@ncukondo/reference-manager 0.27.1 → 0.27.2

package/dist/chunks/{index-D6flikkH.js → index-SwsAKyQr.js}

@@ -1,5 +1,5 @@
-import { a } from "./index-DUpYvm-W.js";
-import { d, g, l, o, s } from "./index-B1pKaejY.js";
+import { a } from "./index-BdLVfbj0.js";
+import { d, g, l, o, s } from "./index-DkJT7s7N.js";
 export {
   a as addAttachment,
   d as detachAttachment,
@@ -8,4 +8,4 @@ export {
   o as openAttachment,
   s as syncAttachments
 };
-//# sourceMappingURL=index-D6flikkH.js.map
+//# sourceMappingURL=index-SwsAKyQr.js.map

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

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

package/dist/chunks/{pubmed-client-mGn5jDIc.js → pubmed-client-DH9y2tEZ.js}

@@ -1,4 +1,4 @@
-import { g as getRateLimiter } from "./index-DUpYvm-W.js";
+import { g as getRateLimiter } from "./index-BdLVfbj0.js";
 const PUBMED_ESUMMARY_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi";
 function buildEsummaryUrl(pmid, config) {
   const url = new URL(PUBMED_ESUMMARY_BASE);
@@ -48,4 +48,4 @@ async function queryPubmed(pmid, config) {
 export {
   queryPubmed
 };
-//# sourceMappingURL=pubmed-client-mGn5jDIc.js.map
+//# sourceMappingURL=pubmed-client-DH9y2tEZ.js.map

package/dist/chunks/{pubmed-client-mGn5jDIc.js.map → pubmed-client-DH9y2tEZ.js.map}

@@ -1 +1 @@
-{"version":3,"file":"pubmed-client-mGn5jDIc.js","sources":["../../src/features/check/pubmed-client.ts"],"sourcesContent":["import { getRateLimiter } from \"../import/rate-limiter.js\";\n\nconst PUBMED_ESUMMARY_BASE = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi\";\n\nexport type PubmedResult =\n  | { success: true; isRetracted: boolean; hasConcern: boolean }\n  | { success: false; error: string };\n\n/**\n * Build PubMed E-utilities esummary URL.\n */\nfunction buildEsummaryUrl(pmid: string, config?: { email?: string; apiKey?: string }): string {\n  const url = new URL(PUBMED_ESUMMARY_BASE);\n  url.searchParams.set(\"db\", \"pubmed\");\n  url.searchParams.set(\"id\", pmid);\n  url.searchParams.set(\"retmode\", \"json\");\n  if (config?.email) {\n    url.searchParams.set(\"email\", config.email);\n  }\n  if (config?.apiKey) {\n    url.searchParams.set(\"api_key\", config.apiKey);\n  }\n  return url.toString();\n}\n\n/**\n * Query PubMed E-utilities for publication status of a PMID.\n *\n * @param pmid - The PubMed ID to query\n * @param config - Optional PubMed config (email, apiKey)\n * @returns PubMed result with retraction status\n */\nexport async function queryPubmed(\n  pmid: string,\n  config?: { email?: string; apiKey?: string }\n): Promise<PubmedResult> {\n  const rateLimiterConfig = config?.apiKey ? { pubmedApiKey: config.apiKey } : {};\n  const rateLimiter = getRateLimiter(\"pubmed\", rateLimiterConfig);\n  await rateLimiter.acquire();\n\n  try {\n    const url = buildEsummaryUrl(pmid, config);\n    const response = await fetch(url);\n\n    if (!response.ok) {\n      return {\n        success: false,\n        error: `PubMed API returned ${response.status} ${response.statusText}`,\n      };\n    }\n\n    const data = (await response.json()) as Record<string, unknown>;\n    const resultObj = data.result as Record<string, unknown> | undefined;\n    const articleData = resultObj?.[pmid] as Record<string, unknown> | undefined;\n\n    if (!articleData) {\n      return { success: true, isRetracted: false, hasConcern: false };\n    }\n\n    const pubTypes = (articleData.pubtype ?? []) as string[];\n    const isRetracted = pubTypes.some(\n      (t) => t === \"Retracted Publication\" || t === \"Retraction of Publication\"\n    );\n    const hasConcern = pubTypes.some((t) => t === \"Expression of Concern\");\n\n    return { success: true, isRetracted, hasConcern };\n  } catch (error) {\n    return {\n      success: false,\n      error: error instanceof Error ? error.message : String(error),\n    };\n  }\n}\n"],"names":[],"mappings":";AAEA,MAAM,uBAAuB;AAS7B,SAAS,iBAAiB,MAAc,QAAsD;AAC5F,QAAM,MAAM,IAAI,IAAI,oBAAoB;AACxC,MAAI,aAAa,IAAI,MAAM,QAAQ;AACnC,MAAI,aAAa,IAAI,MAAM,IAAI;AAC/B,MAAI,aAAa,IAAI,WAAW,MAAM;AACtC,MAAI,QAAQ,OAAO;AACjB,QAAI,aAAa,IAAI,SAAS,OAAO,KAAK;AAAA,EAC5C;AACA,MAAI,QAAQ,QAAQ;AAClB,QAAI,aAAa,IAAI,WAAW,OAAO,MAAM;AAAA,EAC/C;AACA,SAAO,IAAI,SAAA;AACb;AASA,eAAsB,YACpB,MACA,QACuB;AACvB,QAAM,oBAAoB,QAAQ,SAAS,EAAE,cAAc,OAAO,OAAA,IAAW,CAAA;AAC7E,QAAM,cAAc,eAAe,UAAU,iBAAiB;AAC9D,QAAM,YAAY,QAAA;AAElB,MAAI;AACF,UAAM,MAAM,iBAAiB,MAAM,MAAM;AACzC,UAAM,WAAW,MAAM,MAAM,GAAG;AAEhC,QAAI,CAAC,SAAS,IAAI;AAChB,aAAO;AAAA,QACL,SAAS;AAAA,QACT,OAAO,uBAAuB,SAAS,MAAM,IAAI,SAAS,UAAU;AAAA,MAAA;AAAA,IAExE;AAEA,UAAM,OAAQ,MAAM,SAAS,KAAA;AAC7B,UAAM,YAAY,KAAK;AACvB,UAAM,cAAc,YAAY,IAAI;AAEpC,QAAI,CAAC,aAAa;AAChB,aAAO,EAAE,SAAS,MAAM,aAAa,OAAO,YAAY,MAAA;AAAA,IAC1D;AAEA,UAAM,WAAY,YAAY,WAAW,CAAA;AACzC,UAAM,cAAc,SAAS;AAAA,MAC3B,CAAC,MAAM,MAAM,2BAA2B,MAAM;AAAA,IAAA;AAEhD,UAAM,aAAa,SAAS,KAAK,CAAC,MAAM,MAAM,uBAAuB;AAErE,WAAO,EAAE,SAAS,MAAM,aAAa,WAAA;AAAA,EACvC,SAAS,OAAO;AACd,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO,iBAAiB,QAAQ,MAAM,UAAU,OAAO,KAAK;AAAA,IAAA;AAAA,EAEhE;AACF;"}
+{"version":3,"file":"pubmed-client-DH9y2tEZ.js","sources":["../../src/features/check/pubmed-client.ts"],"sourcesContent":["import { getRateLimiter } from \"../import/rate-limiter.js\";\n\nconst PUBMED_ESUMMARY_BASE = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi\";\n\nexport type PubmedResult =\n  | { success: true; isRetracted: boolean; hasConcern: boolean }\n  | { success: false; error: string };\n\n/**\n * Build PubMed E-utilities esummary URL.\n */\nfunction buildEsummaryUrl(pmid: string, config?: { email?: string; apiKey?: string }): string {\n  const url = new URL(PUBMED_ESUMMARY_BASE);\n  url.searchParams.set(\"db\", \"pubmed\");\n  url.searchParams.set(\"id\", pmid);\n  url.searchParams.set(\"retmode\", \"json\");\n  if (config?.email) {\n    url.searchParams.set(\"email\", config.email);\n  }\n  if (config?.apiKey) {\n    url.searchParams.set(\"api_key\", config.apiKey);\n  }\n  return url.toString();\n}\n\n/**\n * Query PubMed E-utilities for publication status of a PMID.\n *\n * @param pmid - The PubMed ID to query\n * @param config - Optional PubMed config (email, apiKey)\n * @returns PubMed result with retraction status\n */\nexport async function queryPubmed(\n  pmid: string,\n  config?: { email?: string; apiKey?: string }\n): Promise<PubmedResult> {\n  const rateLimiterConfig = config?.apiKey ? { pubmedApiKey: config.apiKey } : {};\n  const rateLimiter = getRateLimiter(\"pubmed\", rateLimiterConfig);\n  await rateLimiter.acquire();\n\n  try {\n    const url = buildEsummaryUrl(pmid, config);\n    const response = await fetch(url);\n\n    if (!response.ok) {\n      return {\n        success: false,\n        error: `PubMed API returned ${response.status} ${response.statusText}`,\n      };\n    }\n\n    const data = (await response.json()) as Record<string, unknown>;\n    const resultObj = data.result as Record<string, unknown> | undefined;\n    const articleData = resultObj?.[pmid] as Record<string, unknown> | undefined;\n\n    if (!articleData) {\n      return { success: true, isRetracted: false, hasConcern: false };\n    }\n\n    const pubTypes = (articleData.pubtype ?? []) as string[];\n    const isRetracted = pubTypes.some(\n      (t) => t === \"Retracted Publication\" || t === \"Retraction of Publication\"\n    );\n    const hasConcern = pubTypes.some((t) => t === \"Expression of Concern\");\n\n    return { success: true, isRetracted, hasConcern };\n  } catch (error) {\n    return {\n      success: false,\n      error: error instanceof Error ? error.message : String(error),\n    };\n  }\n}\n"],"names":[],"mappings":";AAEA,MAAM,uBAAuB;AAS7B,SAAS,iBAAiB,MAAc,QAAsD;AAC5F,QAAM,MAAM,IAAI,IAAI,oBAAoB;AACxC,MAAI,aAAa,IAAI,MAAM,QAAQ;AACnC,MAAI,aAAa,IAAI,MAAM,IAAI;AAC/B,MAAI,aAAa,IAAI,WAAW,MAAM;AACtC,MAAI,QAAQ,OAAO;AACjB,QAAI,aAAa,IAAI,SAAS,OAAO,KAAK;AAAA,EAC5C;AACA,MAAI,QAAQ,QAAQ;AAClB,QAAI,aAAa,IAAI,WAAW,OAAO,MAAM;AAAA,EAC/C;AACA,SAAO,IAAI,SAAA;AACb;AASA,eAAsB,YACpB,MACA,QACuB;AACvB,QAAM,oBAAoB,QAAQ,SAAS,EAAE,cAAc,OAAO,OAAA,IAAW,CAAA;AAC7E,QAAM,cAAc,eAAe,UAAU,iBAAiB;AAC9D,QAAM,YAAY,QAAA;AAElB,MAAI;AACF,UAAM,MAAM,iBAAiB,MAAM,MAAM;AACzC,UAAM,WAAW,MAAM,MAAM,GAAG;AAEhC,QAAI,CAAC,SAAS,IAAI;AAChB,aAAO;AAAA,QACL,SAAS;AAAA,QACT,OAAO,uBAAuB,SAAS,MAAM,IAAI,SAAS,UAAU;AAAA,MAAA;AAAA,IAExE;AAEA,UAAM,OAAQ,MAAM,SAAS,KAAA;AAC7B,UAAM,YAAY,KAAK;AACvB,UAAM,cAAc,YAAY,IAAI;AAEpC,QAAI,CAAC,aAAa;AAChB,aAAO,EAAE,SAAS,MAAM,aAAa,OAAO,YAAY,MAAA;AAAA,IAC1D;AAEA,UAAM,WAAY,YAAY,WAAW,CAAA;AACzC,UAAM,cAAc,SAAS;AAAA,MAC3B,CAAC,MAAM,MAAM,2BAA2B,MAAM;AAAA,IAAA;AAEhD,UAAM,aAAa,SAAS,KAAK,CAAC,MAAM,MAAM,uBAAuB;AAErE,WAAO,EAAE,SAAS,MAAM,aAAa,WAAA;AAAA,EACvC,SAAS,OAAO;AACd,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO,iBAAiB,QAAQ,MAAM,UAAU,OAAO,KAAK;AAAA,IAAA;AAAA,EAEhE;AACF;"}

package/dist/chunks/{reference-select-BpTCTnrO.js → reference-select-Ce9pG8cC.js}

@@ -1,8 +1,8 @@
 import { t as tokenize, s as search } from "./file-watcher-Dlx0PolG.js";
 import { render, useApp } from "ink";
 import { createElement } from "react";
-import { r as restoreStdinAfterInk } from "./index-B1pKaejY.js";
-import { t as toChoice, c as calculateEffectiveLimit, S as SearchableMultiSelect } from "./SearchableMultiSelect-CixI0oIE.js";
+import { r as restoreStdinAfterInk } from "./index-DkJT7s7N.js";
+import { t as toChoice, c as calculateEffectiveLimit, S as SearchableMultiSelect } from "./SearchableMultiSelect-0cyizees.js";
 import { checkTTY } from "./tty-BMyaEOhX.js";
 function SearchPromptApp({
   choices,
@@ -126,4 +126,4 @@ export {
   selectReferenceItemsOrExit,
   selectReferencesOrExit
 };
-//# sourceMappingURL=reference-select-BpTCTnrO.js.map
+//# sourceMappingURL=reference-select-Ce9pG8cC.js.map

package/dist/chunks/{reference-select-BpTCTnrO.js.map → reference-select-Ce9pG8cC.js.map}

@@ -1 +1 @@
-{"version":3,"file":"reference-select-BpTCTnrO.js","sources":["../../src/features/interactive/search-prompt.ts","../../src/features/interactive/reference-select.ts"],"sourcesContent":["/**\n * Interactive search prompt using React Ink\n *\n * Provides real-time incremental search with multiple selection support.\n */\n\nimport { render, useApp } from \"ink\";\nimport type React from \"react\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { SearchResult } from \"../search/types.js\";\nimport { restoreStdinAfterInk } from \"./alternate-screen.js\";\nimport { toChoice } from \"./choice-builder.js\";\nimport {\n  type Choice,\n  SearchableMultiSelect,\n  type SortOption,\n  calculateEffectiveLimit,\n  getTerminalHeight,\n  getTerminalWidth,\n} from \"./components/index.js\";\n\n/**\n * Configuration for the search prompt\n */\nexport interface SearchPromptConfig {\n  /** Maximum number of results to display */\n  limit: number;\n  /** Debounce delay in milliseconds (not used in Ink version, kept for API compatibility) */\n  debounceMs: number;\n}\n\n/**\n * Search function type for filtering references\n */\nexport type SearchFunction = (query: string) => SearchResult[];\n\n/**\n * Result from the search prompt\n */\nexport interface SearchPromptResult {\n  /** Selected references */\n  selected: CslItem[];\n  /** Whether the prompt was cancelled */\n  cancelled: boolean;\n}\n\nexport { calculateEffectiveLimit, getTerminalHeight, getTerminalWidth };\n\n/**\n * Props for the SearchPromptApp component\n */\ninterface SearchPromptAppProps {\n  choices: Choice<CslItem>[];\n  filterFn: (query: string, choices: Choice<CslItem>[]) => Choice<CslItem>[];\n  visibleCount: number;\n  defaultSort: SortOption;\n  onSubmit: (selected: Choice<CslItem>[]) => void;\n  onCancel: () => void;\n}\n\n/**\n * SearchPromptApp component - wraps SearchableMultiSelect for search prompt\n */\nfunction SearchPromptApp({\n  choices,\n  filterFn,\n  visibleCount,\n  defaultSort,\n  onSubmit,\n  onCancel,\n}: SearchPromptAppProps): React.ReactElement {\n  const { exit } = useApp();\n\n  const handleSubmit = (selected: Choice<CslItem>[]): void => {\n    onSubmit(selected);\n    exit();\n  };\n\n  const handleCancel = (): void => {\n    onCancel();\n    exit();\n  };\n\n  return createElement(SearchableMultiSelect<CslItem>, {\n    choices,\n    filterFn,\n    visibleCount,\n    onSubmit: handleSubmit,\n    onCancel: handleCancel,\n    header: \"Search references\",\n    placeholder: \"Type to search...\",\n    defaultSort,\n  });\n}\n\n/**\n * Creates and runs an interactive search prompt\n */\nexport async function runSearchPrompt(\n  allReferences: CslItem[],\n  searchFn: SearchFunction,\n  config: SearchPromptConfig,\n  _initialQuery = \"\" // kept for API compatibility, not used in Ink version\n): Promise<SearchPromptResult> {\n  // Convert references to choices\n  const choices = allReferences.map(toChoice);\n\n  // Calculate effective visible count\n  const effectiveLimit = calculateEffectiveLimit(config.limit);\n\n  // Create filter function using the provided search function\n  const filterFn = (query: string, choices: Choice<CslItem>[]): Choice<CslItem>[] => {\n    if (!query.trim()) return choices;\n\n    const results = searchFn(query);\n    return results.map((r) => toChoice(r.reference));\n  };\n\n  // Create a promise to capture the result\n  return new Promise<SearchPromptResult>((resolve) => {\n    let result: SearchPromptResult = { selected: [], cancelled: true };\n\n    const handleSubmit = (selected: Choice<CslItem>[]): void => {\n      result = {\n        selected: selected.map((c) => c.value),\n        cancelled: false,\n      };\n    };\n\n    const handleCancel = (): void => {\n      result = {\n        selected: [],\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app\n    const { waitUntilExit, clear } = render(\n      createElement(SearchPromptApp, {\n        choices,\n        filterFn,\n        visibleCount: effectiveLimit,\n        defaultSort: \"updated-desc\",\n        onSubmit: handleSubmit,\n        onCancel: handleCancel,\n      })\n    );\n\n    // Wait for the app to exit, clear the screen, then resolve\n    waitUntilExit()\n      .then(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve(result);\n      })\n      .catch(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve({\n          selected: [],\n          cancelled: true,\n        });\n      });\n  });\n}\n","/**\n * Shared reference selection utility for interactive ID selection.\n *\n * This module provides a reusable function to select references interactively\n * using the existing search prompt infrastructure.\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { search } from \"../search/matcher.js\";\nimport { tokenize } from \"../search/tokenizer.js\";\nimport { type SearchPromptConfig, runSearchPrompt } from \"./search-prompt.js\";\nimport { checkTTY } from \"./tty.js\";\n\n/**\n * Options for reference selection\n */\nexport interface ReferenceSelectOptions {\n  /** Whether to allow multiple selection (default: true) */\n  multiSelect: boolean;\n  /** Custom prompt message */\n  prompt?: string;\n  /** Initial search query */\n  initialQuery?: string;\n}\n\n/**\n * Result from reference selection\n */\nexport interface ReferenceSelectResult {\n  /** Selected references */\n  selected: CslItem[];\n  /** Whether the selection was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Run interactive reference selection.\n *\n * Launches an interactive search prompt to select references from the library.\n * Supports both single and multiple selection modes.\n *\n * @param allReferences - All references available for selection\n * @param options - Selection options\n * @param config - Interactive prompt configuration\n * @returns Selection result with selected references\n * @throws TTYError if not running in a TTY environment\n */\nexport async function runReferenceSelect(\n  allReferences: CslItem[],\n  options: ReferenceSelectOptions,\n  config: SearchPromptConfig\n): Promise<ReferenceSelectResult> {\n  // Check TTY requirement\n  checkTTY();\n\n  // Create search function for runSearchPrompt\n  const searchFn = (query: string) => {\n    const { tokens } = tokenize(query);\n    return search(allReferences, tokens);\n  };\n\n  // Run search prompt\n  const searchResult = await runSearchPrompt(\n    allReferences,\n    searchFn,\n    config,\n    options.initialQuery ?? \"\"\n  );\n\n  if (searchResult.cancelled) {\n    return { selected: [], cancelled: true };\n  }\n\n  // For single-select mode, return only the first selected item\n  const selected = options.multiSelect ? searchResult.selected : searchResult.selected.slice(0, 1);\n\n  return {\n    selected,\n    cancelled: false,\n  };\n}\n\n/**\n * Options for selectReferencesOrExit helper\n */\nexport interface SelectReferencesOrExitOptions {\n  /** Whether to allow multiple selection */\n  multiSelect: boolean;\n  /** Initial search query */\n  initialQuery?: string;\n}\n\n/**\n * Select references interactively or exit if cancelled/empty.\n *\n * This is a convenience wrapper around runReferenceSelect that handles\n * common patterns:\n * - Exits with code 0 if library is empty\n * - Exits with code 0 if selection is cancelled\n * - Returns selected identifiers\n *\n * @param allReferences - All references available for selection\n * @param options - Selection options\n * @param config - Interactive prompt configuration\n * @returns Array of selected reference IDs (never empty)\n */\nexport async function selectReferencesOrExit(\n  allReferences: CslItem[],\n  options: SelectReferencesOrExitOptions,\n  config: SearchPromptConfig\n): Promise<string[]> {\n  if (allReferences.length === 0) {\n    process.stderr.write(\"No references in library.\\n\");\n    process.exit(0);\n  }\n\n  const selectResult = await runReferenceSelect(allReferences, options, config);\n\n  if (selectResult.cancelled || selectResult.selected.length === 0) {\n    process.exit(0);\n  }\n\n  return selectResult.selected.map((item) => item.id);\n}\n\n/**\n * Select reference items interactively or exit if cancelled/empty.\n *\n * Similar to selectReferencesOrExit but returns full CslItem objects\n * instead of just identifiers. 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+{"version":3,"file":"reference-select-Ce9pG8cC.js","sources":["../../src/features/interactive/search-prompt.ts","../../src/features/interactive/reference-select.ts"],"sourcesContent":["/**\n * Interactive search prompt using React Ink\n *\n * Provides real-time incremental search with multiple selection support.\n */\n\nimport { render, useApp } from \"ink\";\nimport type React from \"react\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { SearchResult } from \"../search/types.js\";\nimport { restoreStdinAfterInk } from \"./alternate-screen.js\";\nimport { toChoice } from \"./choice-builder.js\";\nimport {\n  type Choice,\n  SearchableMultiSelect,\n  type SortOption,\n  calculateEffectiveLimit,\n  getTerminalHeight,\n  getTerminalWidth,\n} from \"./components/index.js\";\n\n/**\n * Configuration for the search prompt\n */\nexport interface SearchPromptConfig {\n  /** Maximum number of results to display */\n  limit: number;\n  /** Debounce delay in milliseconds (not used in Ink version, kept for API compatibility) */\n  debounceMs: number;\n}\n\n/**\n * Search function type for filtering references\n */\nexport type SearchFunction = (query: string) => SearchResult[];\n\n/**\n * Result from the search prompt\n */\nexport interface SearchPromptResult {\n  /** Selected references */\n  selected: CslItem[];\n  /** Whether the prompt was cancelled */\n  cancelled: boolean;\n}\n\nexport { calculateEffectiveLimit, getTerminalHeight, getTerminalWidth };\n\n/**\n * Props for the SearchPromptApp component\n */\ninterface SearchPromptAppProps {\n  choices: Choice<CslItem>[];\n  filterFn: (query: string, choices: Choice<CslItem>[]) => Choice<CslItem>[];\n  visibleCount: number;\n  defaultSort: SortOption;\n  onSubmit: (selected: Choice<CslItem>[]) => void;\n  onCancel: () => void;\n}\n\n/**\n * SearchPromptApp component - wraps SearchableMultiSelect for search prompt\n */\nfunction SearchPromptApp({\n  choices,\n  filterFn,\n  visibleCount,\n  defaultSort,\n  onSubmit,\n  onCancel,\n}: SearchPromptAppProps): React.ReactElement {\n  const { exit } = useApp();\n\n  const handleSubmit = (selected: Choice<CslItem>[]): void => {\n    onSubmit(selected);\n    exit();\n  };\n\n  const handleCancel = (): void => {\n    onCancel();\n    exit();\n  };\n\n  return createElement(SearchableMultiSelect<CslItem>, {\n    choices,\n    filterFn,\n    visibleCount,\n    onSubmit: handleSubmit,\n    onCancel: handleCancel,\n    header: \"Search references\",\n    placeholder: \"Type to search...\",\n    defaultSort,\n  });\n}\n\n/**\n * Creates and runs an interactive search prompt\n */\nexport async function runSearchPrompt(\n  allReferences: CslItem[],\n  searchFn: SearchFunction,\n  config: SearchPromptConfig,\n  _initialQuery = \"\" // kept for API compatibility, not used in Ink version\n): Promise<SearchPromptResult> {\n  // Convert references to choices\n  const choices = allReferences.map(toChoice);\n\n  // Calculate effective visible count\n  const effectiveLimit = calculateEffectiveLimit(config.limit);\n\n  // Create filter function using the provided search function\n  const filterFn = (query: string, choices: Choice<CslItem>[]): Choice<CslItem>[] => {\n    if (!query.trim()) return choices;\n\n    const results = searchFn(query);\n    return results.map((r) => toChoice(r.reference));\n  };\n\n  // Create a promise to capture the result\n  return new Promise<SearchPromptResult>((resolve) => {\n    let result: SearchPromptResult = { selected: [], cancelled: true };\n\n    const handleSubmit = (selected: Choice<CslItem>[]): void => {\n      result = {\n        selected: selected.map((c) => c.value),\n        cancelled: false,\n      };\n    };\n\n    const handleCancel = (): void => {\n      result = {\n        selected: [],\n        cancelled: true,\n      };\n    };\n\n    // Render the Ink app\n    const { waitUntilExit, clear } = render(\n      createElement(SearchPromptApp, {\n        choices,\n        filterFn,\n        visibleCount: effectiveLimit,\n        defaultSort: \"updated-desc\",\n        onSubmit: handleSubmit,\n        onCancel: handleCancel,\n      })\n    );\n\n    // Wait for the app to exit, clear the screen, then resolve\n    waitUntilExit()\n      .then(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve(result);\n      })\n      .catch(() => {\n        clear();\n        restoreStdinAfterInk();\n        resolve({\n          selected: [],\n          cancelled: true,\n        });\n      });\n  });\n}\n","/**\n * Shared reference selection utility for interactive ID selection.\n *\n * This module provides a reusable function to select references interactively\n * using the existing search prompt infrastructure.\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { search } from \"../search/matcher.js\";\nimport { tokenize } from \"../search/tokenizer.js\";\nimport { type SearchPromptConfig, runSearchPrompt } from \"./search-prompt.js\";\nimport { checkTTY } from \"./tty.js\";\n\n/**\n * Options for reference selection\n */\nexport interface ReferenceSelectOptions {\n  /** Whether to allow multiple selection (default: true) */\n  multiSelect: boolean;\n  /** Custom prompt message */\n  prompt?: string;\n  /** Initial search query */\n  initialQuery?: string;\n}\n\n/**\n * Result from reference selection\n */\nexport interface ReferenceSelectResult {\n  /** Selected references */\n  selected: CslItem[];\n  /** Whether the selection was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Run interactive reference selection.\n *\n * Launches an interactive search prompt to select references from the library.\n * Supports both single and multiple selection modes.\n *\n * @param allReferences - All references available for selection\n * @param options - Selection options\n * @param config - Interactive prompt configuration\n * @returns Selection result with selected references\n * @throws TTYError if not running in a TTY environment\n */\nexport async function runReferenceSelect(\n  allReferences: CslItem[],\n  options: ReferenceSelectOptions,\n  config: SearchPromptConfig\n): Promise<ReferenceSelectResult> {\n  // Check TTY requirement\n  checkTTY();\n\n  // Create search function for runSearchPrompt\n  const searchFn = (query: string) => {\n    const { tokens } = tokenize(query);\n    return search(allReferences, tokens);\n  };\n\n  // Run search prompt\n  const searchResult = await runSearchPrompt(\n    allReferences,\n    searchFn,\n    config,\n    options.initialQuery ?? \"\"\n  );\n\n  if (searchResult.cancelled) {\n    return { selected: [], cancelled: true };\n  }\n\n  // For single-select mode, return only the first selected item\n  const selected = options.multiSelect ? searchResult.selected : searchResult.selected.slice(0, 1);\n\n  return {\n    selected,\n    cancelled: false,\n  };\n}\n\n/**\n * Options for selectReferencesOrExit helper\n */\nexport interface SelectReferencesOrExitOptions {\n  /** Whether to allow multiple selection */\n  multiSelect: boolean;\n  /** Initial search query */\n  initialQuery?: string;\n}\n\n/**\n * Select references interactively or exit if cancelled/empty.\n *\n * This is a convenience wrapper around runReferenceSelect that handles\n * common patterns:\n * - 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package/dist/chunks/{style-select-RS-lt5lQ.js → style-select-AvDsSnlB.js}

@@ -2,8 +2,8 @@ import * as fs from "node:fs";
 import * as path from "node:path";
 import "ink";
 import "react";
-import { B as BUILTIN_STYLES } from "./index-DUpYvm-W.js";
-import "./index-B1pKaejY.js";
+import { B as BUILTIN_STYLES } from "./index-BdLVfbj0.js";
+import "./index-DkJT7s7N.js";
 function expandTilde(filePath) {
   if (filePath.startsWith("~/")) {
     const home = process.env.HOME || process.env.USERPROFILE || "";
@@ -58,4 +58,4 @@ export {
   buildStyleChoices,
   listCustomStyles
 };
-//# sourceMappingURL=style-select-RS-lt5lQ.js.map
+//# sourceMappingURL=style-select-AvDsSnlB.js.map

package/dist/chunks/{style-select-RS-lt5lQ.js.map → style-select-AvDsSnlB.js.map}

@@ -1 +1 @@
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cslDirectory : [cslDirectory];\n  const styles = new Set<string>();\n\n  for (const dir of directories) {\n    const expandedDir = expandTilde(dir);\n\n    if (!fs.existsSync(expandedDir)) {\n      continue;\n    }\n\n    try {\n      const files = fs.readdirSync(expandedDir);\n      for (const file of files) {\n        if (file.endsWith(\".csl\")) {\n          styles.add(file.slice(0, -4)); // Remove .csl extension\n        }\n      }\n    } catch {\n      // Ignore read errors\n    }\n  }\n\n  return Array.from(styles).sort();\n}\n\n/**\n * Build style choices for the selection prompt.\n *\n * @param customStyles - Custom style names from csl_directory\n * @param defaultStyle - Default style to show first\n * @returns Array of SelectOption for Ink Select prompt\n */\nexport function buildStyleChoices(\n  customStyles: string[],\n  defaultStyle = \"apa\"\n): SelectOption<string>[] {\n  const choices: SelectOption<string>[] = [];\n  const addedStyles = new Set<string>();\n\n  // Helper to add a style choice\n  const addChoice = (styleName: string, isDefault: boolean): void => {\n    if (addedStyles.has(styleName)) return;\n    addedStyles.add(styleName);\n\n    choices.push({\n      label: isDefault ? 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+{"version":3,"file":"style-select-AvDsSnlB.js","sources":["../../src/features/interactive/style-select.ts"],"sourcesContent":["/**\n * Style selection prompt for citation style selection.\n *\n * Lists built-in styles and custom styles from csl_directory,\n * with the default style shown first.\n */\n\nimport * as fs from \"node:fs\";\nimport * as path from \"node:path\";\nimport { render, useApp } from \"ink\";\nimport { createElement } from \"react\";\nimport type React from \"react\";\nimport { BUILTIN_STYLES } from \"../../config/csl-styles.js\";\nimport { restoreStdinAfterInk } from \"./alternate-screen.js\";\nimport { Select, type SelectOption } from \"./components/index.js\";\n\n/**\n * Options for style selection\n */\nexport interface StyleSelectOptions {\n  /** Directory or directories containing custom CSL files */\n  cslDirectory?: string | string[];\n  /** Default style to show first */\n  defaultStyle?: string;\n}\n\n/**\n * Result from style selection\n */\nexport interface StyleSelectResult {\n  /** Selected style name */\n  style?: string;\n  /** Whether the selection was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Expand tilde (~) in path to home directory\n */\nfunction expandTilde(filePath: string): string {\n  if (filePath.startsWith(\"~/\")) {\n    const home = process.env.HOME || process.env.USERPROFILE || \"\";\n    return path.join(home, filePath.slice(2));\n  }\n  return filePath;\n}\n\n/**\n * List custom CSL style names from the specified directory/directories.\n *\n * @param cslDirectory - Directory or directories to search for CSL files\n * @returns Array of style names (without .csl extension)\n */\nexport function listCustomStyles(cslDirectory: string | string[] | undefined): string[] {\n  if (!cslDirectory) {\n    return [];\n  }\n\n  const directories = Array.isArray(cslDirectory) ? 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package/dist/cli/commands/fulltext.d.ts.map

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

@@ -1,5 +1,5 @@
 import "commander";
-import { c, m } from "./chunks/index-B1pKaejY.js";
+import { c, m } from "./chunks/index-DkJT7s7N.js";
 import "./chunks/file-watcher-Dlx0PolG.js";
 export {
   c as createProgram,

package/dist/features/operations/fulltext/fetch.d.ts

@@ -20,15 +20,38 @@ export interface FulltextFetchOptions {
     /** Force overwrite existing fulltext */
     force?: boolean | undefined;
 }
+export interface FetchAttempt {
+    source: string;
+    phase: "download" | "convert" | "attach";
+    url?: string;
+    fileType: "pdf" | "xml" | "html" | "markdown";
+    error: string;
+}
 export interface FulltextFetchResult {
     success: boolean;
-    error?: string;
+    error?: string | undefined;
     /** The reference ID used for display */
-    referenceId?: string;
+    referenceId?: string | undefined;
     /** Which source was used */
-    source?: string;
+    source?: string | undefined;
     /** Which file types were attached */
-    attachedFiles?: string[];
+    attachedFiles?: string[] | undefined;
+    /** Discovery-phase errors from discoverOA */
+    discoveryErrors?: Array<{
+        source: string;
+        error: string;
+    }> | undefined;
+    /** Per-download-attempt details */
+    attempts?: FetchAttempt[] | undefined;
+    /** Which OA sources were checked */
+    checkedSources?: string[] | undefined;
+    /** Sources that were skipped (e.g., missing credentials or identifiers) */
+    skipped?: Array<{
+        source: string;
+        reason: string;
+    }> | undefined;
+    /** User-facing hint (e.g., suggesting manual download) */
+    hint?: string | undefined;
 }
 export declare function fulltextFetch(library: ILibrary, options: FulltextFetchOptions): Promise<FulltextFetchResult>;
 //# sourceMappingURL=fetch.d.ts.map

package/dist/features/operations/fulltext/fetch.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"fetch.d.ts","sourceRoot":"","sources":["../../../../src/features/operations/fulltext/fetch.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAgBH,OAAO,KAAK,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAEhF,OAAO,KAAK,EAAE,QAAQ,EAAE,cAAc,EAAE,MAAM,oCAAoC,CAAC;AAInF,MAAM,WAAW,oBAAoB;IACnC,wCAAwC;IACxC,UAAU,EAAE,MAAM,CAAC;IACnB,wEAAwE;IACxE,MAAM,CAAC,EAAE,cAAc,GAAG,SAAS,CAAC;IACpC,6BAA6B;IAC7B,cAAc,EAAE,cAAc,CAAC;IAC/B,yCAAyC;IACzC,iBAAiB,EAAE,MAAM,CAAC;IAC1B,qCAAqC;IACrC,MAAM,CAAC,EAAE,cAAc,GAAG,SAAS,CAAC;IACpC,wCAAwC;IACxC,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CAC7B;AAED,MAAM,WAAW,mBAAmB;IAClC,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,4BAA4B;IAC5B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,qCAAqC;IACrC,aAAa,CAAC,EAAE,MAAM,EAAE,CAAC;CAC1B;AAsJD,wBAAsB,aAAa,CACjC,OAAO,EAAE,QAAQ,EACjB,OAAO,EAAE,oBAAoB,GAC5B,OAAO,CAAC,mBAAmB,CAAC,CAqD9B"}
+{"version":3,"file":"fetch.d.ts","sourceRoot":"","sources":["../../../../src/features/operations/fulltext/fetch.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAgBH,OAAO,KAAK,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAEhF,OAAO,KAAK,EAAE,QAAQ,EAAE,cAAc,EAAE,MAAM,oCAAoC,CAAC;AAInF,MAAM,WAAW,oBAAoB;IACnC,wCAAwC;IACxC,UAAU,EAAE,MAAM,CAAC;IACnB,wEAAwE;IACxE,MAAM,CAAC,EAAE,cAAc,GAAG,SAAS,CAAC;IACpC,6BAA6B;IAC7B,cAAc,EAAE,cAAc,CAAC;IAC/B,yCAAyC;IACzC,iBAAiB,EAAE,MAAM,CAAC;IAC1B,qCAAqC;IACrC,MAAM,CAAC,EAAE,cAAc,GAAG,SAAS,CAAC;IACpC,wCAAwC;IACxC,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CAC7B;AAED,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,UAAU,GAAG,SAAS,GAAG,QAAQ,CAAC;IACzC,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,KAAK,GAAG,KAAK,GAAG,MAAM,GAAG,UAAU,CAAC;IAC9C,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,mBAAmB;IAClC,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC3B,wCAAwC;IACxC,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACjC,4BAA4B;IAC5B,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC5B,qCAAqC;IACrC,aAAa,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACrC,6CAA6C;IAC7C,eAAe,CAAC,EAAE,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,GAAG,SAAS,CAAC;IACvE,mCAAmC;IACnC,QAAQ,CAAC,EAAE,YAAY,EAAE,GAAG,SAAS,CAAC;IACtC,oCAAoC;IACpC,cAAc,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACtC,2EAA2E;IAC3E,OAAO,CAAC,EAAE,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC,GAAG,SAAS,CAAC;IAChE,0DAA0D;IAC1D,IAAI,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CAC3B;AA6OD,wBAAsB,aAAa,CACjC,OAAO,EAAE,QAAQ,EACjB,OAAO,EAAE,oBAAoB,GAC5B,OAAO,CAAC,mBAAmB,CAAC,CAyE9B"}

package/dist/mcp/tools/fulltext.d.ts.map

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

@@ -1,6 +1,6 @@
 import "hono";
 import "./chunks/file-watcher-Dlx0PolG.js";
-import { v, u } from "./chunks/index-DUpYvm-W.js";
+import { v, u } from "./chunks/index-BdLVfbj0.js";
 export {
   v as createServer,
   u as startServerWithFileWatcher

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ncukondo/reference-manager",
-  "version": "0.27.1",
+  "version": "0.27.2",
   "description": "A local reference management tool using CSL-JSON as the single source of truth",
   "publishConfig": {
     "access": "public"
@@ -54,7 +54,7 @@
     "@citation-js/plugin-ris": "^0.7.21",
     "@iarna/toml": "^2.2.5",
     "@modelcontextprotocol/sdk": "^1.25.1",
-    "@ncukondo/academic-fulltext": "^0.2.2",
+    "@ncukondo/academic-fulltext": "^0.2.6",
     "chokidar": "^5.0.0",
     "commander": "^12.1.0",
     "env-paths": "^3.0.0",