\n */\n\nimport { render } from \"ink\";\nimport { createElement } from \"react\";\nimport type { CitationKeyFormat } from \"../../../config/schema.js\";\nimport type { CslItem } from \"../../../core/csl-json/types.js\";\nimport type { SearchResult } from \"../../search/types.js\";\nimport type { ActionMenuResult } from \"../action-menu.js\";\nimport { restoreStdinAfterInk } from \"../alternate-screen.js\";\nimport { toChoice } from \"../choice-builder.js\";\nimport { type Choice, type SortOption, calculateEffectiveLimit } from \"../components/index.js\";\nimport { SearchFlowApp } from \"./SearchFlowApp.js\";\n\n/**\n * Configuration for the search flow\n */\nexport interface SearchFlowConfig {\n  /** Maximum number of results to display */\n  limit: number;\n  /** Debounce delay in milliseconds for search filtering */\n  debounceMs: number;\n  /** Default citation key format */\n  defaultKeyFormat?: CitationKeyFormat;\n  /** Default citation style */\n  defaultStyle?: string;\n}\n\n/**\n * Search function type for filtering references\n */\nexport type SearchFunction = (query: string) => SearchResult[];\n\n/**\n * Run the search flow (search → action → style if needed)\n *\n * This is the main entry point for the `search -t` command.\n */\nexport async function runSearchFlow(\n  allReferences: CslItem[],\n  searchFn: SearchFunction,\n  config: SearchFlowConfig\n): Promise<ActionMenuResult> {\n  // Convert references to choices and build lookup map\n  const choices = allReferences.map(toChoice);\n  const choiceMap = new Map(choices.map((c) => [c.id, c]));\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.flatMap((r) => {\n      const choice = choiceMap.get(r.reference.id);\n      return choice ? [choice] : [];\n    });\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<ActionMenuResult>((resolve) => {\n    let flowResult: ActionMenuResult = {\n      action: \"cancel\",\n      output: \"\",\n      cancelled: true,\n    };\n\n    const handleComplete = (result: ActionMenuResult): void => {\n      flowResult = result;\n    };\n\n    const handleCancel = (): void => {\n      flowResult = {\n        action: \"cancel\",\n        output: \"\",\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app (single render for entire flow)\n    const { waitUntilExit } = render(\n      createElement(SearchFlowApp, {\n        choices,\n        filterFn,\n        visibleCount: effectiveLimit,\n        defaultSort,\n        defaultKeyFormat: config.defaultKeyFormat ?? \"pandoc\",\n        defaultStyle: config.defaultStyle ?? \"apa\",\n        debounceMs: config.debounceMs,\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          action: \"cancel\",\n          output: \"\",\n          cancelled: true,\n        });\n      });\n  });\n}\n","/**\n * CiteFlowApp - Single App for cite command flow\n *\n * Implements the Single App Pattern (ADR-015) for the cite command.\n * Manages state transitions: reference selection → style selection → exiting\n */\n\nimport { Box, useApp } from \"ink\";\nimport type React from \"react\";\nimport { createElement, useEffect, useState } from \"react\";\nimport type { CslItem } from \"../../../core/csl-json/types.js\";\nimport { SearchableMultiSelect } from \"../components/SearchableMultiSelect.js\";\nimport { Select, type SelectOption } from \"../components/Select.js\";\nimport type { Choice, SortOption } from \"../components/index.js\";\n\n// Flow states\ntype FlowState = \"search\" | \"style\" | \"exiting\";\n\n/**\n * Result from the cite flow\n */\nexport interface CiteFlowResult {\n  /** Selected reference IDs */\n  identifiers: string[];\n  /** Selected style (if style selection was shown) */\n  style?: string;\n  /** Whether the flow was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Props for CiteFlowApp\n */\nexport interface CiteFlowAppProps {\n  /** All reference choices */\n  choices: Choice<CslItem>[];\n  /** Filter function for search */\n  filterFn: (query: string, choices: Choice<CslItem>[]) => Choice<CslItem>[];\n  /** Number of visible items */\n  visibleCount: number;\n  /** Default sort option */\n  defaultSort: SortOption;\n  /** Style options for style selection */\n  styleOptions: SelectOption<string>[];\n  /** Whether to show style selection (false if style already specified) */\n  showStyleSelect: boolean;\n  /** Callback when flow completes */\n  onComplete: (result: CiteFlowResult) => void;\n  /** Callback when flow is cancelled */\n  onCancel: () => void;\n}\n\n/**\n * CiteFlowApp component\n *\n * Single Ink app that handles the entire cite flow:\n * 1. 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    return createElement(Box);\n  }\n\n  if (state === \"search\") {\n    return createElement(SearchableMultiSelect<CslItem>, {\n      choices,\n      filterFn,\n      visibleCount,\n      onSubmit: handleSearchSubmit,\n      onCancel: handleSearchCancel,\n      header: \"Select references to cite\",\n      placeholder: \"Type to search...\",\n      defaultSort,\n    });\n  }\n\n  // state === \"style\"\n  const count = selectedItems.length;\n  const refWord = count === 1 ? \"reference\" : \"references\";\n  return createElement(Select<string>, {\n    options: styleOptions,\n    message: `Select citation style for ${count} ${refWord}:`,\n    onSelect: handleStyleSelect,\n    onCancel: handleStyleCancel,\n  });\n}\n","/**\n * Runner for CiteFlowApp\n *\n * Provides the public API for running the cite flow.\n */\n\nimport { render } from \"ink\";\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 { 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 undefined;\n  return firstDatePart[0];\n}\n\n/**\n * Extract published date from CSL item\n */\nfunction extractPublishedDate(item: CslItem): Date | 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 undefined;\n  const [year, month = 1, day = 1] = firstDatePart;\n  if (year === undefined) return undefined;\n  return new Date(year, month - 1, day);\n}\n\n/**\n * Extract updated date from CSL item (from custom.timestamp)\n */\nfunction extractUpdatedDate(item: CslItem): Date | undefined {\n  const dateStr = item.custom?.timestamp;\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 * Extract created date from CSL item (from custom.created_at)\n */\nfunction extractCreatedDate(item: CslItem): 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  });\n}\n"],"names":["toChoice","choices"],"mappings":";;;;;AA+DO,SAAS,cAAc;AAAA,EAC5B;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF,GAA2C;AACzC,QAAM,EAAE,KAAA,IAAS,OAAA;AACjB,QAAM,CAAC,OAAO,QAAQ,IAAI,SAAoB,QAAQ;AACtD,QAAM,CAAC,eAAe,gBAAgB,IAAI,SAAoB,CAAA,CAAE;AAChE,QAAM,CAAC,eAAe,gBAAgB,IAAI,SAAkC,IAAI;AAGhF,YAAU,MAAM;AACd,QAAI,UAAU,aAAa,eAAe;AACxC,WAAA;AACA,UAAI,cAAc,WAAW;AAC3B,iBAAA;AAAA,MACF,OAAO;AACL,mBAAW,aAAa;AAAA,MAC1B;AAAA,IACF;AAAA,EACF,GAAG,CAAC,OAAO,eAAe,MAAM,UAAU,UAAU,CAAC;AAGrD,QAAM,WAAW,CAAC,WAA6B;AAC7C,qBAAiB,MAAM;AACvB,aAAS,SAAS;AAAA,EACpB;AAGA,QAAM,qBAAqB,CAAC,aAAgC;AAC1D,QAAI,SAAS,WAAW,GAAG;AACzB,eAAS,EAAE,QAAQ,UAAU,QAAQ,IAAI,WAAW,MAAM;AAC1D;AAAA,IACF;AACA,qBAAiB,SAAS,IAAI,CAAC,MAAM,EAAE,KAAK,CAAC;AAC7C,aAAS,QAAQ;AAAA,EACnB;AAGA,QAAM,qBAAqB,MAAM;AAC/B,aAAS,EAAE,QAAQ,UAAU,QAAQ,IAAI,WAAW,MAAM;AAAA,EAC5D;AAGA,QAAM,qBAAqB,CAAC,WAAuB;AACjD,QAAI,WAAW,UAAU;AACvB,eAAS,EAAE,QAAQ,UAAU,QAAQ,IAAI,WAAW,MAAM;AAC1D;AAAA,IACF;AAGA,QAAI,WAAW,eAAe;AAC5B,eAAS,OAAO;AAChB;AAAA,IACF;AAGA,QAAI,WAAW,iBAAiB;AAC9B,eAAS,eAAe;AACxB;AAAA,IACF;AAGA,QAAI,mBAAmB,MAAM,GAAG;AAC9B,eAAS,EAAE,QAAQ,QAAQ,IAAI,WAAW,OAAO,eAAe;AAChE;AAAA,IACF;AAGA,UAAM,SAAS,eAAe,QAAQ,eAAe;AAAA,MACnD;AAAA,MACA;AAAA,IAAA,CACD;AACD,aAAS,EAAE,QAAQ,QAAQ,WAAW,OAAO;AAAA,EAC/C;AAGA,QAAM,qBAAqB,MAAM;AAC/B,aAAS,QAAQ;AAAA,EACnB;AAGA,QAAM,oBAAoB,CAAC,UAAkB;AAC3C,UAAM,SAAS,eAAe,eAAe,eAAe;AAAA,MAC1D;AAAA,MACA,cAAc;AAAA,IAAA,CACf;AACD,aAAS,EAAE,QAAQ,eAAe,QAAQ,WAAW,OAAO;AAAA,EAC9D;AAGA,QAAM,oBAAoB,MAAM;AAC9B,aAAS,QAAQ;AAAA,EACnB;AAGA,QAAM,2BAA2B,CAAC,WAA6B;AAC7D,QAAI,WAAW,UAAU;AACvB,eAAS,QAAQ;AACjB;AAAA,IACF;AAEA,UAAM,SAAS,eAAe,QAAQ,eAAe;AAAA,MACnD;AAAA,MACA;AAAA,IAAA,CACD;AACD,aAAS,EAAE,QAAQ,iBAAiB,QAAQ,WAAW,OAAO;AAAA,EAChE;AAGA,QAAM,2BAA2B,MAAM;AACrC,aAAS,QAAQ;AAAA,EACnB;AAGA,MAAI,UAAU,WAAW;AAEvB,WAAO,cAAc,GAAG;AAAA,EAC1B;AAEA,MAAI,UAAU,UAAU;AACtB,WAAO,cAAc,uBAAgC;AAAA,MACnD;AAAA,MACA;AAAA,MACA;AAAA,MACA,UAAU;AAAA,MACV,UAAU;AAAA,MACV,QAAQ;AAAA,MACR,aAAa;AAAA,MACb;AAAA,MACA,GAAI,eAAe,UAAa,EAAE,WAAA;AAAA,IAAW,CAC9C;AAAA,EACH;AAEA,MAAI,UAAU,UAAU;AACtB,UAAM,QAAQ,cAAc;AAC5B,UAAM,UAAU,UAAU,IAAI,cAAc;AAC5C,WAAO,cAAc,QAAoB;AAAA,MACvC,KAAK;AAAA,MACL,SAAS,iBAAiB,OAAO,EAAE,kBAAkB;AAAA,MACrD,SAAS,cAAc,KAAK,aAAa,OAAO;AAAA,MAChD,UAAU;AAAA,MACV,UAAU;AAAA,IAAA,CACX;AAAA,EACH;AAEA,MAAI,UAAU,iBAAiB;AAC7B,WAAO,cAAc,QAA0B;AAAA,MAC7C,KAAK;AAAA,MACL,SAAS;AAAA,MACT,SAAS;AAAA,MACT,UAAU;AAAA,MACV,UAAU;AAAA,IAAA,CACX;AAAA,EACH;AAGA,SAAO,cAAc,QAAgB;AAAA,IACnC,KAAK;AAAA,IACL,SAAS;AAAA,IACT,SAAS;AAAA,IACT,UAAU;AAAA,IACV,UAAU;AAAA,EAAA,CACX;AACH;AChMA,eAAsB,cACpB,eACA,UACA,QAC2B;AAE3B,QAAM,UAAU,cAAc,IAAIA,UAAQ;AAC1C,QAAM,YAAY,IAAI,IAAI,QAAQ,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC;AAGvD,QAAM,iBAAiB,wBAAwB,OAAO,KAAK;AAG3D,QAAM,WAAW,CAAC,OAAeC,aAAkD;AACjF,QAAI,CAAC,MAAM,KAAA,EAAQ,QAAOA;AAE1B,UAAM,UAAU,SAAS,KAAK;AAC9B,WAAO,QAAQ,QAAQ,CAAC,MAAM;AAC5B,YAAM,SAAS,UAAU,IAAI,EAAE,UAAU,EAAE;AAC3C,aAAO,SAAS,CAAC,MAAM,IAAI,CAAA;AAAA,IAC7B,CAAC;AAAA,EACH;AAGA,QAAM,cAA0B;AAGhC,SAAO,IAAI,QAA0B,CAAC,YAAY;AAChD,QAAI,aAA+B;AAAA,MACjC,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,WAAW;AAAA,IAAA;AAGb,UAAM,iBAAiB,CAAC,WAAmC;AACzD,mBAAa;AAAA,IACf;AAEA,UAAM,eAAe,MAAY;AAC/B,mBAAa;AAAA,QACX,QAAQ;AAAA,QACR,QAAQ;AAAA,QACR,WAAW;AAAA,MAAA;AAAA,IAEf;AAGA,UAAM,EAAE,kBAAkB;AAAA,MACxB,cAAc,eAAe;AAAA,QAC3B;AAAA,QACA;AAAA,QACA,cAAc;AAAA,QACd;AAAA,QACA,kBAAkB,OAAO,oBAAoB;AAAA,QAC7C,cAAc,OAAO,gBAAgB;AAAA,QACrC,YAAY,OAAO;AAAA,QACnB,YAAY;AAAA,QACZ,UAAU;AAAA,MAAA,CACX;AAAA,IAAA;AAIH,kBAAA,EACG,KAAK,MAAM;AACV,2BAAA;AACA,cAAQ,UAAU;AAAA,IACpB,CAAC,EACA,MAAM,MAAM;AACX,2BAAA;AACA,cAAQ;AAAA,QACN,QAAQ;AAAA,QACR,QAAQ;AAAA,QACR,WAAW;AAAA,MAAA,CACZ;AAAA,IACH,CAAC;AAAA,EACL,CAAC;AACH;ACzDO,SAAS,YAAY;AAAA,EAC1B;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF,GAAyC;AACvC,QAAM,EAAE,KAAA,IAAS,OAAA;AACjB,QAAM,CAAC,OAAO,QAAQ,IAAI,SAAoB,QAAQ;AACtD,QAAM,CAAC,eAAe,gBAAgB,IAAI,SAAoB,CAAA,CAAE;AAChE,QAAM,CAAC,eAAe,gBAAgB,IAAI,SAAgC,IAAI;AAG9E,YAAU,MAAM;AACd,QAAI,UAAU,aAAa,eAAe;AACxC,WAAA;AACA,UAAI,cAAc,WAAW;AAC3B,iBAAA;AAAA,MACF,OAAO;AACL,mBAAW,aAAa;AAAA,MAC1B;AAAA,IACF;AAAA,EACF,GAAG,CAAC,OAAO,eAAe,MAAM,UAAU,UAAU,CAAC;AAGrD,QAAM,WAAW,CAAC,WAA2B;AAC3C,qBAAiB,MAAM;AACvB,aAAS,SAAS;AAAA,EACpB;AAGA,QAAM,qBAAqB,CAAC,aAAgC;AAC1D,QAAI,SAAS,WAAW,GAAG;AACzB,eAAS,EAAE,aAAa,CAAA,GAAI,WAAW,MAAM;AAC7C;AAAA,IACF;AACA,UAAM,QAAQ,SAAS,IAAI,CAAC,MAAM,EAAE,KAAK;AACzC,qBAAiB,KAAK;AAEtB,QAAI,iBAAiB;AACnB,eAAS,OAAO;AAAA,IAClB,OAAO;AAEL,eAAS;AAAA,QACP,aAAa,MAAM,IAAI,CAAC,SAAS,KAAK,EAAE;AAAA,QACxC,WAAW;AAAA,MAAA,CACZ;AAAA,IACH;AAAA,EACF;AAGA,QAAM,qBAAqB,MAAM;AAC/B,aAAS,EAAE,aAAa,CAAA,GAAI,WAAW,MAAM;AAAA,EAC/C;AAGA,QAAM,oBAAoB,CAAC,UAAkB;AAC3C,aAAS;AAAA,MACP,aAAa,cAAc,IAAI,CAAC,SAAS,KAAK,EAAE;AAAA,MAChD;AAAA,MACA,WAAW;AAAA,IAAA,CACZ;AAAA,EACH;AAGA,QAAM,oBAAoB,MAAM;AAC9B,aAAS,QAAQ;AAAA,EACnB;AAGA,MAAI,UAAU,WAAW;AACvB,WAAO,cAAc,GAAG;AAAA,EAC1B;AAEA,MAAI,UAAU,UAAU;AACtB,WAAO,cAAc,uBAAgC;AAAA,MACnD;AAAA,MACA;AAAA,MACA;AAAA,MACA,UAAU;AAAA,MACV,UAAU;AAAA,MACV,QAAQ;AAAA,MACR,aAAa;AAAA,MACb;AAAA,IAAA,CACD;AAAA,EACH;AAGA,QAAM,QAAQ,cAAc;AAC5B,QAAM,UAAU,UAAU,IAAI,cAAc;AAC5C,SAAO,cAAc,QAAgB;AAAA,IACnC,SAAS;AAAA,IACT,SAAS,6BAA6B,KAAK,IAAI,OAAO;AAAA,IACtD,UAAU;AAAA,IACV,UAAU;AAAA,EAAA,CACX;AACH;AC1HA,SAAS,YAAY,MAAmC;AACtD,QAAM,YAAY,KAAK,SAAS,YAAY;AAC5C,MAAI,CAAC,aAAa,UAAU,WAAW,EAAG,QAAO;AACjD,QAAM,gBAAgB,UAAU,CAAC;AACjC,MAAI,CAAC,iBAAiB,cAAc,WAAW,EAAG,QAAO;AACzD,SAAO,cAAc,CAAC;AACxB;AAKA,SAAS,qBAAqB,MAAiC;AAC7D,QAAM,YAAY,KAAK,SAAS,YAAY;AAC5C,MAAI,CAAC,aAAa,UAAU,WAAW,EAAG,QAAO;AACjD,QAAM,gBAAgB,UAAU,CAAC;AACjC,MAAI,CAAC,iBAAiB,cAAc,WAAW,EAAG,QAAO;AACzD,QAAM,CAAC,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI;AACnC,MAAI,SAAS,OAAW,QAAO;AAC/B,SAAO,IAAI,KAAK,MAAM,QAAQ,GAAG,GAAG;AACtC;AAKA,SAAS,mBAAmB,MAAiC;AAC3D,QAAM,UAAU,KAAK,QAAQ;AAC7B,MAAI,CAAC,WAAW,OAAO,YAAY,SAAU,QAAO;AACpD,QAAM,OAAO,IAAI,KAAK,OAAO;AAC7B,SAAO,OAAO,MAAM,KAAK,QAAA,CAAS,IAAI,SAAY;AACpD;AAKA,SAAS,mBAAmB,MAAiC;AAC3D,QAAM,UAAU,KAAK,QAAQ;AAC7B,MAAI,CAAC,WAAW,OAAO,YAAY,SAAU,QAAO;AACpD,QAAM,OAAO,IAAI,KAAK,OAAO;AAC7B,SAAO,OAAO,MAAM,KAAK,QAAA,CAAS,IAAI,SAAY;AACpD;AAKA,SAAS,WAAW,MAAsB;AACxC,QAAM,UAAkC;AAAA,IACtC,mBAAmB;AAAA,IACnB,oBAAoB;AAAA,IACpB,qBAAqB;AAAA,IACrB,MAAM;AAAA,IACN,SAAS;AAAA,IACT,oBAAoB;AAAA,IACpB,QAAQ;AAAA,IACR,QAAQ;AAAA,IACR,SAAS;AAAA,EAAA;AAEX,SAAO,QAAQ,IAAI,KAAK;AAC1B;AAKA,SAAS,SAAS,MAAgC;AAChD,QAAM,UAAU,cAAc,KAAK,MAAM;AACzC,QAAM,OAAO,YAAY,IAAI;AAC7B,QAAM,cAAc,kBAAkB,IAAI;AAC1C,QAAM,WAAW,WAAW,KAAK,IAAI;AAGrC,QAAM,YAAsB,CAAA;AAC5B,MAAI,KAAM,WAAU,KAAK,OAAO,IAAI,CAAC;AACrC,YAAU,KAAK,QAAQ;AACvB,MAAI,YAAa,WAAU,KAAK,WAAW;AAE3C,QAAM,cAAc,mBAAmB,IAAI;AAC3C,QAAM,cAAc,mBAAmB,IAAI;AAC3C,QAAM,gBAAgB,qBAAqB,IAAI;AAE/C,SAAO;AAAA,IACL,IAAI,KAAK;AAAA,IACT,OAAO,KAAK,SAAS;AAAA,IACrB,UAAU,WAAW;AAAA,IACrB,MAAM,UAAU,KAAK,KAAK;AAAA,IAC1B,OAAO;AAAA,IACP,GAAI,eAAe,EAAE,YAAA;AAAA,IACrB,GAAI,eAAe,EAAE,YAAA;AAAA,IACrB,GAAI,iBAAiB,EAAE,cAAA;AAAA,EAAc;AAEzC;AAuBA,eAAsB,YAAY,SAAsD;AACtF,QAAM,EAAE,eAAe,UAAU,QAAQ,cAAc,oBAAoB;AAG3E,QAAM,UAAU,cAAc,IAAI,QAAQ;AAG1C,QAAM,iBAAiB,wBAAwB,OAAO,KAAK;AAG3D,QAAM,WAAW,CAAC,OAAeA,aAAkD;AACjF,QAAI,CAAC,MAAM,KAAA,EAAQ,QAAOA;AAE1B,UAAM,UAAU,SAAS,KAAK;AAC9B,WAAO,QAAQ,IAAI,CAAC,MAAM,SAAS,EAAE,SAAS,CAAC;AAAA,EACjD;AAGA,QAAM,cAA0B;AAGhC,SAAO,IAAI,QAAwB,CAAC,YAAY;AAC9C,QAAI,aAA6B;AAAA,MAC/B,aAAa,CAAA;AAAA,MACb,WAAW;AAAA,IAAA;AAGb,UAAM,iBAAiB,CAAC,WAAiC;AACvD,mBAAa;AAAA,IACf;AAEA,UAAM,eAAe,MAAY;AAC/B,mBAAa;AAAA,QACX,aAAa,CAAA;AAAA,QACb,WAAW;AAAA,MAAA;AAAA,IAEf;AAGA,UAAM,EAAE,kBAAkB;AAAA,MACxB,cAAc,aAAa;AAAA,QACzB;AAAA,QACA;AAAA,QACA,cAAc;AAAA,QACd;AAAA,QACA;AAAA,QACA;AAAA,QACA,YAAY;AAAA,QACZ,UAAU;AAAA,MAAA,CACX;AAAA,IAAA;AAIH,kBAAA,EACG,KAAK,MAAM;AACV,2BAAA;AACA,cAAQ,UAAU;AAAA,IACpB,CAAC,EACA,MAAM,MAAM;AACX,2BAAA;AACA,cAAQ;AAAA,QACN,aAAa,CAAA;AAAA,QACb,WAAW;AAAA,MAAA,CACZ;AAAA,IACH,CAAC;AAAA,EACL,CAAC;AACH;"}

package/dist/chunks/{index-DCBYzNj-.js → index-CmkN2-2A.js}

@@ -1,11 +1,12 @@
 import { Command, Option } from "commander";
-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 packageJson, u as getFulltextAttachmentTypes, v as startServerWithFileWatcher, w as BUILTIN_CONVERTER_NAMES, x as BUILTIN_CONVERTER_INFO } from "./index-CS8S6gE4.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 packageJson, u as getFulltextAttachmentTypes, v as startServerWithFileWatcher, w as BUILTIN_CONVERTER_NAMES, x as BUILTIN_CONVERTER_INFO } from "./index-B4-i4PrU.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 { promises, readFileSync, existsSync, mkdirSync, writeFileSync, lstatSync, unlinkSync, rmSync, symlinkSync } from "node:fs";
 import * as os from "node:os";
+import { homedir } from "node:os";
 import * as path from "node:path";
-import path__default, { join, basename, dirname } from "node:path";
+import path__default, { join, basename, dirname, relative } from "node:path";
 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-BG2eomDC.js";
 import { spawn, spawnSync } from "node:child_process";
@@ -893,15 +894,15 @@ class OperationsLibrary {
   }
   // High-level operations
   async search(options) {
-    const { searchReferences } = await import("./index-CS8S6gE4.js").then((n) => n.H);
+    const { searchReferences } = await import("./index-B4-i4PrU.js").then((n) => n.H);
     return searchReferences(this.library, options);
   }
   async list(options) {
-    const { listReferences } = await import("./index-CS8S6gE4.js").then((n) => n.G);
+    const { listReferences } = await import("./index-B4-i4PrU.js").then((n) => n.G);
     return listReferences(this.library, options ?? {});
   }
   async cite(options) {
-    const { citeReferences } = await import("./index-CS8S6gE4.js").then((n) => n.F);
+    const { citeReferences } = await import("./index-B4-i4PrU.js").then((n) => n.F);
     const defaultStyle = options.defaultStyle ?? this.citationConfig?.defaultStyle;
     const cslDirectory = options.cslDirectory ?? this.citationConfig?.cslDirectory;
     const mergedOptions = {
@@ -912,36 +913,36 @@ class OperationsLibrary {
     return citeReferences(this.library, mergedOptions);
   }
   async import(inputs, options) {
-    const { addReferences } = await import("./index-CS8S6gE4.js").then((n) => n.D);
+    const { addReferences } = await import("./index-B4-i4PrU.js").then((n) => n.D);
     return addReferences(inputs, this.library, options ?? {});
   }
   async check(options) {
-    const { checkReferences } = await import("./index-CS8S6gE4.js").then((n) => n.E);
+    const { checkReferences } = await import("./index-B4-i4PrU.js").then((n) => n.E);
     return checkReferences(this.library, options);
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-Cqss7VR_.js");
+    const { addAttachment: addAttachment2 } = await import("./index-B8iEozpf.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-Cqss7VR_.js");
+    const { listAttachments: listAttachments2 } = await import("./index-B8iEozpf.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-Cqss7VR_.js");
+    const { getAttachment: getAttachment2 } = await import("./index-B8iEozpf.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-Cqss7VR_.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-B8iEozpf.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-Cqss7VR_.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-B8iEozpf.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-Cqss7VR_.js");
+    const { openAttachment: openAttachment2 } = await import("./index-B8iEozpf.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1806,7 +1807,7 @@ function getAttachExitCode(result) {
 }
 async function executeInteractiveSelect$3(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B9b9Ez7Q.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2471,7 +2472,7 @@ 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-h15RI_Ae.js");
+      const { runFixInteraction } = await import("./fix-interaction-DWUzp9Ri.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 +2540,7 @@ function outputCheckError(error, format2) {
 }
 async function selectReferencesInteractively(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-B9b9Ez7Q.js");
   const allReferences = await context.library.getAll();
   if (allReferences.length === 0) {
     process.stderr.write("No references in library.\n");
@@ -2607,8 +2608,8 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-BG3Ef4Pd.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-D8beMum_.js");
+  const { runCiteFlow } = await import("./index-BuQm8A5F.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-aXByJLOo.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");
@@ -7291,7 +7292,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B9b9Ez7Q.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10867,7 +10868,7 @@ function getFulltextExitCode(result) {
 }
 async function executeInteractiveSelect$2(context, config2, multiSelect = false) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B9b9Ez7Q.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect }, config2.cli.tui)
@@ -11290,6 +11291,79 @@ const fulltext = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProp
   handleFulltextGetAction,
   handleFulltextOpenAction
 }, Symbol.toStringTag, { value: "Module" }));
+const skillMd = '---\nname: ref\ndescription: Manage academic references in CSL-JSON format. Add papers by DOI/PMID/ISBN/arXiv, search and list references, generate citations, manage full-text PDFs, and check for retractions.\nallowed-tools:\n  - Bash\n  - Read\n  - Write\n  - Edit\n  - Glob\n  - Grep\n---\n\n# ref — Reference Manager\n\nA CLI tool for managing academic references using CSL-JSON as the single source of truth.\n\n## Quick Reference\n\n| Task | Command |\n|------|---------|\n| Add by DOI | `ref add 10.1234/example` |\n| Add by PMID | `ref add 12345678` |\n| Add by ISBN | `ref add 978-0-123456-78-9` |\n| Add by arXiv | `ref add 2301.12345` |\n| Add from BibTeX | `ref add references.bib` |\n| Add from RIS | `ref add references.ris` |\n| Search | `ref search "query"` |\n| List all | `ref list` |\n| Show details | `ref show <id>` |\n| Generate citation | `ref cite <id>` |\n| Export | `ref export <id> --output bibtex` |\n| Attach full-text | `ref fulltext attach <id> paper.pdf` |\n| Fetch full-text | `ref fulltext fetch <id>` |\n| Check retractions | `ref check <id>` |\n| Remove | `ref remove <id>` |\n| Update fields | `ref update <id> --set "title=New Title"` |\n| Configure | `ref config set <key> <value>` |\n\n## Search Syntax\n\n- Simple text: `ref search "machine learning"`\n- By author: `ref search "author:Smith"`\n- By year: `ref search "year:2024"`\n- By type: `ref search "type:article-journal"`\n- By tag: `ref search "tag:review"`\n- Combined: `ref search "author:Smith year:2024"`\n- Case-sensitive: prefix with `C/` (e.g., `ref search "C/RNA"`)\n\n## Output Formats\n\nMost commands support `--output` or `--json` flags:\n\n- `--json` — JSON output for programmatic use\n- `--output bibtex` — BibTeX format\n- `--output yaml` — YAML format\n\n## Full Help\n\nRun `ref --help` for all commands and options.\nRun `ref <command> --help` for command-specific help.\n';
+const fulltextMd = '---\nname: ref/fulltext\ndescription: Guide for managing full-text PDFs and Markdown files. Covers fetching, attaching, converting, and organizing full-text content.\n---\n\n# Full-Text Management\n\nGuide for working with full-text files (PDFs and Markdown) using `ref`.\n\n## Attach Files\n\n```bash\n# Attach a PDF\nref fulltext attach <id> paper.pdf\n\n# Attach Markdown\nref fulltext attach <id> paper.md\n```\n\n## Fetch Open Access\n\n```bash\n# Auto-discover and download OA full text\nref fulltext fetch <id>\n\n# Fetch with auto-attach on add\nref add 10.1234/example --fetch-fulltext\n```\n\n## Convert Formats\n\n```bash\n# Convert PDF to Markdown (requires external converter)\nref fulltext convert <id>\n\n# Supported converters: marker, docling, mineru, pymupdf\n# Configure custom converter:\nref config set fulltext.pdfConverter.command "marker"\nref config set fulltext.pdfConverter.args "{input} --output {output_dir}"\n```\n\n## Retrieve Full Text\n\n```bash\n# Get file path\nref fulltext get <id>\n\n# Get Markdown content to stdout\nref fulltext get <id> --stdout\n\n# Prefer specific format\nref fulltext get <id> --markdown\nref fulltext get <id> --pdf\n\n# Open in default system viewer\nref fulltext open <id>\n```\n\n## Check Availability\n\n```bash\n# Discover OA sources without downloading\nref fulltext discover <id>\n```\n\n## Detach\n\n```bash\n# Remove full-text association (file remains on disk)\nref fulltext detach <id>\n```\n\n## Tips\n\n- Use `ref fulltext get <id> --stdout` to pipe content to other tools\n- Full-text files are stored in the attachments directory (see `ref config get attachments.directory`)\n- Use `ref show <id>` to see full-text status alongside metadata\n- Markdown is preferred for AI-readable content; use `ref fulltext convert` after attaching PDF\n';
+const manuscriptWritingMd = "---\nname: ref/manuscript-writing\ndescription: Workflow for managing references while writing academic manuscripts. Covers citation generation, bibliography export, and reference verification.\n---\n\n# Manuscript Writing Workflow\n\nGuide for managing references during academic manuscript writing with `ref`.\n\n## 1. Find and Cite\n\n```bash\n# Search your library\nref search \"Smith 2024\"\n\n# Generate an inline citation\nref cite <id>\n\n# Generate citation in specific style\nref cite <id> --style apa\nref cite <id> --style vancouver\n\n# Get Pandoc/LaTeX citation key\nref cite <id> --key\n```\n\n## 2. Build Bibliography\n\n```bash\n# Export all cited references as BibTeX\nref export <id1> <id2> <id3> --output bibtex > references.bib\n\n# Export by search query\nref search \"tag:cited\" --output bibtex > references.bib\n\n# Export all references\nref export --all --output bibtex > library.bib\n```\n\n## 3. Add New References During Writing\n\n```bash\n# Quick add by DOI from a paper you're reading\nref add 10.1234/example\n\n# Add from clipboard BibTeX (pipe from stdin)\necho '<bibtex>' | ref add -\n\n# Add and immediately get citation key\nref add 10.1234/example --json | jq -r '.added[0].id'\n```\n\n## 4. Verify Before Submission\n\n```bash\n# Check all cited references for retractions\nref check <id1> <id2> <id3>\n\n# Verify metadata accuracy\nref check <id> --metadata\n\n# Show full details for final review\nref show <id>\n```\n\n## 5. Full-Text Management\n\n```bash\n# Attach supplementary files\nref fulltext attach <id> paper.pdf\nref fulltext attach <id> supplement.pdf\n\n# Get full-text path for reading\nref fulltext get <id>\n\n# Open in default viewer\nref fulltext open <id>\n```\n\n## Tips\n\n- Use `ref cite <id> --key` to get `@AuthorYear` keys for Pandoc\n- Use `ref show <id> --output yaml` for quick metadata overview\n- Use `ref url <id>` to get DOI/PubMed URLs for linking\n- Tag references with `ref update <id> --set \"tags=cited\"` to track what's in the manuscript\n";
+const systematicReviewMd = '---\nname: ref/systematic-review\ndescription: Workflow for conducting systematic literature reviews using reference-manager. Covers search strategy, screening, and evidence synthesis.\n---\n\n# Systematic Review Workflow\n\nGuide for conducting systematic literature reviews with `ref`.\n\n## 1. Build Search Set\n\nAdd references from multiple sources:\n\n```bash\n# From DOIs (e.g., exported from database search)\nref add 10.1234/study1 10.1234/study2 10.1234/study3\n\n# From BibTeX exported by PubMed/Scopus/Web of Science\nref add pubmed-results.bib\nref add scopus-results.ris\n\n# By PMID list\nref add 12345678 23456789 34567890\n```\n\n## 2. Tag and Organize\n\nUse tags to track screening stages:\n\n```bash\n# Tag references for screening\nref update <id> --set "tags=screening"\n\n# After title/abstract screening\nref update <id> --set "tags=included"\nref update <id> --set "tags=excluded"\n\n# After full-text review\nref update <id> --set "tags=final-included"\n```\n\n## 3. Full-Text Collection\n\n```bash\n# Auto-fetch open access full texts\nref fulltext fetch <id>\n\n# Attach manually obtained PDFs\nref fulltext attach <id> path/to/paper.pdf\n\n# Convert PDF to Markdown for text analysis\nref fulltext convert <id>\n```\n\n## 4. Quality Check\n\n```bash\n# Check for retractions or corrections\nref check <id>\n\n# Verify metadata against upstream sources\nref check <id> --metadata\n```\n\n## 5. Export for Analysis\n\n```bash\n# Export included studies as BibTeX\nref search "tag:final-included" --output bibtex > included.bib\n\n# Export as JSON for custom analysis\nref search "tag:final-included" --json > included.json\n```\n\n## Tips\n\n- Use `ref list --sort date-desc` to review chronologically\n- Use `ref search "tag:screening"` to find unprocessed references\n- Use `ref show <id>` to inspect full metadata before decisions\n- Duplicates are auto-detected on `ref add` — review skip messages\n';
+const SKILL_FILES = [
+  ["SKILL.md", skillMd],
+  ["references/systematic-review.md", systematicReviewMd],
+  ["references/manuscript-writing.md", manuscriptWritingMd],
+  ["references/fulltext.md", fulltextMd]
+];
+async function writeSkills(options) {
+  const { targetDir, force = false, user = false } = options;
+  const baseDir = user ? homedir() : targetDir;
+  const agentsDir = join(baseDir, ".agents", "skills", "ref");
+  const claudeDir = join(baseDir, ".claude", "skills");
+  const claudeLink = join(claudeDir, "ref");
+  const written = [];
+  const skipped = [];
+  mkdirSync(join(agentsDir, "references"), { recursive: true });
+  for (const [relativePath, content] of SKILL_FILES) {
+    const filePath = join(agentsDir, relativePath);
+    if (existsSync(filePath) && !force) {
+      skipped.push(relativePath);
+      continue;
+    }
+    writeFileSync(filePath, content, "utf-8");
+    written.push(relativePath);
+  }
+  let linkCreated = false;
+  mkdirSync(claudeDir, { recursive: true });
+  if (force && existsSync(claudeLink)) {
+    const stat2 = lstatSync(claudeLink);
+    if (stat2.isSymbolicLink()) {
+      unlinkSync(claudeLink);
+    } else if (stat2.isDirectory()) {
+      rmSync(claudeLink, { recursive: true, force: true });
+    }
+  }
+  if (!existsSync(claudeLink)) {
+    const linkTarget = relative(claudeDir, agentsDir);
+    symlinkSync(linkTarget, claudeLink, "junction");
+    linkCreated = true;
+  }
+  return { written, skipped, linkCreated };
+}
+async function executeInstallSkills(options) {
+  return writeSkills({
+    targetDir: process.cwd(),
+    force: options.force,
+    ...options.user != null && { user: options.user }
+  });
+}
+function formatInstallSkillsOutput(result) {
+  const lines = [];
+  if (result.written.length === 0 && result.skipped.length > 0) {
+    lines.push("Skills already up-to-date. Use --force to overwrite.");
+    lines.push(`  ${result.skipped.length} files skipped`);
+    return lines.join("\n");
+  }
+  if (result.written.length > 0) {
+    lines.push(`Installed ${result.written.length} skill files to .agents/skills/ref/`);
+    for (const file of result.written) {
+      lines.push(`  + ${file}`);
+    }
+  }
+  if (result.skipped.length > 0) {
+    lines.push(`  ${result.skipped.length} files skipped (already exist)`);
+  }
+  if (result.linkCreated) {
+    lines.push("Created symlink: .claude/skills/ref -> .agents/skills/ref");
+  }
+  return lines.join("\n");
+}
 function buildResourceIndicators(item) {
   const labels = [];
   const attachments = item.custom?.attachments;
@@ -26836,49 +26910,49 @@ function requireFastUri() {
     schemelessOptions.skipEscape = true;
     return serialize2(resolved, schemelessOptions);
   }
-  function resolveComponent(base, relative, options, skipNormalization) {
+  function resolveComponent(base, relative2, options, skipNormalization) {
     const target = {};
     if (!skipNormalization) {
       base = parse2(serialize2(base, options), options);
-      relative = parse2(serialize2(relative, options), options);
+      relative2 = parse2(serialize2(relative2, options), options);
     }
     options = options || {};
-    if (!options.tolerant && relative.scheme) {
-      target.scheme = relative.scheme;
-      target.userinfo = relative.userinfo;
-      target.host = relative.host;
-      target.port = relative.port;
-      target.path = removeDotSegments(relative.path || "");
-      target.query = relative.query;
+    if (!options.tolerant && relative2.scheme) {
+      target.scheme = relative2.scheme;
+      target.userinfo = relative2.userinfo;
+      target.host = relative2.host;
+      target.port = relative2.port;
+      target.path = removeDotSegments(relative2.path || "");
+      target.query = relative2.query;
     } else {
-      if (relative.userinfo !== void 0 || relative.host !== void 0 || relative.port !== void 0) {
-        target.userinfo = relative.userinfo;
-        target.host = relative.host;
-        target.port = relative.port;
-        target.path = removeDotSegments(relative.path || "");
-        target.query = relative.query;
+      if (relative2.userinfo !== void 0 || relative2.host !== void 0 || relative2.port !== void 0) {
+        target.userinfo = relative2.userinfo;
+        target.host = relative2.host;
+        target.port = relative2.port;
+        target.path = removeDotSegments(relative2.path || "");
+        target.query = relative2.query;
       } else {
-        if (!relative.path) {
+        if (!relative2.path) {
           target.path = base.path;
-          if (relative.query !== void 0) {
-            target.query = relative.query;
+          if (relative2.query !== void 0) {
+            target.query = relative2.query;
           } else {
             target.query = base.query;
           }
         } else {
-          if (relative.path[0] === "/") {
-            target.path = removeDotSegments(relative.path);
+          if (relative2.path[0] === "/") {
+            target.path = removeDotSegments(relative2.path);
           } else {
             if ((base.userinfo !== void 0 || base.host !== void 0 || base.port !== void 0) && !base.path) {
-              target.path = "/" + relative.path;
+              target.path = "/" + relative2.path;
             } else if (!base.path) {
-              target.path = relative.path;
+              target.path = relative2.path;
             } else {
-              target.path = base.path.slice(0, base.path.lastIndexOf("/") + 1) + relative.path;
+              target.path = base.path.slice(0, base.path.lastIndexOf("/") + 1) + relative2.path;
             }
             target.path = removeDotSegments(target.path);
           }
-          target.query = relative.query;
+          target.query = relative2.query;
         }
         target.userinfo = base.userinfo;
         target.host = base.host;
@@ -26886,7 +26960,7 @@ function requireFastUri() {
       }
       target.scheme = base.scheme;
     }
-    target.fragment = relative.fragment;
+    target.fragment = relative2.fragment;
     return target;
   }
   function equal2(uriA, uriB, options) {
@@ -32451,7 +32525,7 @@ 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-CS8S6gE4.js").then((n) => n.A);
+    const { removeReference } = await import("./index-B4-i4PrU.js").then((n) => n.A);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -32506,7 +32580,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-B9b9Ez7Q.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32731,7 +32805,7 @@ 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-BG3Ef4Pd.js");
+  const { runSearchFlow } = await import("./index-BuQm8A5F.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();
@@ -32750,7 +32824,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-D5s90TfM.js");
+    const { isSideEffectAction } = await import("./action-menu-DLEwSKrj.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -33048,7 +33122,7 @@ function formatShowOutput(item, options, attachmentsDirectory) {
 }
 async function executeInteractiveSelect$1(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B9b9Ez7Q.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33297,7 +33371,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B9b9Ez7Q.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33592,7 +33666,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-B9b9Ez7Q.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -34040,6 +34114,7 @@ function createProgram() {
   registerAttachCommand(program);
   registerMcpCommand(program);
   registerUrlCommand(program);
+  registerInstallCommand(program);
   registerConfigCommand(program);
   registerCompletionCommand(program);
   return program;
@@ -34204,7 +34279,7 @@ function shouldAutoFetch(cliFlag, configEnabled) {
   return configEnabled;
 }
 async function performAutoFetch(addedItems, context, config2) {
-  const { fulltextFetch: fulltextFetch2 } = await import("./index-CS8S6gE4.js").then((n) => n.z);
+  const { fulltextFetch: fulltextFetch2 } = await import("./index-B4-i4PrU.js").then((n) => n.z);
   const fetchResults = await autoFetchFulltext(addedItems, context, {
     fulltextConfig: config2.fulltext,
     fulltextDirectory: config2.attachments.directory,
@@ -34470,6 +34545,25 @@ function registerUrlCommand(program) {
     await handleUrlAction(identifiers.length > 0 ? identifiers : void 0, options, globalOpts);
   });
 }
+function registerInstallCommand(program) {
+  const installCmd = program.command("install").description("Install tools and integrations");
+  installCmd.command("skills").description("Install Agent Skills (SKILL.md) for AI coding agents").option("-f, --force", "Overwrite existing files").option("-u, --user", "Install to user-level directory (~/.agents/skills/)").action(async (options) => {
+    try {
+      const result = await executeInstallSkills({
+        force: options.force ?? false,
+        ...options.user != null && { user: options.user }
+      });
+      const output = formatInstallSkillsOutput(result);
+      process.stdout.write(`${output}
+`);
+      setExitCode(ExitCode.SUCCESS);
+    } catch (error) {
+      process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}
+`);
+      setExitCode(ExitCode.INTERNAL_ERROR);
+    }
+  });
+}
 async function main(argv) {
   const program = createProgram();
   if (process.env.COMP_LINE) {
@@ -34499,4 +34593,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-DCBYzNj-.js.map
+//# sourceMappingURL=index-CmkN2-2A.js.map