@ncukondo/reference-manager 0.5.1 → 0.5.3

package/README.md

@@ -27,6 +27,7 @@ Automate the tedious parts of literature reviews:
 # Import references from multiple sources
 ref add pmid:12345678 pmid:23456789
 ref add "10.1234/example.doi"
+ref add "ISBN:978-4-00-000000-0"
 ref add exported-from-pubmed.nbib
 
 # AI-assisted screening (with Claude Code)
@@ -102,6 +103,9 @@ ref add "10.1038/nature12373"
 # Add from PubMed
 ref add pmid:25056061
 
+# Add a book by ISBN
+ref add "ISBN:978-4-00-000000-0"
+
 # Search your library
 ref search "author:smith machine learning"
 
@@ -184,7 +188,7 @@ With a custom library:
 |------|-------------|------------|
 | `search` | Search references by query | `query`: Search string (e.g., `"author:smith 2024"`) |
 | `list` | List all references | `format?`: `"json"` \| `"bibtex"` \| `"pretty"` |
-| `add` | Add new reference(s) | `input`: DOI, PMID, BibTeX, RIS, or CSL-JSON |
+| `add` | Add new reference(s) | `input`: DOI, PMID, ISBN, BibTeX, RIS, or CSL-JSON |
 | `remove` | Remove a reference | `id`: Reference ID, `force`: must be `true` |
 | `cite` | Generate formatted citation | `ids`: Array of reference IDs, `style?`: Citation style, `format?`: `"text"` \| `"html"` |
 | `fulltext_attach` | Attach PDF/Markdown to reference | `id`: Reference ID, `path`: File path |
@@ -221,6 +225,7 @@ ref add references.bib                # From BibTeX
 ref add export.ris                    # From RIS
 ref add "10.1038/nature12373"         # From DOI
 ref add pmid:25056061                 # From PubMed ID
+ref add "ISBN:978-4-00-000000-0"      # From ISBN
 cat references.json | ref add         # From stdin
 
 # Remove a reference

package/dist/chunks/{file-watcher-Dqkw6R7-.js → file-watcher-CBAbblss.js}

@@ -226,6 +226,9 @@ class Reference {
   getPmid() {
     return this.item.PMID;
   }
+  getIsbn() {
+    return this.item.ISBN;
+  }
   /**
    * Get the PMCID
    */
@@ -432,6 +435,7 @@ class Library {
   idIndex = /* @__PURE__ */ new Map();
   doiIndex = /* @__PURE__ */ new Map();
   pmidIndex = /* @__PURE__ */ new Map();
+  isbnIndex = /* @__PURE__ */ new Map();
   constructor(filePath, items) {
     this.filePath = filePath;
     for (const item of items) {
@@ -506,8 +510,25 @@ class Library {
    * @returns Remove result with removed status and the removed item
    */
   async remove(identifier, options = {}) {
-    const { byUuid = false } = options;
-    const ref = byUuid ? this.uuidIndex.get(identifier) : this.idIndex.get(identifier);
+    const { idType = "id" } = options;
+    let ref;
+    switch (idType) {
+      case "uuid":
+        ref = this.uuidIndex.get(identifier);
+        break;
+      case "doi":
+        ref = this.doiIndex.get(identifier);
+        break;
+      case "pmid":
+        ref = this.pmidIndex.get(identifier);
+        break;
+      case "isbn":
+        ref = this.isbnIndex.get(identifier);
+        break;
+      default:
+        ref = this.idIndex.get(identifier);
+        break;
+    }
     if (!ref) {
       return { removed: false };
     }
@@ -523,8 +544,25 @@ class Library {
    * @returns Update result with updated item, success status, and any ID changes
    */
   async update(identifier, updates, options = {}) {
-    const { byUuid = false, ...updateOptions } = options;
-    const ref = byUuid ? this.uuidIndex.get(identifier) : this.idIndex.get(identifier);
+    const { idType = "id", ...updateOptions } = options;
+    let ref;
+    switch (idType) {
+      case "uuid":
+        ref = this.uuidIndex.get(identifier);
+        break;
+      case "doi":
+        ref = this.doiIndex.get(identifier);
+        break;
+      case "pmid":
+        ref = this.pmidIndex.get(identifier);
+        break;
+      case "isbn":
+        ref = this.isbnIndex.get(identifier);
+        break;
+      default:
+        ref = this.idIndex.get(identifier);
+        break;
+    }
     if (!ref) {
       return { updated: false };
     }
@@ -537,22 +575,27 @@ class Library {
    * @returns The CSL item if found, undefined otherwise
    */
   async find(identifier, options = {}) {
-    const { byUuid = false } = options;
-    const ref = byUuid ? this.uuidIndex.get(identifier) : this.idIndex.get(identifier);
+    const { idType = "id" } = options;
+    let ref;
+    switch (idType) {
+      case "uuid":
+        ref = this.uuidIndex.get(identifier);
+        break;
+      case "doi":
+        ref = this.doiIndex.get(identifier);
+        break;
+      case "pmid":
+        ref = this.pmidIndex.get(identifier);
+        break;
+      case "isbn":
+        ref = this.isbnIndex.get(identifier);
+        break;
+      default:
+        ref = this.idIndex.get(identifier);
+        break;
+    }
     return ref?.getItem();
   }
-  /**
-   * Find a reference by DOI
-   */
-  findByDoi(doi) {
-    return this.doiIndex.get(doi);
-  }
-  /**
-   * Find a reference by PMID
-   */
-  findByPmid(pmid) {
-    return this.pmidIndex.get(pmid);
-  }
   /**
    * Get all references
    */
@@ -586,6 +629,10 @@ class Library {
     if (pmid) {
       this.pmidIndex.set(pmid, ref);
     }
+    const isbn = ref.getIsbn();
+    if (isbn) {
+      this.isbnIndex.set(isbn, ref);
+    }
   }
   /**
    * Remove reference from all indices and array
@@ -682,6 +729,10 @@ class Library {
     if (pmid) {
       this.pmidIndex.delete(pmid);
     }
+    const isbn = ref.getIsbn();
+    if (isbn) {
+      this.isbnIndex.delete(isbn);
+    }
   }
   /**
    * Generate an alphabetic suffix for ID collision resolution.
@@ -1322,6 +1373,52 @@ function checkPmidMatch(item, existing) {
   }
   return null;
 }
+function normalizeIsbn(isbn) {
+  return isbn.replace(/[-\s]/g, "").toUpperCase();
+}
+const BOOK_TYPES = ["book"];
+const BOOK_SECTION_TYPES = ["chapter"];
+function checkIsbnMatch(item, existing) {
+  if (!item.ISBN || !existing.ISBN) {
+    return null;
+  }
+  const normalizedItemIsbn = normalizeIsbn(item.ISBN);
+  const normalizedExistingIsbn = normalizeIsbn(existing.ISBN);
+  if (normalizedItemIsbn !== normalizedExistingIsbn) {
+    return null;
+  }
+  if (BOOK_TYPES.includes(item.type) || BOOK_TYPES.includes(existing.type)) {
+    return {
+      type: "isbn",
+      existing,
+      details: {
+        isbn: normalizedExistingIsbn
+      }
+    };
+  }
+  if (BOOK_SECTION_TYPES.includes(item.type) || BOOK_SECTION_TYPES.includes(existing.type)) {
+    const itemTitle = item.title ? normalize(item.title) : null;
+    const existingTitle = existing.title ? normalize(existing.title) : null;
+    if (itemTitle && existingTitle && itemTitle === existingTitle) {
+      return {
+        type: "isbn",
+        existing,
+        details: {
+          isbn: normalizedExistingIsbn,
+          normalizedTitle: existingTitle
+        }
+      };
+    }
+    return null;
+  }
+  return {
+    type: "isbn",
+    existing,
+    details: {
+      isbn: normalizedExistingIsbn
+    }
+  };
+}
 function checkTitleAuthorYearMatch(item, existing) {
   const itemTitle = item.title ? normalize(item.title) : null;
   const existingTitle = existing.title ? normalize(existing.title) : null;
@@ -1354,6 +1451,10 @@ function checkSingleDuplicate(item, existing) {
   if (pmidMatch) {
     return pmidMatch;
   }
+  const isbnMatch = checkIsbnMatch(item, existing);
+  if (isbnMatch) {
+    return isbnMatch;
+  }
   return checkTitleAuthorYearMatch(item, existing);
 }
 function detectDuplicate(item, existingReferences) {
@@ -1560,4 +1661,4 @@ export {
   tokenize as t,
   writeCslJson as w
 };
-//# sourceMappingURL=file-watcher-Dqkw6R7-.js.map
+//# sourceMappingURL=file-watcher-CBAbblss.js.map

package/dist/chunks/file-watcher-CBAbblss.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"file-watcher-CBAbblss.js","sources":["../../src/core/identifier/normalize.ts","../../src/core/identifier/generator.ts","../../src/core/identifier/uuid.ts","../../src/core/reference.ts","../../src/utils/hash.ts","../../src/core/csl-json/types.ts","../../src/core/csl-json/parser.ts","../../src/core/csl-json/serializer.ts","../../src/core/library.ts","../../src/features/search/tokenizer.ts","../../src/features/search/normalizer.ts","../../src/features/search/uppercase.ts","../../src/features/search/matcher.ts","../../src/features/search/sorter.ts","../../src/features/duplicate/detector.ts","../../src/features/file-watcher/file-watcher.ts"],"sourcesContent":["/**\n * Normalize text for identifier generation\n * Converts to lowercase, converts spaces to underscores, keeps only alphanumeric and underscores\n * @param text - Text to normalize\n * @returns Normalized text (ASCII alphanumeric and underscores only)\n */\nexport function normalizeText(text: string): string {\n  return text\n    .toLowerCase()\n    .replace(/\\s+/g, \"_\") // Convert spaces to underscores\n    .replace(/[^a-z0-9_]/g, \"\") // Keep only alphanumeric and underscores\n    .replace(/_+/g, \"_\") // Collapse multiple underscores\n    .replace(/^_|_$/g, \"\"); // Remove leading/trailing underscores\n}\n\n/**\n * Normalize author name for identifier\n * @param name - Author name to normalize\n * @returns Normalized name (max 32 chars)\n */\nexport function normalizeAuthorName(name: string): string {\n  const normalized = normalizeText(name);\n  return normalized.slice(0, 32);\n}\n\n/**\n * Create a title slug for identifier\n * @param title - Title to create slug from\n * @returns Title slug (max 32 chars)\n */\nexport function normalizeTitleSlug(title: string): string {\n  const normalized = normalizeText(title);\n  return normalized.slice(0, 32);\n}\n","import type { CslItem } from \"../csl-json/types\";\nimport { normalizeAuthorName, normalizeTitleSlug } from \"./normalize\";\n\n/**\n * Extract author name from CSL-JSON item\n * Returns family name, literal name, or empty string\n */\nfunction extractAuthorName(item: CslItem): string {\n  if (!item.author || item.author.length === 0) {\n    return \"\";\n  }\n\n  const firstAuthor = item.author[0];\n  if (!firstAuthor) {\n    return \"\";\n  }\n\n  // Try family name first\n  if (firstAuthor.family) {\n    return normalizeAuthorName(firstAuthor.family);\n  }\n\n  // Try literal name (e.g., institutional authors)\n  if (firstAuthor.literal) {\n    return normalizeAuthorName(firstAuthor.literal);\n  }\n\n  return \"\";\n}\n\n/**\n * Extract year from CSL-JSON item\n * Returns year string or empty string\n */\nfunction extractYear(item: CslItem): string {\n  if (!item.issued || !item.issued[\"date-parts\"] || item.issued[\"date-parts\"].length === 0) {\n    return \"\";\n  }\n\n  const dateParts = item.issued[\"date-parts\"][0];\n  if (!dateParts || dateParts.length === 0) {\n    return \"\";\n  }\n\n  const year = dateParts[0];\n  return year ? year.toString() : \"\";\n}\n\n/**\n * Determine the title part of the ID based on author, year, and title availability\n * @param hasAuthor - Whether author is available\n * @param hasYear - Whether year is available\n * @param title - Title slug\n * @returns Title part of the ID\n */\nfunction determineTitlePart(hasAuthor: boolean, hasYear: boolean, title: string): string {\n  // No title part needed if both author and year are present\n  if (hasAuthor && hasYear) {\n    return \"\";\n  }\n\n  // Add title if available\n  if (title) {\n    return `-${title}`;\n  }\n\n  // Add \"untitled\" only if both author and year are missing\n  if (!hasAuthor && !hasYear) {\n    return \"-untitled\";\n  }\n\n  return \"\";\n}\n\n/**\n * Generate a BibTeX-style ID for a CSL-JSON item\n * Format: <FirstAuthorFamily>-<Year>[<TitleSlug>][a-z suffix]\n * @param item - CSL-JSON item\n * @returns Generated ID\n */\nexport function generateId(item: CslItem): string {\n  const author = extractAuthorName(item);\n  const year = extractYear(item);\n  const title = item.title ? normalizeTitleSlug(item.title) : \"\";\n\n  // Build base ID with fallbacks\n  const authorPart = author || \"anon\";\n  const yearPart = year || \"nd\"; // no date\n  const titlePart = determineTitlePart(Boolean(author), Boolean(year), title);\n\n  return `${authorPart}-${yearPart}${titlePart}`;\n}\n\n/**\n * Generate suffix for collision handling\n * a, b, c, ..., z, aa, ab, ...\n * @param index - Collision index (0 = no suffix, 1 = 'a', 2 = 'b', ...)\n * @returns Suffix string\n */\nfunction generateSuffix(index: number): string {\n  if (index === 0) {\n    return \"\";\n  }\n\n  let suffix = \"\";\n  let num = index;\n\n  while (num > 0) {\n    num--; // Adjust for 0-based indexing\n    suffix = String.fromCharCode(97 + (num % 26)) + suffix;\n    num = Math.floor(num / 26);\n  }\n\n  return suffix;\n}\n\n/**\n * Generate ID with collision check\n * Appends a, b, c, ... suffix if the base ID already exists\n * @param item - CSL-JSON item\n * @param existingIds - Array of existing IDs\n * @returns Generated ID with collision handling\n */\nexport function generateIdWithCollisionCheck(item: CslItem, existingIds: string[]): string {\n  const baseId = generateId(item);\n\n  // Normalize existing IDs to lowercase for case-insensitive comparison\n  const normalizedExistingIds = existingIds.map((id) => id.toLowerCase());\n\n  // Check for collisions\n  let candidate = baseId;\n  let suffixIndex = 0;\n\n  while (normalizedExistingIds.includes(candidate.toLowerCase())) {\n    suffixIndex++;\n    const suffix = generateSuffix(suffixIndex);\n    candidate = `${baseId}${suffix}`;\n  }\n\n  return candidate;\n}\n","import { randomUUID } from \"node:crypto\";\nimport type { CslCustom } from \"../csl-json/types\";\n\nconst UUID_REGEX = /^[0-9a-f]{8}-[0-9a-f]{4}-4[0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}$/i;\n\n/**\n * Validate if a string is a valid UUID v4\n */\nexport function isValidUuid(uuid: string): boolean {\n  return UUID_REGEX.test(uuid);\n}\n\n/**\n * Generate a new UUID v4\n */\nexport function generateUuid(): string {\n  return randomUUID();\n}\n\n/**\n * Generate a new ISO 8601 timestamp\n */\nexport function generateTimestamp(): string {\n  return new Date().toISOString();\n}\n\n/**\n * Extract UUID from custom field\n */\nexport function extractUuidFromCustom(custom: CslCustom | undefined): string | null {\n  if (!custom || !custom.uuid) {\n    return null;\n  }\n\n  return isValidUuid(custom.uuid) ? custom.uuid : null;\n}\n\n/**\n * Ensure custom metadata has a valid UUID\n * Generates a new UUID if missing or invalid\n */\nfunction ensureUuid(custom: CslCustom | undefined): Partial<CslCustom> & { uuid: string } {\n  const existingUuid = extractUuidFromCustom(custom);\n\n  if (existingUuid && custom) {\n    return custom as Partial<CslCustom> & { uuid: string };\n  }\n\n  const newUuid = generateUuid();\n  return {\n    ...custom,\n    uuid: newUuid,\n  };\n}\n\n/**\n * Ensure custom metadata has a valid created_at timestamp\n * Migrates from legacy timestamp field if needed\n * Generates a new timestamp if missing\n */\nfunction ensureCreatedAt(\n  custom: Partial<CslCustom> & { uuid: string }\n): Partial<CslCustom> & { uuid: string; created_at: string } {\n  // Already has created_at\n  if (custom.created_at) {\n    return custom as Partial<CslCustom> & { uuid: string; created_at: string };\n  }\n\n  // Legacy migration: move timestamp to created_at if timestamp exists but created_at doesn't\n  if (custom.timestamp) {\n    return {\n      ...custom,\n      created_at: custom.timestamp,\n    };\n  }\n\n  // Generate new created_at\n  const newTimestamp = generateTimestamp();\n  return {\n    ...custom,\n    created_at: newTimestamp,\n  };\n}\n\n/**\n * Ensure custom metadata has a valid timestamp (last modification time)\n * Defaults to created_at if missing\n */\nfunction ensureTimestamp(\n  custom: Partial<CslCustom> & { uuid: string; created_at: string }\n): CslCustom {\n  // Already has timestamp\n  if (custom.timestamp) {\n    return custom as CslCustom;\n  }\n\n  // Default to created_at (new item, not yet modified)\n  return {\n    ...custom,\n    timestamp: custom.created_at,\n  };\n}\n\n/**\n * Ensure custom metadata has valid UUID, created_at, and timestamp\n * Handles legacy migration from old timestamp-only format\n * Generates new values if missing or invalid\n */\nexport function ensureCustomMetadata(custom: CslCustom | undefined): CslCustom {\n  const withUuid = ensureUuid(custom);\n  const withCreatedAt = ensureCreatedAt(withUuid);\n  const withTimestamp = ensureTimestamp(withCreatedAt);\n  return withTimestamp;\n}\n","import type { CslItem } from \"./csl-json/types\";\nimport { generateIdWithCollisionCheck } from \"./identifier/generator\";\nimport { ensureCustomMetadata, extractUuidFromCustom } from \"./identifier/uuid\";\n\n/**\n * Options for creating a Reference\n */\nexport interface ReferenceCreateOptions {\n  /** Existing IDs to check for collision */\n  existingIds?: Set<string>;\n}\n\n/**\n * Reference entity wrapping a CSL-JSON item\n */\nexport class Reference {\n  private item: CslItem;\n  private uuid: string;\n\n  constructor(item: CslItem) {\n    // Ensure UUID and timestamp are present and valid in custom field\n    const customMetadata = ensureCustomMetadata(item.custom);\n    this.item = { ...item, custom: customMetadata };\n\n    // Extract UUID from the custom field\n    const extractedUuid = extractUuidFromCustom(customMetadata);\n    if (!extractedUuid) {\n      throw new Error(\"Failed to extract UUID after ensureCustomMetadata\");\n    }\n    this.uuid = extractedUuid;\n  }\n\n  /**\n   * Factory method to create a Reference with UUID and ID generation\n   */\n  static create(item: CslItem, options?: ReferenceCreateOptions): Reference {\n    const existingIds = options?.existingIds || new Set<string>();\n\n    // Generate ID if not provided or empty\n    let updatedItem = item;\n    if (!item.id || item.id.trim() === \"\") {\n      const generatedId = generateIdWithCollisionCheck(item, Array.from(existingIds));\n      updatedItem = { ...item, id: generatedId };\n    }\n\n    return new Reference(updatedItem);\n  }\n\n  /**\n   * Get the underlying CSL-JSON item\n   */\n  getItem(): CslItem {\n    return this.item;\n  }\n\n  /**\n   * Get the UUID (internal stable identifier)\n   */\n  getUuid(): string {\n    return this.uuid;\n  }\n\n  /**\n   * Get the ID (Pandoc citation key / BibTeX-key)\n   */\n  getId(): string {\n    return this.item.id;\n  }\n\n  /**\n   * Get the title\n   */\n  getTitle(): string | undefined {\n    return this.item.title;\n  }\n\n  /**\n   * Get the authors\n   */\n  getAuthors(): CslItem[\"author\"] {\n    return this.item.author;\n  }\n\n  /**\n   * Get the year from issued date\n   */\n  getYear(): number | undefined {\n    const issued = this.item.issued;\n    if (!issued || !issued[\"date-parts\"] || issued[\"date-parts\"].length === 0) {\n      return undefined;\n    }\n    const firstDate = issued[\"date-parts\"][0];\n    return firstDate && firstDate.length > 0 ? firstDate[0] : undefined;\n  }\n\n  /**\n   * Get the DOI\n   */\n  getDoi(): string | undefined {\n    return this.item.DOI;\n  }\n\n  /**\n   * Get the PMID\n   */\n  getPmid(): string | undefined {\n    return this.item.PMID;\n  }\n\n  getIsbn(): string | undefined {\n    return this.item.ISBN;\n  }\n\n  /**\n   * Get the PMCID\n   */\n  getPmcid(): string | undefined {\n    return this.item.PMCID;\n  }\n\n  /**\n   * Get the URL\n   */\n  getUrl(): string | undefined {\n    return this.item.URL;\n  }\n\n  /**\n   * Get the keyword\n   */\n  getKeyword(): string[] | undefined {\n    return this.item.keyword;\n  }\n\n  /**\n   * Get additional URLs from custom metadata\n   */\n  getAdditionalUrls(): string[] | undefined {\n    return this.item.custom?.additional_urls;\n  }\n\n  /**\n   * Get the creation timestamp from custom metadata (immutable)\n   */\n  getCreatedAt(): string {\n    if (!this.item.custom?.created_at) {\n      throw new Error(\"created_at is missing from custom metadata\");\n    }\n    return this.item.custom.created_at;\n  }\n\n  /**\n   * Get the last modification timestamp from custom metadata\n   */\n  getTimestamp(): string {\n    if (!this.item.custom?.timestamp) {\n      throw new Error(\"timestamp is missing from custom metadata\");\n    }\n    return this.item.custom.timestamp;\n  }\n\n  /**\n   * Update the timestamp to current time\n   * Call this whenever the reference is modified\n   */\n  touch(): void {\n    if (!this.item.custom) {\n      throw new Error(\"custom metadata is missing\");\n    }\n    this.item.custom.timestamp = new Date().toISOString();\n  }\n\n  /**\n   * Get the type\n   */\n  getType(): string {\n    return this.item.type;\n  }\n}\n","import { createHash } from \"node:crypto\";\nimport { createReadStream } from \"node:fs\";\n\n/**\n * Compute SHA-256 hash of a string\n */\nexport function computeHash(input: string): string {\n  return createHash(\"sha256\").update(input, \"utf-8\").digest(\"hex\");\n}\n\n/**\n * Compute SHA-256 hash of a file\n */\nexport async function computeFileHash(filePath: string): Promise<string> {\n  return new Promise((resolve, reject) => {\n    const hash = createHash(\"sha256\");\n    const stream = createReadStream(filePath);\n\n    stream.on(\"data\", (chunk) => hash.update(chunk));\n    stream.on(\"end\", () => resolve(hash.digest(\"hex\")));\n    stream.on(\"error\", (error) => reject(error));\n  });\n}\n","import { z } from \"zod\";\n\n// CSL-JSON Name (Person)\nconst CslNameSchema = z.object({\n  family: z.string().optional(),\n  given: z.string().optional(),\n  literal: z.string().optional(),\n  \"dropping-particle\": z.string().optional(),\n  \"non-dropping-particle\": z.string().optional(),\n  suffix: z.string().optional(),\n});\n\n// CSL-JSON Date\nconst CslDateSchema = z.object({\n  \"date-parts\": z.array(z.array(z.number())).optional(),\n  raw: z.string().optional(),\n  season: z.string().optional(),\n  circa: z.boolean().optional(),\n  literal: z.string().optional(),\n});\n\n// CSL-JSON Fulltext Metadata\nconst CslFulltextSchema = z.object({\n  pdf: z.string().optional(),\n  markdown: z.string().optional(),\n});\n\n// CSL-JSON Custom Metadata\nconst CslCustomSchema = z\n  .object({\n    uuid: z.string(),\n    created_at: z.string(),\n    timestamp: z.string(),\n    additional_urls: z.array(z.string()).optional(),\n    fulltext: CslFulltextSchema.optional(),\n    tags: z.array(z.string()).optional(),\n  })\n  .passthrough();\n\n// CSL-JSON Item\nexport const CslItemSchema = z\n  .object({\n    id: z.string(),\n    type: z.string(),\n    title: z.string().optional(),\n    author: z.array(CslNameSchema).optional(),\n    editor: z.array(CslNameSchema).optional(),\n    issued: CslDateSchema.optional(),\n    accessed: CslDateSchema.optional(),\n    \"container-title\": z.string().optional(),\n    volume: z.string().optional(),\n    issue: z.string().optional(),\n    page: z.string().optional(),\n    DOI: z.string().optional(),\n    PMID: z.string().optional(),\n    PMCID: z.string().optional(),\n    ISBN: z.string().optional(),\n    ISSN: z.string().optional(),\n    URL: z.string().optional(),\n    abstract: z.string().optional(),\n    publisher: z.string().optional(),\n    \"publisher-place\": z.string().optional(),\n    note: z.string().optional(),\n    keyword: z.array(z.string()).optional(),\n    custom: CslCustomSchema.optional(),\n    // Allow additional fields\n  })\n  .passthrough();\n\n// CSL-JSON Library (array of items)\nexport const CslLibrarySchema = z.array(CslItemSchema);\n\nexport type CslCustom = z.infer<typeof CslCustomSchema>;\nexport type CslItem = z.infer<typeof CslItemSchema>;\nexport type CslLibrary = z.infer<typeof CslLibrarySchema>;\n","import { readFile } from \"node:fs/promises\";\nimport { ensureCustomMetadata } from \"../identifier/uuid\";\nimport { type CslLibrary, CslLibrarySchema } from \"./types\";\n\n/**\n * Convert keyword field from semicolon-separated string to array\n * @param keyword - Semicolon-separated string or undefined\n * @returns Array of keywords or undefined\n */\nfunction parseKeyword(keyword: unknown): string[] | undefined {\n  if (typeof keyword !== \"string\") {\n    return undefined;\n  }\n\n  if (keyword.trim() === \"\") {\n    return undefined;\n  }\n\n  const keywords = keyword\n    .split(\";\")\n    .map((k) => k.trim())\n    .filter((k) => k !== \"\");\n\n  return keywords.length > 0 ? keywords : undefined;\n}\n\n/**\n * Parse a CSL-JSON file and ensure all entries have valid UUIDs and timestamps\n * @param filePath - Path to the CSL-JSON file\n * @returns Array of CSL-JSON items with guaranteed UUIDs and timestamps\n * @throws Error if file cannot be read or JSON is invalid\n */\nexport async function parseCslJson(filePath: string): Promise<CslLibrary> {\n  // Read file\n  const content = await readFile(filePath, \"utf-8\");\n\n  // Parse JSON\n  let rawData: unknown;\n  try {\n    rawData = JSON.parse(content);\n  } catch (error) {\n    throw new Error(\n      `Failed to parse JSON: ${error instanceof Error ? error.message : String(error)}`\n    );\n  }\n\n  // Convert keyword fields from string to array before validation\n  if (Array.isArray(rawData)) {\n    rawData = rawData.map((item: unknown) => {\n      if (item && typeof item === \"object\" && \"keyword\" in item) {\n        const itemWithKeyword = item as Record<string, unknown>;\n        return {\n          ...itemWithKeyword,\n          keyword: parseKeyword(itemWithKeyword.keyword),\n        };\n      }\n      return item;\n    });\n  }\n\n  // Validate with zod\n  const parseResult = CslLibrarySchema.safeParse(rawData);\n\n  if (!parseResult.success) {\n    throw new Error(`Invalid CSL-JSON structure: ${parseResult.error.message}`);\n  }\n\n  const library = parseResult.data;\n\n  // Ensure all entries have valid UUIDs and timestamps\n  const processedLibrary: CslLibrary = library.map((item) => {\n    const updatedCustom = ensureCustomMetadata(item.custom);\n\n    return {\n      ...item,\n      custom: updatedCustom,\n    };\n  });\n\n  return processedLibrary;\n}\n","import { mkdir, writeFile } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\nimport type { CslLibrary } from \"./types\";\n\n/**\n * Convert keyword array to semicolon-separated string\n * @param keywords - Array of keywords or undefined\n * @returns Semicolon-separated string or undefined\n */\nfunction serializeKeyword(keywords: string[] | undefined): string | undefined {\n  if (!keywords || keywords.length === 0) {\n    return undefined;\n  }\n\n  return keywords.join(\"; \");\n}\n\n/**\n * Serialize a CSL-JSON library to a formatted JSON string\n * @param library - CSL-JSON library (array of items)\n * @returns Formatted JSON string with 2-space indentation\n */\nexport function serializeCslJson(library: CslLibrary): string {\n  // Convert keyword arrays to semicolon-separated strings\n  const libraryForJson = library.map((item) => {\n    const { keyword, ...rest } = item;\n    const serializedKeyword = serializeKeyword(keyword);\n\n    if (serializedKeyword === undefined) {\n      return rest;\n    }\n\n    return {\n      ...rest,\n      keyword: serializedKeyword,\n    };\n  });\n\n  return JSON.stringify(libraryForJson, null, 2);\n}\n\n/**\n * Write a CSL-JSON library to a file\n * @param filePath - Path to write the CSL-JSON file\n * @param library - CSL-JSON library to write\n * @throws Error if file cannot be written\n */\nexport async function writeCslJson(filePath: string, library: CslLibrary): Promise<void> {\n  // Ensure parent directory exists\n  const dir = dirname(filePath);\n  await mkdir(dir, { recursive: true });\n\n  // Serialize and write\n  const content = serializeCslJson(library);\n  await writeFile(filePath, content, \"utf-8\");\n}\n","import { existsSync } from \"node:fs\";\nimport { mkdir } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\nimport { computeFileHash } from \"../utils/hash\";\nimport { parseCslJson } from \"./csl-json/parser\";\nimport { writeCslJson } from \"./csl-json/serializer\";\nimport type { CslItem } from \"./csl-json/types\";\nimport type {\n  FindOptions,\n  ILibrary,\n  RemoveOptions,\n  RemoveResult,\n  UpdateOptions,\n  UpdateResult,\n} from \"./library-interface.js\";\nimport { Reference } from \"./reference\";\n\n// Re-export types from library-interface for backward compatibility\nexport type {\n  FindOptions,\n  IdentifierType,\n  ILibrary,\n  UpdateOptions,\n  UpdateResult,\n} from \"./library-interface.js\";\n\n/**\n * Library manager for CSL-JSON references.\n * Implements ILibrary interface for use with operations layer.\n */\nexport class Library implements ILibrary {\n  private filePath: string;\n  private references: Reference[] = [];\n  private currentHash: string | null = null;\n\n  // Indices for fast lookup\n  private uuidIndex: Map<string, Reference> = new Map();\n  private idIndex: Map<string, Reference> = new Map();\n  private doiIndex: Map<string, Reference> = new Map();\n  private pmidIndex: Map<string, Reference> = new Map();\n  private isbnIndex: Map<string, Reference> = new Map();\n\n  private constructor(filePath: string, items: CslItem[]) {\n    this.filePath = filePath;\n\n    // Create references and build indices\n    for (const item of items) {\n      const ref = new Reference(item);\n      this.references.push(ref);\n      this.addToIndices(ref);\n    }\n  }\n\n  /**\n   * Load library from file.\n   * If the file does not exist, creates an empty library file.\n   */\n  static async load(filePath: string): Promise<Library> {\n    // Check if file exists, create empty library if not\n    if (!existsSync(filePath)) {\n      // Create parent directories if needed\n      const dir = dirname(filePath);\n      await mkdir(dir, { recursive: true });\n      // Create empty library file\n      await writeCslJson(filePath, []);\n    }\n\n    const items = await parseCslJson(filePath);\n    const library = new Library(filePath, items);\n    // Compute and store file hash after loading\n    library.currentHash = await computeFileHash(filePath);\n    return library;\n  }\n\n  /**\n   * Save library to file\n   */\n  async save(): Promise<void> {\n    const items = this.references.map((ref) => ref.getItem());\n    await writeCslJson(this.filePath, items);\n    // Update file hash after saving\n    this.currentHash = await computeFileHash(this.filePath);\n  }\n\n  /**\n   * Reloads the library from file if it was modified externally.\n   * Self-writes (detected via hash comparison) are skipped.\n   * @returns true if reload occurred, false if skipped (self-write detected)\n   */\n  async reload(): Promise<boolean> {\n    const newHash = await computeFileHash(this.filePath);\n\n    if (newHash === this.currentHash) {\n      // Self-write detected, skip reload\n      return false;\n    }\n\n    // External change detected, reload\n    const items = await parseCslJson(this.filePath);\n\n    // Clear and rebuild indices\n    this.references = [];\n    this.uuidIndex.clear();\n    this.idIndex.clear();\n    this.doiIndex.clear();\n    this.pmidIndex.clear();\n\n    for (const item of items) {\n      const ref = new Reference(item);\n      this.references.push(ref);\n      this.addToIndices(ref);\n    }\n\n    // Update hash\n    this.currentHash = newHash;\n\n    return true;\n  }\n\n  /**\n   * Add a reference to the library\n   * @param item - The CSL item to add\n   * @returns The added CSL item (with generated ID and UUID)\n   */\n  async add(item: CslItem): Promise<CslItem> {\n    // Collect existing IDs for collision check\n    const existingIds = new Set(this.references.map((ref) => ref.getId()));\n\n    // Create reference with collision check\n    const ref = Reference.create(item, { existingIds });\n\n    // Add to library\n    this.references.push(ref);\n    this.addToIndices(ref);\n\n    // Return the added item\n    return ref.getItem();\n  }\n\n  /**\n   * Remove a reference by citation ID or UUID.\n   * @param identifier - The citation ID or UUID of the reference to remove\n   * @param options - Remove options (byUuid to use UUID lookup)\n   * @returns Remove result with removed status and the removed item\n   */\n  async remove(identifier: string, options: RemoveOptions = {}): Promise<RemoveResult> {\n    const { idType = \"id\" } = options;\n    let ref: Reference | undefined;\n    switch (idType) {\n      case \"uuid\":\n        ref = this.uuidIndex.get(identifier);\n        break;\n      case \"doi\":\n        ref = this.doiIndex.get(identifier);\n        break;\n      case \"pmid\":\n        ref = this.pmidIndex.get(identifier);\n        break;\n      case \"isbn\":\n        ref = this.isbnIndex.get(identifier);\n        break;\n      default: // \"id\" or unknown\n        ref = this.idIndex.get(identifier);\n        break;\n    }\n    if (!ref) {\n      return { removed: false };\n    }\n    const removedItem = ref.getItem();\n    const removed = this.removeReference(ref);\n    return { removed, removedItem };\n  }\n\n  /**\n   * Update a reference by citation ID or UUID.\n   * @param identifier - The citation ID or UUID of the reference to update\n   * @param updates - Partial updates to apply to the reference\n   * @param options - Update options (byUuid to use UUID lookup, onIdCollision for collision handling)\n   * @returns Update result with updated item, success status, and any ID changes\n   */\n  async update(\n    identifier: string,\n    updates: Partial<CslItem>,\n    options: UpdateOptions = {}\n  ): Promise<UpdateResult> {\n    const { idType = \"id\", ...updateOptions } = options;\n    let ref: Reference | undefined;\n    switch (idType) {\n      case \"uuid\":\n        ref = this.uuidIndex.get(identifier);\n        break;\n      case \"doi\":\n        ref = this.doiIndex.get(identifier);\n        break;\n      case \"pmid\":\n        ref = this.pmidIndex.get(identifier);\n        break;\n      case \"isbn\":\n        ref = this.isbnIndex.get(identifier);\n        break;\n      default: // \"id\" or unknown\n        ref = this.idIndex.get(identifier);\n        break;\n    }\n\n    if (!ref) {\n      return { updated: false };\n    }\n\n    return this.updateReference(ref, updates, updateOptions);\n  }\n\n  /**\n   * Find a reference by citation ID or UUID.\n   * @param identifier - The citation ID or UUID of the reference to find\n   * @param options - Find options (byUuid to use UUID lookup)\n   * @returns The CSL item if found, undefined otherwise\n   */\n  async find(identifier: string, options: FindOptions = {}): Promise<CslItem | undefined> {\n    const { idType = \"id\" } = options;\n\n    let ref: Reference | undefined;\n    switch (idType) {\n      case \"uuid\":\n        ref = this.uuidIndex.get(identifier);\n        break;\n      case \"doi\":\n        ref = this.doiIndex.get(identifier);\n        break;\n      case \"pmid\":\n        ref = this.pmidIndex.get(identifier);\n        break;\n      case \"isbn\":\n        ref = this.isbnIndex.get(identifier);\n        break;\n      default: // \"id\" or unknown\n        ref = this.idIndex.get(identifier);\n        break;\n    }\n\n    return ref?.getItem();\n  }\n\n  /**\n   * Get all references\n   */\n  async getAll(): Promise<CslItem[]> {\n    return this.references.map((ref) => ref.getItem());\n  }\n\n  /**\n   * Get the file path\n   */\n  getFilePath(): string {\n    return this.filePath;\n  }\n\n  /**\n   * Get the current file hash\n   * Returns null if the library has not been loaded or saved yet\n   */\n  getCurrentHash(): string | null {\n    return this.currentHash;\n  }\n\n  /**\n   * Add reference to all indices\n   */\n  private addToIndices(ref: Reference): void {\n    // UUID index\n    this.uuidIndex.set(ref.getUuid(), ref);\n\n    // ID index\n    this.idIndex.set(ref.getId(), ref);\n\n    // DOI index\n    const doi = ref.getDoi();\n    if (doi) {\n      this.doiIndex.set(doi, ref);\n    }\n\n    // PMID index\n    const pmid = ref.getPmid();\n    if (pmid) {\n      this.pmidIndex.set(pmid, ref);\n    }\n\n    // ISBN index\n    const isbn = ref.getIsbn();\n    if (isbn) {\n      this.isbnIndex.set(isbn, ref);\n    }\n  }\n\n  /**\n   * Remove reference from all indices and array\n   */\n  private removeReference(ref: Reference): boolean {\n    const index = this.references.indexOf(ref);\n    if (index === -1) {\n      return false;\n    }\n    this.references.splice(index, 1);\n    this.removeFromIndices(ref);\n    return true;\n  }\n\n  /**\n   * Update a reference with partial updates.\n   * Preserves uuid and created_at, updates timestamp.\n   */\n  private updateReference(\n    ref: Reference,\n    updates: Partial<CslItem>,\n    options: UpdateOptions = {}\n  ): UpdateResult {\n    const index = this.references.indexOf(ref);\n    if (index === -1) {\n      return { updated: false };\n    }\n\n    const existingItem = ref.getItem();\n    const currentId = ref.getId();\n    const { newId, idChanged, collision } = this.resolveNewId(\n      updates.id ?? existingItem.id,\n      currentId,\n      options\n    );\n\n    if (collision) {\n      return { updated: false, idCollision: true };\n    }\n\n    const updatedItem = this.buildUpdatedItem(existingItem, updates, newId);\n\n    // Remove old reference from indices\n    this.removeFromIndices(ref);\n\n    // Create new reference and replace in array\n    const newRef = new Reference(updatedItem);\n    this.references[index] = newRef;\n    this.addToIndices(newRef);\n\n    const result: UpdateResult = { updated: true, item: newRef.getItem() };\n    if (idChanged) {\n      result.idChanged = true;\n      result.newId = newId;\n    }\n    return result;\n  }\n\n  /**\n   * Resolve the new ID, handling collisions based on options.\n   */\n  private resolveNewId(\n    requestedId: string,\n    currentId: string,\n    options: UpdateOptions\n  ): { newId: string; idChanged: boolean; collision: boolean } {\n    if (requestedId === currentId) {\n      return { newId: requestedId, idChanged: false, collision: false };\n    }\n\n    const conflictingRef = this.idIndex.get(requestedId);\n    if (!conflictingRef) {\n      return { newId: requestedId, idChanged: false, collision: false };\n    }\n\n    const onIdCollision = options.onIdCollision ?? \"fail\";\n    if (onIdCollision === \"fail\") {\n      return { newId: requestedId, idChanged: false, collision: true };\n    }\n\n    // onIdCollision === \"suffix\": resolve by adding suffix\n    const existingIds = new Set(this.references.map((r) => r.getId()));\n    existingIds.delete(currentId);\n    const resolvedId = this.resolveIdCollision(requestedId, existingIds);\n    return { newId: resolvedId, idChanged: true, collision: false };\n  }\n\n  /**\n   * Build the updated CslItem, preserving uuid and created_at.\n   */\n  private buildUpdatedItem(\n    existingItem: CslItem,\n    updates: Partial<CslItem>,\n    newId: string\n  ): CslItem {\n    return {\n      ...existingItem,\n      ...updates,\n      id: newId,\n      type: updates.type ?? existingItem.type,\n      custom: {\n        ...(existingItem.custom || {}),\n        ...(updates.custom || {}),\n        uuid: existingItem.custom?.uuid || \"\",\n        created_at: existingItem.custom?.created_at || new Date().toISOString(),\n        timestamp: new Date().toISOString(),\n      },\n    };\n  }\n\n  /**\n   * Remove a reference from all indices.\n   */\n  private removeFromIndices(ref: Reference): void {\n    this.uuidIndex.delete(ref.getUuid());\n    this.idIndex.delete(ref.getId());\n\n    const doi = ref.getDoi();\n    if (doi) {\n      this.doiIndex.delete(doi);\n    }\n\n    const pmid = ref.getPmid();\n    if (pmid) {\n      this.pmidIndex.delete(pmid);\n    }\n\n    const isbn = ref.getIsbn();\n    if (isbn) {\n      this.isbnIndex.delete(isbn);\n    }\n  }\n\n  /**\n   * Generate an alphabetic suffix for ID collision resolution.\n   * 0 -> 'a', 1 -> 'b', ..., 25 -> 'z', 26 -> 'aa', etc.\n   */\n  private generateSuffix(index: number): string {\n    const alphabet = \"abcdefghijklmnopqrstuvwxyz\";\n    let suffix = \"\";\n    let n = index;\n\n    do {\n      suffix = alphabet[n % 26] + suffix;\n      n = Math.floor(n / 26) - 1;\n    } while (n >= 0);\n\n    return suffix;\n  }\n\n  /**\n   * Resolve ID collision by appending alphabetic suffix.\n   */\n  private resolveIdCollision(baseId: string, existingIds: Set<string>): string {\n    if (!existingIds.has(baseId)) {\n      return baseId;\n    }\n\n    let index = 0;\n    let newId: string;\n\n    do {\n      const suffix = this.generateSuffix(index);\n      newId = `${baseId}${suffix}`;\n      index++;\n    } while (existingIds.has(newId));\n\n    return newId;\n  }\n}\n","import type { FieldSpecifier, SearchQuery, SearchToken } from \"./types.js\";\n\nconst VALID_FIELDS: Set<FieldSpecifier> = new Set([\n  \"author\",\n  \"title\",\n  \"year\",\n  \"doi\",\n  \"pmid\",\n  \"pmcid\",\n  \"url\",\n  \"keyword\",\n  \"tag\",\n]);\n\n/**\n * Check if character at index is whitespace\n */\nfunction isWhitespace(query: string, index: number): boolean {\n  return /\\s/.test(query.charAt(index));\n}\n\n/**\n * Check if character at index is a quote\n */\nfunction isQuote(query: string, index: number): boolean {\n  return query.charAt(index) === '\"';\n}\n\n/**\n * Tokenize a search query string\n */\nexport function tokenize(query: string): SearchQuery {\n  const tokens: SearchToken[] = [];\n  let i = 0;\n\n  while (i < query.length) {\n    // Skip whitespace\n    if (isWhitespace(query, i)) {\n      i++;\n      continue;\n    }\n\n    // Parse next token\n    const result = parseNextToken(query, i);\n    if (result.token) {\n      tokens.push(result.token);\n    }\n    i = result.nextIndex;\n  }\n\n  return {\n    original: query,\n    tokens,\n  };\n}\n\ntype TokenResult = { token: SearchToken | null; nextIndex: number };\n\n/**\n * Check if there's whitespace between two indices\n */\nfunction hasWhitespaceBetween(query: string, start: number, end: number): boolean {\n  for (let j = start; j < end; j++) {\n    if (isWhitespace(query, j)) {\n      return true;\n    }\n  }\n  return false;\n}\n\n/**\n * Try to parse a field:value pattern starting at the given index\n * Returns null if not a valid field:value pattern\n */\nfunction tryParseFieldValue(query: string, startIndex: number): TokenResult | null {\n  const colonIndex = query.indexOf(\":\", startIndex);\n  if (colonIndex === -1) {\n    return null;\n  }\n\n  // Check if there's whitespace before colon (invalid field pattern)\n  if (hasWhitespaceBetween(query, startIndex, colonIndex)) {\n    return null;\n  }\n\n  const fieldName = query.substring(startIndex, colonIndex);\n  if (!VALID_FIELDS.has(fieldName as FieldSpecifier)) {\n    return null;\n  }\n\n  // Valid field specifier found\n  const afterColon = colonIndex + 1;\n\n  // Check if value is empty\n  if (afterColon >= query.length || isWhitespace(query, afterColon)) {\n    return { token: null, nextIndex: afterColon };\n  }\n\n  // Check if value is a quoted phrase\n  if (isQuote(query, afterColon)) {\n    const quoteResult = parseQuotedValue(query, afterColon);\n    if (quoteResult.value !== null) {\n      return {\n        token: {\n          raw: query.substring(startIndex, quoteResult.nextIndex),\n          value: quoteResult.value,\n          field: fieldName as FieldSpecifier,\n          isPhrase: true,\n        },\n        nextIndex: quoteResult.nextIndex,\n      };\n    }\n    // If quote parsing failed, return null to try other parsing\n    return null;\n  }\n\n  // Regular unquoted value\n  const valueResult = parseUnquotedValue(query, afterColon);\n  return {\n    token: {\n      raw: query.substring(startIndex, valueResult.nextIndex),\n      value: valueResult.value,\n      field: fieldName as FieldSpecifier,\n      isPhrase: false,\n    },\n    nextIndex: valueResult.nextIndex,\n  };\n}\n\n/**\n * Parse a quoted token (phrase without field specifier)\n */\nfunction parseQuotedToken(query: string, startIndex: number): TokenResult {\n  const quoteResult = parseQuotedValue(query, startIndex);\n  if (quoteResult.value !== null) {\n    return {\n      token: {\n        raw: query.substring(startIndex, quoteResult.nextIndex),\n        value: quoteResult.value,\n        isPhrase: true,\n      },\n      nextIndex: quoteResult.nextIndex,\n    };\n  }\n\n  // If quote parsing failed (empty or unclosed), skip it\n  if (quoteResult.nextIndex > startIndex) {\n    // Empty quote - skip it\n    return { token: null, nextIndex: quoteResult.nextIndex };\n  }\n\n  // Unclosed quote - treat as regular text including the quote character\n  const valueResult = parseUnquotedValue(query, startIndex, true);\n  return {\n    token: {\n      raw: valueResult.value,\n      value: valueResult.value,\n      isPhrase: false,\n    },\n    nextIndex: valueResult.nextIndex,\n  };\n}\n\n/**\n * Parse a regular unquoted token\n */\nfunction parseRegularToken(query: string, startIndex: number): TokenResult {\n  const valueResult = parseUnquotedValue(query, startIndex);\n  return {\n    token: {\n      raw: valueResult.value,\n      value: valueResult.value,\n      isPhrase: false,\n    },\n    nextIndex: valueResult.nextIndex,\n  };\n}\n\n/**\n * Parse the next token starting at the given index\n */\nfunction parseNextToken(query: string, startIndex: number): TokenResult {\n  // Try to parse field:value pattern first\n  const fieldResult = tryParseFieldValue(query, startIndex);\n  if (fieldResult !== null) {\n    return fieldResult;\n  }\n\n  // Check if it's a quoted phrase\n  if (isQuote(query, startIndex)) {\n    return parseQuotedToken(query, startIndex);\n  }\n\n  // Regular unquoted token\n  return parseRegularToken(query, startIndex);\n}\n\n/**\n * Parse a quoted value starting at a quote character\n */\nfunction parseQuotedValue(\n  query: string,\n  startIndex: number\n): { value: string | null; nextIndex: number } {\n  if (!isQuote(query, startIndex)) {\n    return { value: null, nextIndex: startIndex };\n  }\n\n  let i = startIndex + 1; // Skip opening quote\n  const valueStart = i;\n\n  // Find closing quote\n  while (i < query.length && !isQuote(query, i)) {\n    i++;\n  }\n\n  // No closing quote found\n  if (i >= query.length) {\n    return { value: null, nextIndex: startIndex };\n  }\n\n  const value = query.substring(valueStart, i);\n  i++; // Skip closing quote\n\n  // Return null for empty quotes\n  if (value.trim() === \"\") {\n    return { value: null, nextIndex: i };\n  }\n\n  return { value, nextIndex: i };\n}\n\n/**\n * Parse an unquoted value\n * @param includeQuotes - If true, don't stop at quote characters (for unclosed quotes)\n */\nfunction parseUnquotedValue(\n  query: string,\n  startIndex: number,\n  includeQuotes = false\n): { value: string; nextIndex: number } {\n  let i = startIndex;\n\n  // Read until whitespace (and optionally until quote)\n  while (i < query.length && !isWhitespace(query, i)) {\n    if (!includeQuotes && isQuote(query, i)) {\n      break;\n    }\n    i++;\n  }\n\n  return {\n    value: query.substring(startIndex, i),\n    nextIndex: i,\n  };\n}\n","/**\n * Normalize text for search matching\n *\n * Applies the following transformations:\n * 1. Unicode NFKC normalization\n * 2. Lowercase conversion\n * 3. Remove diacritics (accents)\n * 4. Punctuation removal\n * 5. Whitespace normalization\n */\nexport function normalize(text: string): string {\n  // Step 1: Unicode NFKC normalization (compatibility normalization)\n  let normalized = text.normalize(\"NFKC\");\n\n  // Step 2: Lowercase\n  normalized = normalized.toLowerCase();\n\n  // Step 3: Remove diacritics\n  // Use NFD to decompose, then remove combining diacritical marks\n  normalized = normalized.normalize(\"NFD\").replace(/\\p{M}/gu, \"\");\n\n  // Step 4: Remove punctuation\n  // Replace all punctuation and special characters with spaces\n  // Keep: letters (including Unicode), numbers, slashes, and whitespace\n  normalized = normalized.replace(/[^\\p{L}\\p{N}/\\s]/gu, \" \");\n\n  // Step 5: Normalize whitespace\n  // - Replace all whitespace sequences (spaces, tabs, newlines) with a single space\n  // - Trim leading and trailing whitespace\n  normalized = normalized.replace(/\\s+/g, \" \").trim();\n\n  return normalized;\n}\n\n/**\n * Normalize text for matching while preserving case\n *\n * Applies the following transformations:\n * 1. Unicode NFKC normalization\n * 2. Remove diacritics (accents)\n * 3. Normalize whitespace\n *\n * Unlike `normalize`, this function preserves letter case\n * for use with uppercase-sensitive matching.\n */\nexport function normalizePreservingCase(text: string): string {\n  // Step 1: Unicode NFKC normalization (compatibility normalization)\n  let normalized = text.normalize(\"NFKC\");\n\n  // Step 2: Remove diacritics\n  // Use NFD to decompose, then remove combining diacritical marks\n  normalized = normalized.normalize(\"NFD\").replace(/\\p{M}/gu, \"\");\n\n  // Step 3: Normalize whitespace\n  // - Replace all whitespace sequences (spaces, tabs, newlines) with a single space\n  // - Trim leading and trailing whitespace\n  normalized = normalized.replace(/\\s+/g, \" \").trim();\n\n  return normalized;\n}\n","/**\n * Represents a segment of consecutive uppercase letters in a string.\n */\nexport interface UppercaseSegment {\n  /** The uppercase segment text */\n  segment: string;\n  /** Start index (inclusive) */\n  start: number;\n  /** End index (exclusive) */\n  end: number;\n}\n\n/**\n * Checks if the text contains 2 or more consecutive uppercase letters.\n * Pattern: /[A-Z]{2,}/\n *\n * @param text - The text to check\n * @returns true if text contains consecutive uppercase letters\n */\nexport function hasConsecutiveUppercase(text: string): boolean {\n  const pattern = /[A-Z]{2,}/;\n  return pattern.test(text);\n}\n\n/**\n * Extracts all segments of 2 or more consecutive uppercase letters from text.\n * Pattern: /[A-Z]{2,}/g\n *\n * @param text - The text to extract segments from\n * @returns Array of uppercase segments with their positions\n */\nexport function extractUppercaseSegments(text: string): UppercaseSegment[] {\n  const pattern = /[A-Z]{2,}/g;\n  const segments: UppercaseSegment[] = [];\n\n  for (const match of text.matchAll(pattern)) {\n    segments.push({\n      segment: match[0],\n      start: match.index,\n      end: match.index + match[0].length,\n    });\n  }\n\n  return segments;\n}\n\n/**\n * Escapes special regex characters in a string.\n */\nfunction escapeRegex(str: string): string {\n  return str.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n}\n\n/**\n * Normalizes whitespace in a string (collapses multiple spaces, trims).\n */\nfunction normalizeWhitespace(text: string): string {\n  return text.replace(/\\s+/g, \" \").trim();\n}\n\n/**\n * Checks if all uppercase segments from the query exist in the target (case-sensitive).\n */\nfunction allUppercaseSegmentsExist(segments: UppercaseSegment[], target: string): boolean {\n  return segments.every((seg) => target.includes(seg.segment));\n}\n\n/**\n * Builds a regex pattern from query and its uppercase segments.\n * Uppercase segments are matched literally, other parts flexibly.\n */\nfunction buildMatchPattern(query: string, segments: UppercaseSegment[]): string {\n  const patternParts: string[] = [];\n  let lastEnd = 0;\n\n  for (const seg of segments) {\n    if (seg.start > lastEnd) {\n      const beforePart = query.slice(lastEnd, seg.start);\n      if (beforePart.trim()) {\n        patternParts.push(escapeRegex(beforePart));\n      }\n    }\n    patternParts.push(`(?:${escapeRegex(seg.segment)})`);\n    lastEnd = seg.end;\n  }\n\n  if (lastEnd < query.length) {\n    const afterPart = query.slice(lastEnd);\n    if (afterPart.trim()) {\n      patternParts.push(escapeRegex(afterPart));\n    }\n  }\n\n  return patternParts.join(\".*?\");\n}\n\n/**\n * Matches a query string against a target string with case sensitivity\n * for consecutive uppercase segments in the query.\n *\n * - If query contains 2+ consecutive uppercase letters (e.g., AI, RNA),\n *   those portions must match exactly in the target.\n * - Other portions are matched case-insensitively.\n *\n * @param query - The search query\n * @param target - The target string to match against\n * @returns true if query matches target according to the rules\n */\nexport function matchWithUppercaseSensitivity(query: string, target: string): boolean {\n  if (query === \"\") {\n    return true;\n  }\n  if (target === \"\") {\n    return false;\n  }\n\n  const normalizedQuery = normalizeWhitespace(query);\n  const normalizedTarget = normalizeWhitespace(target);\n\n  if (!hasConsecutiveUppercase(normalizedQuery)) {\n    return normalizedTarget.toLowerCase().includes(normalizedQuery.toLowerCase());\n  }\n\n  const segments = extractUppercaseSegments(normalizedQuery);\n\n  if (!allUppercaseSegmentsExist(segments, target)) {\n    return false;\n  }\n\n  const pattern = buildMatchPattern(normalizedQuery, segments);\n\n  try {\n    const regex = new RegExp(pattern, \"i\");\n    return regex.test(normalizedTarget);\n  } catch {\n    return normalizedTarget.toLowerCase().includes(normalizedQuery.toLowerCase());\n  }\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport { normalizePreservingCase } from \"./normalizer.js\";\nimport type { FieldMatch, MatchStrength, SearchResult, SearchToken } from \"./types.js\";\nimport { matchWithUppercaseSensitivity } from \"./uppercase.js\";\n\n/**\n * ID fields require exact match (case-sensitive)\n */\nconst ID_FIELDS = new Set([\"DOI\", \"PMID\", \"PMCID\", \"URL\"]);\n\n/**\n * Extract year from CSL-JSON issued field\n */\nfunction extractYear(reference: CslItem): string {\n  if (reference.issued?.[\"date-parts\"]?.[0]?.[0]) {\n    return String(reference.issued[\"date-parts\"][0][0]);\n  }\n  return \"0000\";\n}\n\n/**\n * Extract and format author names\n * Returns \"family given\" format for all authors\n */\nfunction extractAuthors(reference: CslItem): string {\n  if (!reference.author || reference.author.length === 0) {\n    return \"\";\n  }\n\n  return reference.author\n    .map((author) => {\n      const family = author.family || \"\";\n      const given = author.given || \"\";\n      return given ? `${family} ${given}` : family;\n    })\n    .join(\" \");\n}\n\n/**\n * Get field value from reference\n */\nfunction getFieldValue(reference: CslItem, field: string): string | null {\n  // Handle special fields\n  if (field === \"year\") {\n    return extractYear(reference);\n  }\n\n  if (field === \"author\") {\n    return extractAuthors(reference);\n  }\n\n  // Handle direct field access\n  const value = reference[field as keyof CslItem];\n  if (typeof value === \"string\") {\n    return value;\n  }\n\n  // Handle nested custom fields\n  if (field.startsWith(\"custom.\")) {\n    const customField = field.substring(7); // Remove \"custom.\" prefix\n    const customValue = (reference.custom as Record<string, unknown>)?.[customField];\n    if (typeof customValue === \"string\") {\n      return customValue;\n    }\n  }\n\n  return null;\n}\n\n/**\n * Check if URL matches in primary URL or additional_urls array\n */\nfunction matchUrl(queryValue: string, reference: CslItem): FieldMatch | null {\n  // Check primary URL field\n  if (reference.URL === queryValue) {\n    return {\n      field: \"URL\",\n      strength: \"exact\",\n      value: reference.URL,\n    };\n  }\n\n  // Check additional_urls in custom field\n  const additionalUrls = (reference.custom as Record<string, unknown>)?.additional_urls;\n  if (Array.isArray(additionalUrls)) {\n    for (const url of additionalUrls) {\n      if (typeof url === \"string\" && url === queryValue) {\n        return {\n          field: \"custom.additional_urls\",\n          strength: \"exact\",\n          value: url,\n        };\n      }\n    }\n  }\n\n  return null;\n}\n\n/**\n * Check if query matches any keyword in the keyword array\n * Performs partial match with normalization on each keyword element\n */\nfunction matchKeyword(queryValue: string, reference: CslItem): FieldMatch | null {\n  // Check if keyword field exists and is an array\n  if (!reference.keyword || !Array.isArray(reference.keyword)) {\n    return null;\n  }\n\n  // Normalize query value (preserving case for uppercase-sensitive matching)\n  const normalizedQuery = normalizePreservingCase(queryValue);\n\n  // Search through each keyword element\n  for (const keyword of reference.keyword) {\n    if (typeof keyword === \"string\") {\n      const normalizedKeyword = normalizePreservingCase(keyword);\n      // Use uppercase-sensitive matching\n      if (matchWithUppercaseSensitivity(normalizedQuery, normalizedKeyword)) {\n        return {\n          field: \"keyword\",\n          strength: \"partial\",\n          value: keyword,\n        };\n      }\n    }\n  }\n\n  return null;\n}\n\n/**\n * Match a tag field against custom.tags array\n * Similar to matchKeyword but accesses custom.tags\n */\nfunction matchTag(queryValue: string, reference: CslItem): FieldMatch | null {\n  // Check if custom.tags field exists and is an array\n  if (!reference.custom?.tags || !Array.isArray(reference.custom.tags)) {\n    return null;\n  }\n\n  // Normalize query value (preserving case for uppercase-sensitive matching)\n  const normalizedQuery = normalizePreservingCase(queryValue);\n\n  // Search through each tag element\n  for (const tag of reference.custom.tags) {\n    if (typeof tag === \"string\") {\n      const normalizedTag = normalizePreservingCase(tag);\n      // Use uppercase-sensitive matching\n      if (matchWithUppercaseSensitivity(normalizedQuery, normalizedTag)) {\n        return {\n          field: \"tag\",\n          strength: \"partial\",\n          value: tag,\n        };\n      }\n    }\n  }\n\n  return null;\n}\n\n/**\n * Map field specifier to actual CSL-JSON field name\n */\nconst FIELD_MAP: Record<string, string> = {\n  author: \"author\",\n  title: \"title\",\n  doi: \"DOI\",\n  pmid: \"PMID\",\n  pmcid: \"PMCID\",\n};\n\n/**\n * Match a year field against a reference\n */\nfunction matchYearField(tokenValue: string, reference: CslItem): FieldMatch | null {\n  const year = extractYear(reference);\n  if (year === tokenValue) {\n    return {\n      field: \"year\",\n      strength: \"exact\",\n      value: year,\n    };\n  }\n  return null;\n}\n\n/**\n * Match a content or ID field against a reference\n */\nfunction matchFieldValue(field: string, tokenValue: string, reference: CslItem): FieldMatch | null {\n  const fieldValue = getFieldValue(reference, field);\n  if (fieldValue === null) {\n    return null;\n  }\n\n  // Check if this is an ID field (exact match, case-sensitive)\n  if (ID_FIELDS.has(field)) {\n    if (fieldValue === tokenValue) {\n      return {\n        field,\n        strength: \"exact\",\n        value: fieldValue,\n      };\n    }\n    return null;\n  }\n\n  // Content field: use uppercase-sensitive matching\n  // Normalize both values (remove diacritics, normalize whitespace) while preserving case\n  const normalizedFieldValue = normalizePreservingCase(fieldValue);\n  const normalizedQuery = normalizePreservingCase(tokenValue);\n\n  // If query contains consecutive uppercase (e.g., \"AI\", \"RNA\"), match case-sensitively\n  // Otherwise, match case-insensitively\n  if (matchWithUppercaseSensitivity(normalizedQuery, normalizedFieldValue)) {\n    return {\n      field,\n      strength: \"partial\",\n      value: fieldValue,\n    };\n  }\n  return null;\n}\n\n/**\n * Match token against a specific field\n */\nfunction matchSpecificField(token: SearchToken, reference: CslItem): FieldMatch[] {\n  const matches: FieldMatch[] = [];\n  const fieldToSearch = token.field as string;\n\n  // Handle URL field specially (search both URL and additional_urls)\n  if (fieldToSearch === \"url\") {\n    const urlMatch = matchUrl(token.value, reference);\n    if (urlMatch) matches.push(urlMatch);\n    return matches;\n  }\n\n  // Handle year field\n  if (fieldToSearch === \"year\") {\n    const yearMatch = matchYearField(token.value, reference);\n    if (yearMatch) matches.push(yearMatch);\n    return matches;\n  }\n\n  // Handle keyword field specially (search array elements)\n  if (fieldToSearch === \"keyword\") {\n    const keywordMatch = matchKeyword(token.value, reference);\n    if (keywordMatch) matches.push(keywordMatch);\n    return matches;\n  }\n\n  // Handle tag field specially (search custom.tags array)\n  if (fieldToSearch === \"tag\") {\n    const tagMatch = matchTag(token.value, reference);\n    if (tagMatch) matches.push(tagMatch);\n    return matches;\n  }\n\n  // Standard field matching\n  const actualField = FIELD_MAP[fieldToSearch] || fieldToSearch;\n  const match = matchFieldValue(actualField, token.value, reference);\n  if (match) matches.push(match);\n\n  return matches;\n}\n\n/**\n * Standard fields to search (not special-cased)\n */\nconst STANDARD_SEARCH_FIELDS = [\n  \"title\",\n  \"author\",\n  \"container-title\",\n  \"publisher\",\n  \"DOI\",\n  \"PMID\",\n  \"PMCID\",\n  \"abstract\",\n];\n\n/**\n * Match token against a single field (used for all-fields search)\n */\nfunction matchSingleField(\n  field: string,\n  tokenValue: string,\n  reference: CslItem\n): FieldMatch | null {\n  if (field === \"year\") {\n    return matchYearField(tokenValue, reference);\n  }\n  if (field === \"URL\") {\n    return matchUrl(tokenValue, reference);\n  }\n  if (field === \"keyword\") {\n    return matchKeyword(tokenValue, reference);\n  }\n  if (field === \"tag\") {\n    return matchTag(tokenValue, reference);\n  }\n  return matchFieldValue(field, tokenValue, reference);\n}\n\n/**\n * Match token against all searchable fields\n */\nfunction matchAllFields(token: SearchToken, reference: CslItem): FieldMatch[] {\n  const matches: FieldMatch[] = [];\n\n  // Match special fields\n  const specialFields = [\"year\", \"URL\", \"keyword\", \"tag\"];\n  for (const field of specialFields) {\n    const match = matchSingleField(field, token.value, reference);\n    if (match) matches.push(match);\n  }\n\n  // Match standard fields\n  for (const field of STANDARD_SEARCH_FIELDS) {\n    const match = matchFieldValue(field, token.value, reference);\n    if (match) matches.push(match);\n  }\n\n  return matches;\n}\n\n/**\n * Match a single token against a reference\n * Returns an array of field matches\n */\nexport function matchToken(token: SearchToken, reference: CslItem): FieldMatch[] {\n  // If field is specified, only search that field\n  if (token.field) {\n    return matchSpecificField(token, reference);\n  }\n\n  // No field specified: search all fields\n  return matchAllFields(token, reference);\n}\n\n/**\n * Match a reference against all search tokens\n * Returns a SearchResult if all tokens match (AND logic), null otherwise\n */\nexport function matchReference(reference: CslItem, tokens: SearchToken[]): SearchResult | null {\n  // Empty token array means no match\n  if (tokens.length === 0) {\n    return null;\n  }\n\n  const tokenMatches: SearchResult[\"tokenMatches\"] = [];\n  let overallStrength: MatchStrength = \"none\";\n\n  // Check if all tokens match (AND logic)\n  for (const token of tokens) {\n    const matches = matchToken(token, reference);\n\n    // If any token doesn't match at least one field, no match\n    if (matches.length === 0) {\n      return null;\n    }\n\n    // Determine highest match strength for this token\n    const tokenStrength = matches.some((m) => m.strength === \"exact\") ? \"exact\" : \"partial\";\n\n    // Update overall strength (exact > partial > none)\n    if (tokenStrength === \"exact\") {\n      overallStrength = \"exact\";\n    } else if (tokenStrength === \"partial\" && overallStrength === \"none\") {\n      overallStrength = \"partial\";\n    }\n\n    tokenMatches.push({\n      token,\n      matches,\n    });\n  }\n\n  // Calculate score (higher is better)\n  // Exact matches get higher score than partial matches\n  const score = overallStrength === \"exact\" ? 100 + tokenMatches.length : 50 + tokenMatches.length;\n\n  return {\n    reference,\n    tokenMatches,\n    overallStrength,\n    score,\n  };\n}\n\n/**\n * Search references against search tokens\n * Returns array of SearchResult for all matching references\n */\nexport function search(references: CslItem[], tokens: SearchToken[]): SearchResult[] {\n  const results: SearchResult[] = [];\n\n  for (const reference of references) {\n    const match = matchReference(reference, tokens);\n    if (match) {\n      results.push(match);\n    }\n  }\n\n  return results;\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { MatchStrength, SearchResult } from \"./types.js\";\n\n/**\n * Extract year from CSL-JSON reference\n * Returns \"0000\" for missing year (sorted last)\n */\nfunction extractYear(reference: CslItem): string {\n  if (reference.issued?.[\"date-parts\"]?.[0]?.[0]) {\n    return String(reference.issued[\"date-parts\"][0][0]);\n  }\n  return \"0000\";\n}\n\n/**\n * Extract first author's family name for sorting\n * Returns empty string for missing author (sorted last)\n */\nfunction extractFirstAuthorFamily(reference: CslItem): string {\n  if (!reference.author || reference.author.length === 0) {\n    return \"\";\n  }\n  return reference.author[0]?.family || \"\";\n}\n\n/**\n * Extract title for sorting\n * Returns empty string for missing title (sorted last)\n */\nfunction extractTitle(reference: CslItem): string {\n  return reference.title || \"\";\n}\n\n/**\n * Compare match strength (exact > partial > none)\n * Returns negative if a < b, positive if a > b, 0 if equal\n */\nfunction compareStrength(a: MatchStrength, b: MatchStrength): number {\n  const strengthOrder = { exact: 2, partial: 1, none: 0 };\n  return strengthOrder[b] - strengthOrder[a];\n}\n\n/**\n * Compare years (descending - newer first)\n * Returns negative if a < b, positive if a > b, 0 if equal\n */\nfunction compareYear(a: CslItem, b: CslItem): number {\n  const yearA = extractYear(a);\n  const yearB = extractYear(b);\n  return Number(yearB) - Number(yearA);\n}\n\n/**\n * Compare authors alphabetically (empty comes last)\n * Returns negative if a < b, positive if a > b, 0 if equal\n */\nfunction compareAuthor(a: CslItem, b: CslItem): number {\n  const authorA = extractFirstAuthorFamily(a).toLowerCase();\n  const authorB = extractFirstAuthorFamily(b).toLowerCase();\n  // Empty string (no author) should come after authors\n  if (authorA === \"\" && authorB !== \"\") return 1;\n  if (authorA !== \"\" && authorB === \"\") return -1;\n  return authorA.localeCompare(authorB);\n}\n\n/**\n * Compare titles alphabetically (empty comes last)\n * Returns negative if a < b, positive if a > b, 0 if equal\n */\nfunction compareTitle(a: CslItem, b: CslItem): number {\n  const titleA = extractTitle(a).toLowerCase();\n  const titleB = extractTitle(b).toLowerCase();\n  // Empty string (no title) should come after titles\n  if (titleA === \"\" && titleB !== \"\") return 1;\n  if (titleA !== \"\" && titleB === \"\") return -1;\n  return titleA.localeCompare(titleB);\n}\n\n/**\n * Sort search results according to the specification:\n * 1. Match strength (exact > partial)\n * 2. Year (descending)\n * 3. Author (alphabetical)\n * 4. Title (alphabetical)\n * 5. Registration order (original array order)\n */\nexport function sortResults(results: SearchResult[]): SearchResult[] {\n  // Create a copy with original indices for stable sort\n  const indexed = results.map((result, index) => ({ result, index }));\n\n  // Sort according to the criteria\n  const sorted = indexed.sort((a, b) => {\n    // 1. Match strength (exact > partial)\n    const strengthDiff = compareStrength(a.result.overallStrength, b.result.overallStrength);\n    if (strengthDiff !== 0) return strengthDiff;\n\n    // 2. Year (descending - newer first)\n    const yearDiff = compareYear(a.result.reference, b.result.reference);\n    if (yearDiff !== 0) return yearDiff;\n\n    // 3. Author (alphabetical)\n    const authorDiff = compareAuthor(a.result.reference, b.result.reference);\n    if (authorDiff !== 0) return authorDiff;\n\n    // 4. Title (alphabetical, case-insensitive)\n    const titleDiff = compareTitle(a.result.reference, b.result.reference);\n    if (titleDiff !== 0) return titleDiff;\n\n    // 5. Registration order (original array order)\n    return a.index - b.index;\n  });\n\n  // Return only the results (without indices)\n  return sorted.map((item) => item.result);\n}\n","/**\n * Duplicate detection logic\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { normalize } from \"../search/normalizer.js\";\nimport type { DuplicateMatch, DuplicateResult } from \"./types.js\";\n\n/**\n * Normalize DOI by removing common URL prefixes\n * Returns the DOI in format: 10.xxxx/...\n */\nfunction normalizeDoi(doi: string): string {\n  // Remove common DOI URL prefixes\n  const normalized = doi\n    .replace(/^https?:\\/\\/doi\\.org\\//i, \"\")\n    .replace(/^https?:\\/\\/dx\\.doi\\.org\\//i, \"\")\n    .replace(/^doi:/i, \"\");\n\n  return normalized;\n}\n\n/**\n * Extract year from CSL-JSON issued field\n */\nfunction extractYear(item: CslItem): string | null {\n  const dateParts = item.issued?.[\"date-parts\"]?.[0];\n  if (!dateParts || dateParts.length === 0) {\n    return null;\n  }\n  return String(dateParts[0]);\n}\n\n/**\n * Normalize author names to \"family given-initial\" format\n */\nfunction normalizeAuthors(item: CslItem): string | null {\n  if (!item.author || item.author.length === 0) {\n    return null;\n  }\n\n  // Combine all authors: \"family given-initial\"\n  const authorStrings = item.author.map((author) => {\n    const family = author.family || \"\";\n    const givenInitial = author.given ? author.given.charAt(0) : \"\";\n    return `${family} ${givenInitial}`.trim();\n  });\n\n  // Join and normalize\n  return normalize(authorStrings.join(\" \"));\n}\n\n/**\n * Check if two items match by DOI\n */\nfunction checkDoiMatch(item: CslItem, existing: CslItem): DuplicateMatch | null {\n  if (!item.DOI || !existing.DOI) {\n    return null;\n  }\n\n  const normalizedItemDoi = normalizeDoi(item.DOI);\n  const normalizedExistingDoi = normalizeDoi(existing.DOI);\n\n  // DOI comparison is case-sensitive\n  if (normalizedItemDoi === normalizedExistingDoi) {\n    return {\n      type: \"doi\",\n      existing,\n      details: {\n        doi: normalizedExistingDoi,\n      },\n    };\n  }\n\n  return null;\n}\n\n/**\n * Check if two items match by PMID\n */\nfunction checkPmidMatch(item: CslItem, existing: CslItem): DuplicateMatch | null {\n  if (!item.PMID || !existing.PMID) {\n    return null;\n  }\n\n  // PMID comparison is exact string match\n  if (item.PMID === existing.PMID) {\n    return {\n      type: \"pmid\",\n      existing,\n      details: {\n        pmid: existing.PMID,\n      },\n    };\n  }\n\n  return null;\n}\n\n/**\n * Normalize ISBN by removing hyphens, spaces, and uppercasing X\n */\nfunction normalizeIsbn(isbn: string): string {\n  return isbn.replace(/[-\\s]/g, \"\").toUpperCase();\n}\n\n/**\n * Types that should match by ISBN only (not title)\n */\nconst BOOK_TYPES = [\"book\"];\n\n/**\n * Types that should match by ISBN + title (chapters in the same book can differ)\n */\nconst BOOK_SECTION_TYPES = [\"chapter\"];\n\n/**\n * Check if two items match by ISBN\n * - For book type: ISBN only\n * - For chapter type: ISBN + title\n */\nfunction checkIsbnMatch(item: CslItem, existing: CslItem): DuplicateMatch | null {\n  if (!item.ISBN || !existing.ISBN) {\n    return null;\n  }\n\n  const normalizedItemIsbn = normalizeIsbn(item.ISBN);\n  const normalizedExistingIsbn = normalizeIsbn(existing.ISBN);\n\n  if (normalizedItemIsbn !== normalizedExistingIsbn) {\n    return null;\n  }\n\n  // For book type: ISBN only is enough\n  if (BOOK_TYPES.includes(item.type) || BOOK_TYPES.includes(existing.type)) {\n    return {\n      type: \"isbn\",\n      existing,\n      details: {\n        isbn: normalizedExistingIsbn,\n      },\n    };\n  }\n\n  // For chapter type: ISBN + title must match\n  if (BOOK_SECTION_TYPES.includes(item.type) || BOOK_SECTION_TYPES.includes(existing.type)) {\n    const itemTitle = item.title ? 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