@ncukondo/search-hub 0.16.0 → 0.17.0

package/dist/cli/commands/review/extract.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"extract.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/review/extract.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,OAAO,EAAsD,KAAK,YAAY,EAAE,KAAK,WAAW,EAAE,MAAM,YAAY,CAAC;AAErH,MAAM,MAAM,UAAU,GAAG,MAAM,GAAG,OAAO,GAAG,QAAQ,GAAG,MAAM,CAAC;AAE9D,MAAM,WAAW,oBAAoB;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,YAAY,EAAE,CAAC;IACxB,IAAI,CAAC,EAAE,UAAU,CAAC;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,kGAAkG;IAClG,KAAK,CAAC,EAAE,WAAW,CAAC;IACpB,+EAA+E;IAC/E,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,gFAAgF;IAChF,IAAI,EAAE,MAAM,CAAC;IACb,4FAA4F;IAC5F,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAGD,MAAM,WAAW,mBAAmB;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,cAAc,EAAE,MAAM,CAAC;IACvB,aAAa,EAAE,MAAM,CAAC;CACvB;AAgLD;;GAEG;AACH,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAU/C;AAED;;GAEG;AACH,wBAAsB,oBAAoB,CACxC,OAAO,EAAE,oBAAoB,EAC7B,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,mBAAmB,CAAC,CAkH9B"}

package/dist/cli/commands/review/extract.js

@@ -167,10 +167,14 @@ async function executeReviewExtract(options, sessionsDir) {
     };
     const yamlContent = stringify(outputFile, { lineWidth: 0 });
     const decisionComment = getDecisionInlineComment(options.basis);
-    const yamlWithComments = yamlContent.replace(
+    let yamlWithComments = yamlContent.replace(
       /^(\s*-?\s*)decision: uncertain$/gm,
       `$1decision: uncertain          ${decisionComment}`
     );
+    yamlWithComments = yamlWithComments.replace(
+      /^(\s*)comment: ""$/gm,
+      '$1comment: ""                  # reason for decision'
+    );
     const guidanceComment = getBasisGuidanceComment(options.basis);
     finalContent = guidanceComment + yamlWithComments;
   } else {
@@ -180,10 +184,14 @@ async function executeReviewExtract(options, sessionsDir) {
       articles: paginated.map((article) => buildFinalizeArticle(article, options.basis))
     };
     const yamlContent = stringify(outputFile, { lineWidth: 0 });
-    const yamlWithComments = yamlContent.replace(
+    let yamlWithComments = yamlContent.replace(
       /^(\s*)finalDecision: null$/gm,
       "$1finalDecision: # include / exclude"
     );
+    yamlWithComments = yamlWithComments.replace(
+      /^(\s*)reviews: \[\]$/gm,
+      "$1reviews: []                  # add new reviews here"
+    );
     const guidanceComment = getFinalDecisionGuidanceComment();
     finalContent = guidanceComment + yamlWithComments;
   }

package/dist/cli/commands/review/extract.js.map

@@ -1 +1 @@
-{"version":3,"file":"extract.js","sources":["../../../../src/cli/commands/review/extract.ts"],"sourcesContent":["/**\n * review extract command - Extract subset of articles for distributed review\n */\n\nimport { join, dirname } from 'node:path';\nimport { readFile, writeFile, mkdir, copyFile, access } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport { classifyStatus, type ReviewFile, type ArticleEntry, type ReviewStatus, type ReviewBasis } from './types.js';\n\nexport type SortOption = 'year' | 'title' | 'random' | 'none';\n\nexport interface ReviewExtractOptions {\n  sessionId: string;\n  filter?: ReviewStatus[];\n  sort?: SortOption;\n  seed?: number;\n  limit?: number;\n  offset?: number;\n  /** Basis for the review (title, abstract, fulltext). When specified, outputs screening format. */\n  basis?: ReviewBasis;\n  /** Reviewer identifier (e.g., \"ai:claude\"). Required for all extract modes. */\n  reviewer?: string;\n  /** Name for the review subset (output goes to for-review/<name>/review.yaml) */\n  name: string;\n  /** When true, outputs final decision format with reviewHistory and finalDecision fields. */\n  finalize?: boolean;\n}\n\n\nexport interface ReviewExtractResult {\n  outputPath: string;\n  extractedCount: number;\n  totalMatching: number;\n}\n\n/**\n * Load review file from session directory\n */\nasync function loadReviewFile(sessionDir: string): Promise<ReviewFile> {\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Seeded random number generator (Fisher-Yates shuffle with LCG)\n */\nfunction seededShuffle<T>(array: T[], seed: number): T[] {\n  const result = [...array];\n  let currentSeed = seed;\n\n  // Linear congruential generator\n  function random(): number {\n    currentSeed = (currentSeed * 1664525 + 1013904223) % 4294967296;\n    return currentSeed / 4294967296;\n  }\n\n  // Fisher-Yates shuffle\n  for (let i = result.length - 1; i > 0; i--) {\n    const j = Math.floor(random() * (i + 1));\n    [result[i], result[j]] = [result[j]!, result[i]!];\n  }\n\n  return result;\n}\n\n/**\n * Get the best identifier for an article (doi > pmid > scopusId > arxivId > ericId > title)\n */\nfunction getArticleId(article: ArticleEntry): string {\n  if (article.doi) return article.doi;\n  if (article.pmid) return article.pmid;\n  if (article.scopusId) return article.scopusId;\n  if (article.arxivId) return article.arxivId;\n  if (article.ericId) return article.ericId;\n  return article.title;\n}\n\nfunction getBasisGuidanceComment(basis: ReviewBasis): string {\n  const schemaLine = '# yaml-language-server: $schema=./review.schema.json';\n  switch (basis) {\n    case 'title':\n      return [\n        schemaLine,\n        '# Screening by title only.',\n        '# Mark clearly irrelevant items as \"exclude\" with a comment explaining the reason.',\n        '# Leave everything else as \"uncertain\".',\n        '',\n      ].join('\\n');\n    case 'abstract':\n      return [\n        schemaLine,\n        '# Screening by title and abstract.',\n        '# You should be able to decide \"include\" or \"exclude\" for most items at this stage.',\n        '# Mark remaining ambiguous items as \"uncertain\" with a comment explaining why.',\n        '',\n      ].join('\\n');\n    case 'fulltext':\n      return [\n        schemaLine,\n        '# Screening by full text. This is the final decision stage.',\n        '# Decide \"include\" or \"exclude\" for each item.',\n        '# Use \"uncertain\" only when absolutely unavoidable, with a comment explaining why.',\n        '',\n      ].join('\\n');\n  }\n}\n\nfunction getDecisionInlineComment(basis: ReviewBasis): string {\n  switch (basis) {\n    case 'title':\n      return '# exclude / uncertain';\n    case 'abstract':\n    case 'fulltext':\n      return '# include / exclude / uncertain';\n  }\n}\n\n/** Build a screening article for --basis mode: only include fields relevant to the basis */\nfunction buildScreeningArticle(article: ArticleEntry, basis: ReviewBasis): ArticleEntry {\n  // Start with identifiers\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Include abstract for abstract and fulltext basis\n  if ((basis === 'abstract' || basis === 'fulltext') && article.abstract) {\n    result.abstract = article.abstract;\n  }\n\n  // Include fulltext ref for fulltext basis\n  if (basis === 'fulltext' && article.fulltext) {\n    result.fulltext = article.fulltext;\n  }\n\n  // Pre-populate reviews (reviewer omitted; filled from top-level field on merge)\n  result.reviews = [{ decision: 'uncertain' as const, comment: '' } as ArticleEntry['reviews'][0]];\n\n  return result;\n}\n\n/** Build a finalize article with reviewHistory and finalDecision, optionally scoped by basis */\nfunction buildFinalizeArticle(article: ArticleEntry, basis?: ReviewBasis): ArticleEntry {\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n\n  // Always include identifiers\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Always include bibliographic metadata\n  if (article.authors) result.authors = article.authors;\n  if (article.year) result.year = article.year;\n\n  // Scope content by basis (or include all if no basis)\n  if (!basis || basis === 'abstract' || basis === 'fulltext') {\n    if (article.abstract) result.abstract = article.abstract;\n  }\n  if (!basis || basis === 'fulltext') {\n    if (article.fulltext) result.fulltext = article.fulltext;\n  }\n\n  // Add reviewHistory (existing reviews, read-only)\n  result.reviewHistory = article.reviews ?? [];\n\n  // Empty reviews for new reviews\n  result.reviews = [];\n\n  // Null finalDecision as placeholder\n  result.finalDecision = null;\n\n  return result;\n}\n\nfunction getFinalDecisionGuidanceComment(): string {\n  return [\n    '# yaml-language-server: $schema=./review.schema.json',\n    '# Final decision file: set finalDecision on each article',\n    '# Valid decisions: include / exclude / null',\n    '',\n  ].join('\\n');\n}\n\n/**\n * Sort articles based on sort option\n */\nfunction sortArticles(articles: ArticleEntry[], sort: SortOption, seed?: number): ArticleEntry[] {\n  switch (sort) {\n    case 'year':\n      return [...articles].sort((a, b) => {\n        const yearA = a.year ?? '';\n        const yearB = b.year ?? '';\n        return yearA.localeCompare(yearB);\n      });\n    case 'title':\n      return [...articles].sort((a, b) => a.title.localeCompare(b.title));\n    case 'random':\n      return seededShuffle(articles, seed ?? Date.now());\n    case 'none':\n    default:\n      return articles;\n  }\n}\n\n/**\n * Validate the name parameter for extract\n */\nexport function validateName(name: string): void {\n  if (!name || name.trim() === '') {\n    throw new Error('--name must not be empty');\n  }\n  if (name.includes('/') || name.includes('\\\\')) {\n    throw new Error(`--name must not contain path separators: \"${name}\"`);\n  }\n  if (name.includes('..')) {\n    throw new Error(`--name must not contain \"..\": \"${name}\"`);\n  }\n}\n\n/**\n * Execute review extract command\n */\nexport async function executeReviewExtract(\n  options: ReviewExtractOptions,\n  sessionsDir: string\n): Promise<ReviewExtractResult> {\n  validateName(options.name);\n\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const outputPath = join(sessionDir, 'for-review', options.name, 'review.yaml');\n  const reviewFile = await loadReviewFile(sessionDir);\n\n  // Filter articles by status\n  const reviewers = reviewFile.reviewers;\n  let filtered: ArticleEntry[];\n  if (options.filter && options.filter.length > 0) {\n    filtered = reviewFile.articles.filter((article) => {\n      const status = classifyStatus(article, reviewers);\n      return options.filter!.includes(status);\n    });\n  } else {\n    filtered = [...reviewFile.articles];\n  }\n\n  const totalMatching = filtered.length;\n\n  // Sort articles\n  const sorted = sortArticles(filtered, options.sort ?? 'none', options.seed);\n\n  // Apply pagination\n  let paginated = sorted;\n  if (options.offset !== undefined && options.offset > 0) {\n    paginated = paginated.slice(options.offset);\n  }\n  if (options.limit !== undefined && options.limit > 0) {\n    paginated = paginated.slice(0, options.limit);\n  }\n\n  if (!options.reviewer) {\n    throw new Error('--reviewer is required for review file extract');\n  }\n\n  let finalContent: string;\n\n  if (options.basis && !options.finalize) {\n    // Screening mode: basis-scoped content with pre-populated reviews\n    const outputFile: ReviewFile = {\n      sessionId: options.sessionId,\n      basis: options.basis,\n      reviewer: options.reviewer,\n      articles: paginated.map((article) => buildScreeningArticle(article, options.basis!)),\n    };\n\n    const yamlContent = stringifyYaml(outputFile, { lineWidth: 0 });\n\n    // Add decision inline comments\n    const decisionComment = getDecisionInlineComment(options.basis);\n    const yamlWithComments = yamlContent.replace(\n      /^(\\s*-?\\s*)decision: uncertain$/gm,\n      `$1decision: uncertain          ${decisionComment}`\n    );\n\n    const guidanceComment = getBasisGuidanceComment(options.basis);\n    finalContent = guidanceComment + yamlWithComments;\n  } else {\n    // Final decision mode: --finalize, or no --basis (backward compat)\n    const outputFile: ReviewFile = {\n      sessionId: options.sessionId,\n      reviewer: options.reviewer,\n      articles: paginated.map((article) => buildFinalizeArticle(article, options.basis)),\n    };\n\n    const yamlContent = stringifyYaml(outputFile, { lineWidth: 0 });\n\n    // Replace finalDecision: null with a commented placeholder for user guidance\n    const yamlWithComments = yamlContent.replace(\n      /^(\\s*)finalDecision: null$/gm,\n      '$1finalDecision: # include / exclude'\n    );\n\n    const guidanceComment = getFinalDecisionGuidanceComment();\n    finalContent = guidanceComment + yamlWithComments;\n  }\n\n  // Ensure output directory exists\n  const outputDir = dirname(outputPath);\n  await mkdir(outputDir, { recursive: true });\n\n  // Write output YAML\n  await writeFile(outputPath, finalContent, 'utf-8');\n\n  // Copy schema file to output directory if it exists\n  const schemaSourcePath = join(sessionDir, '.internal', 'review.schema.json');\n  const schemaDestPath = join(outputDir, 'review.schema.json');\n\n  try {\n    await access(schemaSourcePath);\n    await copyFile(schemaSourcePath, schemaDestPath);\n  } catch {\n    // Schema file doesn't exist, skip copying\n  }\n\n  return {\n    outputPath,\n    extractedCount: paginated.length,\n    totalMatching,\n  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Required for all extract modes. */\n  reviewer?: string;\n  /** Name for the review subset (output goes to for-review/<name>/review.yaml) */\n  name: string;\n  /** When true, outputs final decision format with reviewHistory and finalDecision fields. */\n  finalize?: boolean;\n}\n\n\nexport interface ReviewExtractResult {\n  outputPath: string;\n  extractedCount: number;\n  totalMatching: number;\n}\n\n/**\n * Load review file from session directory\n */\nasync function loadReviewFile(sessionDir: string): Promise<ReviewFile> {\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Seeded random number generator (Fisher-Yates shuffle with LCG)\n */\nfunction seededShuffle<T>(array: T[], seed: number): T[] {\n  const result = [...array];\n  let currentSeed = seed;\n\n  // Linear congruential generator\n  function random(): number {\n    currentSeed = (currentSeed * 1664525 + 1013904223) % 4294967296;\n    return currentSeed / 4294967296;\n  }\n\n  // Fisher-Yates shuffle\n  for (let i = result.length - 1; i > 0; i--) {\n    const j = Math.floor(random() * (i + 1));\n    [result[i], result[j]] = [result[j]!, result[i]!];\n  }\n\n  return result;\n}\n\n/**\n * Get the best identifier for an article (doi > pmid > scopusId > arxivId > ericId > title)\n */\nfunction getArticleId(article: ArticleEntry): string {\n  if (article.doi) return article.doi;\n  if (article.pmid) return article.pmid;\n  if (article.scopusId) return article.scopusId;\n  if (article.arxivId) return article.arxivId;\n  if (article.ericId) return article.ericId;\n  return article.title;\n}\n\nfunction getBasisGuidanceComment(basis: ReviewBasis): string {\n  const schemaLine = '# yaml-language-server: $schema=./review.schema.json';\n  switch (basis) {\n    case 'title':\n      return [\n        schemaLine,\n        '# Screening by title only.',\n        '# Mark clearly irrelevant items as \"exclude\" with a comment explaining the reason.',\n        '# Leave everything else as \"uncertain\".',\n        '',\n      ].join('\\n');\n    case 'abstract':\n      return [\n        schemaLine,\n        '# Screening by title and abstract.',\n        '# You should be able to decide \"include\" or \"exclude\" for most items at this stage.',\n        '# Mark remaining ambiguous items as \"uncertain\" with a comment explaining why.',\n        '',\n      ].join('\\n');\n    case 'fulltext':\n      return [\n        schemaLine,\n        '# Screening by full text. This is the final decision stage.',\n        '# Decide \"include\" or \"exclude\" for each item.',\n        '# Use \"uncertain\" only when absolutely unavoidable, with a comment explaining why.',\n        '',\n      ].join('\\n');\n  }\n}\n\nfunction getDecisionInlineComment(basis: ReviewBasis): string {\n  switch (basis) {\n    case 'title':\n      return '# exclude / uncertain';\n    case 'abstract':\n    case 'fulltext':\n      return '# include / exclude / uncertain';\n  }\n}\n\n/** Build a screening article for --basis mode: only include fields relevant to the basis */\nfunction buildScreeningArticle(article: ArticleEntry, basis: ReviewBasis): ArticleEntry {\n  // Start with identifiers\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Include abstract for abstract and fulltext basis\n  if ((basis === 'abstract' || basis === 'fulltext') && article.abstract) {\n    result.abstract = article.abstract;\n  }\n\n  // Include fulltext ref for fulltext basis\n  if (basis === 'fulltext' && article.fulltext) {\n    result.fulltext = article.fulltext;\n  }\n\n  // Pre-populate reviews (reviewer omitted; filled from top-level field on merge)\n  result.reviews = [{ decision: 'uncertain' as const, comment: '' } as ArticleEntry['reviews'][0]];\n\n  return result;\n}\n\n/** Build a finalize article with reviewHistory and finalDecision, optionally scoped by basis */\nfunction buildFinalizeArticle(article: ArticleEntry, basis?: ReviewBasis): ArticleEntry {\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n\n  // Always include identifiers\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Always include bibliographic metadata\n  if (article.authors) result.authors = article.authors;\n  if (article.year) result.year = article.year;\n\n  // Scope content by basis (or include all if no basis)\n  if (!basis || basis === 'abstract' || basis === 'fulltext') {\n    if (article.abstract) result.abstract = article.abstract;\n  }\n  if (!basis || basis === 'fulltext') {\n    if (article.fulltext) result.fulltext = article.fulltext;\n  }\n\n  // Add reviewHistory (existing reviews, read-only)\n  result.reviewHistory = article.reviews ?? 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package/dist/cli/commands/review/finalize.d.ts

@@ -3,6 +3,7 @@ export interface ReviewFinalizeOptions {
     sessionId: string;
     dryRun?: boolean;
     minReviewers?: number;
+    decision?: 'include' | 'exclude';
 }
 export interface ReviewFinalizeResult {
     includedCount: number;
@@ -18,5 +19,6 @@ export declare function executeReviewFinalize(options: ReviewFinalizeOptions, se
  */
 export declare function formatFinalizeOutput(result: ReviewFinalizeResult, options?: {
     dryRun?: boolean;
+    decision?: 'include' | 'exclude';
 }): string;
 //# sourceMappingURL=finalize.d.ts.map

package/dist/cli/commands/review/finalize.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"finalize.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/review/finalize.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,OAAO,EAAmC,KAAK,YAAY,EAAE,MAAM,YAAY,CAAC;AAEhF,MAAM,WAAW,qBAAqB;IACpC,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,EAAE,SAAS,GAAG,SAAS,CAAC;CAClC;AAED,MAAM,WAAW,oBAAoB;IACnC,aAAa,EAAE,MAAM,CAAC;IACtB,aAAa,EAAE,MAAM,CAAC;IACtB,eAAe,EAAE,MAAM,CAAC,YAAY,EAAE,MAAM,CAAC,CAAC;CAC/C;AAcD;;GAEG;AACH,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,qBAAqB,EAC9B,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,oBAAoB,CAAC,CAwD/B;AAED;;GAEG;AACH,wBAAgB,oBAAoB,CAClC,MAAM,EAAE,oBAAoB,EAC5B,OAAO,CAAC,EAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAC;IAAC,QAAQ,CAAC,EAAE,SAAS,GAAG,SAAS,CAAA;CAAE,GAC/D,MAAM,CAuCR"}

package/dist/cli/commands/review/finalize.js

@@ -28,6 +28,11 @@ async function executeReviewFinalize(options, sessionsDir) {
   for (const article of reviewFile.articles) {
     const status = classifyStatus(article, reviewers);
     if (status === "agreed-include" || status === "agreed-exclude") {
+      const consensusDecision = status === "agreed-include" ? "include" : "exclude";
+      if (options.decision && options.decision !== consensusDecision) {
+        result.skippedByStatus[status]++;
+        continue;
+      }
       const reviews = article.reviews ?? [];
       const uniqueReviewers = new Set(reviews.map((r) => r.reviewer));
       if (uniqueReviewers.size < minReviewers) {
@@ -35,7 +40,7 @@ async function executeReviewFinalize(options, sessionsDir) {
         continue;
       }
       if (!options.dryRun) {
-        article.finalDecision = status === "agreed-include" ? "include" : "exclude";
+        article.finalDecision = consensusDecision;
       }
       if (status === "agreed-include") {
         result.includedCount++;
@@ -75,6 +80,12 @@ function formatFinalizeOutput(result, options) {
   if (result.skippedByStatus.conflicting > 0) {
     skippedParts.push(`${result.skippedByStatus.conflicting} conflicting`);
   }
+  if (options?.decision && result.skippedByStatus["agreed-include"] > 0) {
+    skippedParts.push(`${result.skippedByStatus["agreed-include"]} agreed-include (filtered)`);
+  }
+  if (options?.decision && result.skippedByStatus["agreed-exclude"] > 0) {
+    skippedParts.push(`${result.skippedByStatus["agreed-exclude"]} agreed-exclude (filtered)`);
+  }
   if (skippedParts.length > 0) {
     lines.push(`Skipped: ${skippedParts.join(", ")}`);
   }

package/dist/cli/commands/review/finalize.js.map

@@ -1 +1 @@
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+{"version":3,"file":"finalize.js","sources":["../../../../src/cli/commands/review/finalize.ts"],"sourcesContent":["/**\n * review finalize command - Auto-set finalDecision for articles with consensus\n */\n\nimport { join } from 'node:path';\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport { classifyStatus, type ReviewFile, type ReviewStatus } from './types.js';\n\nexport interface ReviewFinalizeOptions {\n  sessionId: string;\n  dryRun?: boolean;\n  minReviewers?: number;\n  decision?: 'include' | 'exclude';\n}\n\nexport interface ReviewFinalizeResult {\n  includedCount: number;\n  excludedCount: number;\n  skippedByStatus: Record<ReviewStatus, number>;\n}\n\nfunction createEmptySkippedByStatus(): Record<ReviewStatus, number> {\n  return {\n    pending: 0,\n    incomplete: 0,\n    uncertain: 0,\n    'agreed-include': 0,\n    'agreed-exclude': 0,\n    conflicting: 0,\n    finalized: 0,\n  };\n}\n\n/**\n * Execute review finalize command\n */\nexport async function executeReviewFinalize(\n  options: ReviewFinalizeOptions,\n  sessionsDir: string\n): Promise<ReviewFinalizeResult> {\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  const reviewFile = parseYaml(content) as ReviewFile;\n\n  const reviewers = reviewFile.reviewers ?? [];\n  const minReviewers = options.minReviewers ?? 1;\n\n  const result: ReviewFinalizeResult = {\n    includedCount: 0,\n    excludedCount: 0,\n    skippedByStatus: createEmptySkippedByStatus(),\n  };\n\n  for (const article of reviewFile.articles) {\n    const status = classifyStatus(article, reviewers);\n\n    if (status === 'agreed-include' || status === 'agreed-exclude') {\n      // Check decision filter\n      const consensusDecision = status === 'agreed-include' ? 'include' : 'exclude';\n      if (options.decision && options.decision !== consensusDecision) {\n        result.skippedByStatus[status]++;\n        continue;\n      }\n\n      // Check minimum reviewer count\n      const reviews = article.reviews ?? 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package/dist/cli/index.d.ts.map

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package/dist/cli/index.js

@@ -1790,13 +1790,21 @@ Examples:
       process.exitCode = EXIT_CODES.SESSION_ERROR;
     }
   });
-  reviewCommand.command("finalize").description("Auto-set finalDecision for articles with reviewer consensus").requiredOption("--session <id>", "session ID").option("--dry-run", "preview without changes", false).option("--min-reviewers <n>", "minimum agreeing reviewers needed", "1").action(async (options) => {
+  reviewCommand.command("finalize").description("Auto-set finalDecision for articles with reviewer consensus").requiredOption("--session <id>", "session ID").option("--dry-run", "preview without changes", false).option("--min-reviewers <n>", "minimum agreeing reviewers needed", "1").option("--decision <type>", "only finalize this decision type (include or exclude)").action(async (options) => {
     const globalOpts = program.opts();
     try {
       const sessionsDir = await getSessionsDir(globalOpts);
+      if (options.decision && options.decision !== "include" && options.decision !== "exclude") {
+        if (!globalOpts.quiet) {
+          console.error(`Error: --decision must be "include" or "exclude", got "${options.decision}"`);
+        }
+        process.exitCode = EXIT_CODES.GENERAL_ERROR;
+        return;
+      }
       const finalizeOptions = {
         sessionId: options.session,
-        ...options.dryRun && { dryRun: options.dryRun }
+        ...options.dryRun && { dryRun: options.dryRun },
+        ...options.decision && { decision: options.decision }
       };
       const minReviewers = parseInt(options.minReviewers, 10);
       if (!Number.isNaN(minReviewers) && minReviewers > 1) {
@@ -1804,7 +1812,10 @@ Examples:
       }
       const result = await executeReviewFinalize(finalizeOptions, sessionsDir);
       if (!globalOpts.quiet) {
-        console.log(formatFinalizeOutput(result, { dryRun: options.dryRun }));
+        console.log(formatFinalizeOutput(result, {
+          dryRun: options.dryRun,
+          ...finalizeOptions.decision && { decision: finalizeOptions.decision }
+        }));
         if (!options.dryRun) {
           const statusResult = await executeReviewStatus({ sessionId: options.session }, sessionsDir);
           const suggestion = formatSuggestion(getSuggestion({

package/dist/cli/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sources":["../../src/cli/index.ts"],"sourcesContent":["#!/usr/bin/env node\n/**\n * CLI entry point for search-hub.\n */\nimport { config as loadDotenv } from 'dotenv';\n\n// Load .env file as early as possible, before any config loading\nloadDotenv({ quiet: true });\nimport { Command } from 'commander';\nimport { VERSION } from '../version.js';\nimport { init } from './commands/init.js';\nimport { EXIT_CODES } from './exit-codes.js';\nimport { loadConfig, saveConfig, getDefaultConfig, type Config } from '../config/index.js';\nimport { getDefaultConfigPath } from '../config/paths.js';\nimport {\n  viewConfig,\n  viewConfigKey,\n  setConfigKey,\n} from './commands/config.js';\nimport {\n  validateQueryCommand,\n  formatValidateResult,\n  formatVocabValidationOutput,\n  hasVocabErrors,\n  detectSchemaLink,\n} from './commands/query/validate.js';\nimport { MeSHLookupClient } from '../query/mesh-lookup.js';\nimport { RateLimiter } from '../providers/base/rate-limiter.js';\nimport { VocabCache } from '../query/vocab-cache.js';\nimport {\n  createEricCountValidator,\n  createEmtreeCountValidator,\n  type CountVocabValidator,\n} from '../query/vocab-validator.js';\nimport { createProviderInstance } from './commands/search-executor.js';\nimport {\n  translateQueryCommand,\n  formatTranslateResult,\n} from './commands/query/translate.js';\nimport {\n  inspectQueryCommand,\n  formatInspectOutput,\n} from './commands/query/inspect.js';\nimport {\n  generateQueryTemplate,\n  writeQueryTemplate,\n} from './commands/query/init.js';\nimport type { ProviderName } from '../providers/base/types.js';\nimport {\n  listSessionsForDisplay,\n  getSessionDetails,\n  computeDeduplicationStats,\n  formatSessionList,\n  formatSessionDetails,\n} from './commands/status.js';\nimport {\n  parseSearchOptions,\n  validateSearchInput,\n  formatDryRunOutput,\n  formatCountOnlyOutput,\n  formatPreviewOutput,\n  formatShortKeywordWarning,\n} from './commands/search.js';\nimport { executeSearch, executeCountOnly, executePreview } from './commands/search-executor.js';\nimport {\n  parseResumeOptions,\n  validateResumeInput,\n  getResumableProvidersForCommand,\n} from './commands/resume.js';\nimport { executeResume } from './commands/resume-executor.js';\nimport { formatVerboseProviderDetails } from './commands/search-utils.js';\nimport {\n  parseExportOptions,\n  validateExportInput,\n  formatIds,\n  formatJson,\n  formatJsonl,\n  formatCslJson,\n  deduplicateArticles,\n  type JsonExportMetadata,\n} from './commands/export.js';\nimport {\n  computeSummary,\n  formatSummary,\n  formatSummaryJson,\n} from './commands/summary.js';\nimport {\n  parseResultsOptions,\n  validateResultsInput,\n  formatResultsList,\n  formatResultsJson,\n} from './commands/results.js';\nimport { filterByQuery } from './commands/query-filter.js';\nimport {\n  loadNotes,\n  addNote,\n  addAssessment,\n  formatNotesList,\n  formatAllSessionNotes,\n  type SessionNotes,\n} from './commands/notes.js';\nimport {\n  computeDiff,\n  computeQueryDiff,\n  formatDiff,\n  formatDiffJson,\n  type ShowFilter,\n} from './commands/diff.js';\nimport {\n  mergeArticles,\n  validateMergeSources,\n  createMergedSession,\n  formatMergeOutput as formatSessionMergeOutput,\n  formatMergeJson as formatSessionMergeJson,\n} from './commands/merge.js';\n\nimport {\n  executeReviewInit,\n  type ReviewInitOptions,\n} from './commands/review/init.js';\nimport {\n  executeReviewStatus,\n  formatStatusOutput,\n  type ReviewStatusOptions,\n} from './commands/review/status.js';\nimport {\n  executeReviewList,\n  formatListOutput,\n  type ReviewListOptions,\n  type ListFilter,\n} from './commands/review/list.js';\nimport {\n  executeReviewExtract,\n  type ReviewExtractOptions,\n  type SortOption,\n} from './commands/review/extract.js';\nimport {\n  executeReviewMerge,\n  formatMergeOutput,\n  type ReviewMergeOptions,\n} from './commands/review/merge.js';\nimport {\n  executeReviewMark,\n  type ReviewMarkOptions,\n} from './commands/review/mark.js';\nimport {\n  executeReviewExport,\n  formatExportOutput,\n  type ReviewExportOptions,\n  type ExportFormat as ReviewExportFormat,\n  type ExportFilter as ReviewExportFilter,\n} from './commands/review/export.js';\nimport {\n  executeReviewFinalize,\n  formatFinalizeOutput,\n  type ReviewFinalizeOptions,\n} from './commands/review/finalize.js';\nimport { type ReviewStatus } from './commands/review/types.js';\nimport { registerFulltextCommands } from './commands/fulltext/index.js';\n\nimport {\n  parseRegisterOptions,\n  validateRegisterInput,\n  formatRegistrationSummary,\n  formatDryRunOutput as formatRegisterDryRunOutput,\n  hasReviewFile,\n  getReviewSummary,\n  getIncludedArticles,\n  formatReviewRequiredMessage,\n  formatNoIncludedArticlesError,\n  formatPendingWarning,\n  formatIgnoringReviewsNote,\n  confirmPrompt,\n} from './commands/register.js';\nimport { formatSuggestion } from './suggestions/index.js';\nimport { getSuggestion } from './suggestions/rules.js';\nimport { registerArticles, saveRegistrationRecord } from '../integration/register.js';\nimport { checkRefAvailable, checkNpmAvailable, installRefManager } from '../integration/ref-cli.js';\nimport { loadSession, sessionExists, listSessions } from '../session/manager.js';\nimport { parseQueryFile, detectShortKeywords } from '../query/parser.js';\nimport { writeFile, readFile } from 'node:fs/promises';\nimport { realpathSync } from 'node:fs';\nimport { join } from 'node:path';\nimport { fileURLToPath } from 'node:url';\nimport { getSessionsDir } from './utils/sessions-dir.js';\nimport { expandPath } from '../utils/path.js';\nimport { loadSessionArticles, loadSessionQuery } from './commands/session-utils.js';\nimport { parseIdentifierFile, checkCoverage, formatCheckResult, formatCheckResultJson } from './commands/check.js';\n\n/**\n * Global CLI options available to all commands.\n */\nexport interface GlobalOptions {\n  /** Path to config file */\n  config?: string;\n  /** Path to session directory */\n  sessionDir?: string;\n  /** Enable verbose output */\n  verbose: boolean;\n  /** Suppress all output except errors */\n  quiet: boolean;\n  /** Enable color output (default: true, use --no-color to disable) */\n  color: boolean;\n}\n\n/**\n * Create and configure the CLI program.\n */\nexport function createProgram(): Command {\n  const program = new Command();\n\n  program\n    .name('search-hub')\n    .version(VERSION)\n    .description(\n      'CLI tool for systematic literature searching across multiple academic databases'\n    )\n    .option('-c, --config <path>', 'path to config file')\n    .option('--session-dir <path>', 'path to session directory')\n    .option('-v, --verbose', 'enable verbose output', false)\n    .option('--quiet', 'suppress all output except errors', false)\n    .option('--no-color', 'disable color output')\n    .addHelpText('after', `\nWorkflow:\n  1. query init → edit → validate / --dry-run        Query preparation\n  2. search --preview → search                       Preview & execute\n  3. results / summary / diff / check                Inspect & verify\n  4. review init → extract → merge → status          Systematic review\n  5. register / export                               Output\n\n  Iterate: search → results -q → check → diff       Query refinement\n\nQuick Start:\n  $ search-hub query init -o search.yaml        # Create query template\n  $ search-hub search search.yaml --count-only  # Check hit counts\n  $ search-hub search search.yaml               # Execute search\n  $ search-hub results <session>                # Review titles`);\n\n  // Register init command\n  program\n    .command('init')\n    .description('Initialize configuration directory')\n    .option('-f, --force', 'overwrite existing configuration', false)\n    .addHelpText('after', `\nExamples:\n  $ search-hub init                 # Initialize with default settings\n  $ search-hub init --force         # Overwrite existing configuration`)\n    .action(async (options: { force: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const result = await init({ force: options.force });\n        if (!globalOpts.quiet) {\n          if (result.success) {\n            console.log(result.message);\n          } else {\n            console.error(result.message);\n          }\n        }\n        process.exitCode = result.success ? EXIT_CODES.SUCCESS : EXIT_CODES.CONFIG_ERROR;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.GENERAL_ERROR;\n      }\n    });\n\n  // Register config command\n  program\n    .command('config')\n    .description('View and edit configuration')\n    .argument('[key]', 'configuration key to view or set')\n    .argument('[value]', 'value to set for the key')\n    .addHelpText('after', `\nExamples:\n  $ search-hub config                              # Show all config\n  $ search-hub config providers.pubmed             # Show PubMed config\n  $ search-hub config providers.pubmed.api_key KEY # Set API key`)\n    .action(async (key?: string, value?: string) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        // Load config - use default if no config file exists\n        let config;\n        try {\n          config = await loadConfig(\n            globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}\n          );\n        } catch {\n          config = getDefaultConfig();\n        }\n\n        if (!key) {\n          // View all config\n          if (!globalOpts.quiet) {\n            console.log(viewConfig(config));\n          }\n        } else if (!value) {\n          // View specific key\n          const result = viewConfigKey(config, key);\n          if (result.success) {\n            if (!globalOpts.quiet) {\n              console.log(result.value);\n            }\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n            }\n            process.exitCode = EXIT_CODES.CONFIG_ERROR;\n            return;\n          }\n        } else {\n          // Set key value\n          const result = setConfigKey(config, key, value);\n          if (result.success) {\n            // Save the modified config to file\n            const configPath = globalOpts.config ? expandPath(globalOpts.config) : getDefaultConfigPath();\n            try {\n              await saveConfig(config, { path: configPath });\n              if (!globalOpts.quiet) {\n                console.log(`Set ${key} = ${result.value}`);\n                console.log(`Saved to ${configPath}`);\n              }\n            } catch (saveError) {\n              if (!globalOpts.quiet) {\n                console.error(\n                  `Error saving config: ${saveError instanceof Error ? saveError.message : saveError}`\n                );\n              }\n              process.exitCode = EXIT_CODES.CONFIG_ERROR;\n              return;\n            }\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n            }\n            process.exitCode = EXIT_CODES.CONFIG_ERROR;\n            return;\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.CONFIG_ERROR;\n      }\n    });\n\n  // Register query command group\n  const queryCommand = program\n    .command('query')\n    .description('Query file utilities')\n    .addHelpText('after', `\nQuery YAML format (minimal):\n  name: my_search\n  query:\n    - field: title_abstract\n      terms:\n        keywords: [\"term1\", \"term2\"]\n      operator: OR\n\nUse \"search-hub query init\" to generate a template.`);\n\n  queryCommand\n    .command('validate')\n    .description('Validate query YAML file (auto-checks controlled vocabulary)')\n    .argument('<file>', 'path to query YAML file')\n    .option('--no-vocab', 'skip controlled vocabulary validation')\n    .option('--no-cache', 'skip vocabulary lookup cache')\n    .addHelpText('after', `\nExamples:\n  $ search-hub query validate ./diabetes-ai.yaml\n  $ search-hub query validate ./diabetes-ai.yaml --no-vocab   # Skip MeSH check\n  $ search-hub query validate ./diabetes-ai.yaml --no-cache   # Ignore cache`)\n    .action(async (file: string, opts: { vocab?: boolean; cache?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const noVocab = opts.vocab === false;\n        const noCache = opts.cache === false;\n\n        let cache: VocabCache | undefined;\n        if (!noVocab && !noCache) {\n          cache = new VocabCache();\n          await cache.load();\n        }\n\n        const hasSchema = await detectSchemaLink(file);\n\n        if (noVocab) {\n          const result = await validateQueryCommand(file, { noVocab });\n\n          if (!globalOpts.quiet) {\n            let output = formatValidateResult(result, file);\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'query validate',\n              queryFile: file,\n              validationSuccess: result.success,\n              hasSchemaLink: hasSchema,\n            }));\n            if (suggestion) output += '\\n' + suggestion;\n            console.log(output);\n          }\n          process.exitCode = !result.success\n            ? EXIT_CODES.QUERY_ERROR\n            : EXIT_CODES.SUCCESS;\n          return;\n        }\n\n        const rateLimiter = new RateLimiter({ tokensPerSecond: 3 });\n        const meshClient = new MeSHLookupClient({\n          rateLimiter,\n          ...(cache ? { cache } : {}),\n        });\n\n        // Create count validators for ERIC/Emtree\n        const countValidators: CountVocabValidator[] = [];\n        let config: Config | undefined;\n        try {\n          config = await loadConfig(\n            globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}\n          );\n        } catch {\n          // Config not available — skip count validators\n        }\n\n        if (config) {\n          const ericProvider = createProviderInstance('eric', config);\n          if (ericProvider) {\n            countValidators.push(\n              createEricCountValidator(ericProvider, cache ? { cache } : undefined)\n            );\n          }\n\n          const scopusProvider = createProviderInstance('scopus', config);\n          if (scopusProvider) {\n            countValidators.push(\n              createEmtreeCountValidator(scopusProvider, cache ? { cache } : undefined)\n            );\n          }\n        }\n\n        const result = await validateQueryCommand(file, {\n          meshClient,\n          ...(countValidators.length > 0 ? { countValidators } : {}),\n        });\n\n        if (cache) {\n          await cache.save();\n        }\n\n        if (!globalOpts.quiet) {\n          let output = formatValidateResult(result, file);\n          if (result.vocabResult) {\n            output += formatVocabValidationOutput(result.vocabResult);\n          }\n          const suggestion = formatSuggestion(getSuggestion({\n            command: 'query validate',\n            queryFile: file,\n            validationSuccess: result.success && !hasVocabErrors(result),\n            hasSchemaLink: hasSchema,\n          }));\n          if (suggestion) output += '\\n' + suggestion;\n          console.log(output);\n        }\n        process.exitCode =\n          !result.success || hasVocabErrors(result)\n            ? EXIT_CODES.QUERY_ERROR\n            : EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.QUERY_ERROR;\n      }\n    });\n\n  queryCommand\n    .command('translate')\n    .description('Show translated queries for each database')\n    .argument('<file>', 'path to query YAML file')\n    .option('--db <provider>', 'show translation for specific provider only')\n    .addHelpText('after', `\nExamples:\n  $ search-hub query translate ./diabetes-ai.yaml            # All databases\n  $ search-hub query translate ./diabetes-ai.yaml --db pubmed # PubMed only`)\n    .action(async (file: string, options: { db?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const translateOptions = options.db\n          ? { providers: [options.db as ProviderName] }\n          : {};\n        const result = await translateQueryCommand(file, translateOptions);\n        if (!globalOpts.quiet) {\n          console.log(formatTranslateResult(result, file));\n        }\n        process.exitCode = result.success\n          ? EXIT_CODES.SUCCESS\n          : EXIT_CODES.QUERY_ERROR;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.QUERY_ERROR;\n      }\n    });\n\n  queryCommand\n    .command('inspect')\n    .description('Show how a query resolves per provider (block replacements and added filters)')\n    .argument('<file>', 'path to query YAML file')\n    .option('--db <provider>', 'show resolution for specific provider only')\n    .addHelpText('after', `\nExamples:\n  $ search-hub query inspect ./diabetes-ai.yaml            # All databases\n  $ search-hub query inspect ./diabetes-ai.yaml --db pubmed # PubMed only`)\n    .action(async (file: string, options: { db?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const inspectOptions = options.db\n          ? { providers: [options.db as ProviderName] }\n          : {};\n        const result = await inspectQueryCommand(file, inspectOptions);\n        if (!result.success) {\n          if (!globalOpts.quiet) {\n            console.error(`\\u2717 Failed to inspect: ${file}\\n  Error: ${result.error}`);\n          }\n          process.exitCode = EXIT_CODES.QUERY_ERROR;\n          return;\n        }\n        if (!globalOpts.quiet) {\n          console.log(formatInspectOutput(result.result!));\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.QUERY_ERROR;\n      }\n    });\n\n  queryCommand\n    .command('init')\n    .description('Generate a template query YAML file')\n    .option('-o, --output <path>', 'write to file (default: stdout)')\n    .option('--force', 'overwrite existing file', false)\n    .action(async (options: { output?: string; force?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        if (options.output) {\n          const result = await writeQueryTemplate(options);\n          if (!globalOpts.quiet) {\n            if (result.success) {\n              console.log(result.message);\n            } else {\n              console.error(result.message);\n            }\n          }\n          process.exitCode = result.success ? EXIT_CODES.SUCCESS : EXIT_CODES.GENERAL_ERROR;\n        } else {\n          const template = generateQueryTemplate();\n          console.log(template);\n          process.exitCode = EXIT_CODES.SUCCESS;\n        }\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.GENERAL_ERROR;\n      }\n    });\n\n  // Register status command\n  program\n    .command('status')\n    .description('Show session status and statistics')\n    .argument('[session-id]', 'session ID to show details for')\n    .option('--json', 'output as JSON')\n    .option('--all', 'include completed sessions')\n    .addHelpText('after', `\nExamples:\n  $ search-hub status                           # List recent sessions\n  $ search-hub status 20240115_diabetes-ai_a3f2 # Show session details\n  $ search-hub status --json                    # JSON output for scripting`)\n    .action(async (sessionId?: string, options?: { json?: boolean; all?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const formatOpts = { json: options?.json ?? false };\n\n        if (sessionId) {\n          // Show specific session details\n          const result = await getSessionDetails(sessionId, sessionsDir);\n          if (result.success && result.session) {\n            // Compute deduplication stats\n            try {\n              const rawSession = await loadSession(sessionId, sessionsDir);\n              const dedupStats = await computeDeduplicationStats(sessionId, sessionsDir, rawSession);\n              result.session.uniqueArticles = dedupStats.uniqueArticles;\n              result.session.duplicatesRemoved = dedupStats.duplicatesRemoved;\n            } catch {\n              // Dedup stats are optional - don't fail the command\n            }\n            if (!globalOpts.quiet) {\n              console.log(formatSessionDetails(result.session, formatOpts));\n            }\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n        } else {\n          // List sessions\n          const listOpts = { all: options?.all ?? false };\n          const sessions = await listSessionsForDisplay(sessionsDir, listOpts);\n          if (!globalOpts.quiet) {\n            console.log(formatSessionList(sessions, formatOpts));\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  // Register search command\n  program\n    .command('search')\n    .description('Execute search across databases')\n    .argument('[query-file]', 'path to query YAML file')\n    .option('--db <providers>', 'target specific database(s), comma-separated')\n    .option('--query <string>', 'direct query in database-native syntax (advanced; requires --db; prefer YAML files)')\n    .option('--name <string>', 'session name')\n    .option('--max-results <n>', 'limit results per database')\n    .option('--dry-run', 'show translated queries without executing')\n    .option('--count-only', 'get hit counts without downloading results')\n    .option('--preview', 'get hit counts and first 5 titles without creating session')\n    .option('--skip-connection-test', 'skip API connection test during dry-run')\n    .option('--no-resume', 'start fresh even if session exists')\n    .option('--strict', 'require all targeted databases to succeed (exit non-zero on partial failure)')\n    .addHelpText('after', `\nWorkflow position:\n  query validate → [this command: search] → results / summary / diff\n\nExamples:\n  $ search-hub search ./diabetes-ai.yaml                # Search all databases\n  $ search-hub search ./query.yaml --db pubmed,eric     # Specific databases\n  $ search-hub search --db pubmed --query \"diabetes[tiab]\"  # Direct query\n  $ search-hub search ./query.yaml --dry-run            # Preview translations\n  $ search-hub search ./query.yaml --count-only         # Get hit counts only\n  $ search-hub search ./query.yaml --max-results 100    # Limit results\n\nQuery features (use \"query init\" to see full template):\n  filters:    year_from, year_to, language, publication_types\n  exclude:    NOT terms per block (terms.exclude)\n  mesh/eric:  controlled vocabulary (terms.mesh, terms.eric)\n  providers:  per-database block replacements and filter additions`)\n    .action(\n      async (\n        queryFile?: string,\n        options?: {\n          db?: string;\n          query?: string;\n          name?: string;\n          maxResults?: string;\n          dryRun?: boolean;\n          countOnly?: boolean;\n          preview?: boolean;\n          skipConnectionTest?: boolean;\n          resume?: boolean;\n          strict?: boolean;\n        }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const searchOpts = parseSearchOptions(queryFile, {\n            db: options?.db,\n            query: options?.query,\n            name: options?.name,\n            maxResults: options?.maxResults,\n            dryRun: options?.dryRun,\n            countOnly: options?.countOnly,\n            preview: options?.preview,\n            noResume: options?.resume === false,\n            strict: options?.strict,\n          });\n\n          const validation = validateSearchInput(searchOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n\n          // Check for short keywords and display warning\n          if (searchOpts.queryFile && !globalOpts.quiet) {\n            try {\n              const ast = await parseQueryFile(searchOpts.queryFile);\n              const shortKeywords = detectShortKeywords(ast);\n              if (shortKeywords.length > 0) {\n                console.error(formatShortKeywordWarning(shortKeywords));\n                console.error('');\n              }\n            } catch {\n              // Ignore parse errors here - they'll be caught later during execution\n            }\n          }\n\n          // Handle dry-run mode\n          if (searchOpts.dryRun) {\n            // Try to load config for provider readiness display\n            let dryRunConfig: Config | undefined;\n            try {\n              dryRunConfig = await loadConfig(globalOpts.config ? { explicitConfigPath: globalOpts.config } : {});\n            } catch {\n              // Config unavailable, readiness section will be omitted\n            }\n\n            if (searchOpts.queryFile) {\n              // Translate from file\n              const translateOpts = searchOpts.providers\n                ? { providers: searchOpts.providers }\n                : {};\n              const result = await translateQueryCommand(\n                searchOpts.queryFile,\n                translateOpts\n              );\n              if (result.success && result.translations) {\n                const translations = Object.entries(result.translations).map(\n                  ([provider, t]) => ({ provider, query: t.native })\n                );\n                const providers = translations.map(t => t.provider) as ProviderName[];\n                if (!globalOpts.quiet) {\n                  const dryRunOpts = dryRunConfig\n                    ? { config: dryRunConfig, providers, skipConnectionTest: options?.skipConnectionTest }\n                    : {};\n                  console.log(await formatDryRunOutput(translations, dryRunOpts));\n                }\n              } else {\n                if (!globalOpts.quiet) {\n                  console.error(`Error: ${result.error}`);\n                }\n                process.exitCode = EXIT_CODES.QUERY_ERROR;\n                return;\n              }\n            } else if (searchOpts.directQuery && searchOpts.providers) {\n              // Direct query\n              const translations = [\n                {\n                  provider: searchOpts.providers[0]!,\n                  query: searchOpts.directQuery,\n                },\n              ];\n              if (!globalOpts.quiet) {\n                const dryRunOpts = dryRunConfig\n                  ? { config: dryRunConfig, providers: searchOpts.providers as ProviderName[], skipConnectionTest: options?.skipConnectionTest }\n                  : {};\n                console.log(await formatDryRunOutput(translations, dryRunOpts));\n              }\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n            return;\n          }\n\n          // Handle preview mode\n          if (searchOpts.preview) {\n            let previewConfig;\n            try {\n              previewConfig = await loadConfig(globalOpts.config ? { explicitConfigPath: globalOpts.config } : {});\n            } catch {\n              previewConfig = getDefaultConfig();\n            }\n\n            const previews = await executePreview(searchOpts, previewConfig);\n\n            if (previews.length === 0) {\n              if (!globalOpts.quiet) {\n                console.error('Error: No providers enabled or selected');\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n\n            if (!globalOpts.quiet) {\n              console.log(formatPreviewOutput(previews, searchOpts.queryFile));\n            }\n\n            const previewHasErrors = previews.some((p) => p.error);\n            const previewAllFailed = previews.every((p) => p.error);\n            if (previewAllFailed) {\n              process.exitCode = EXIT_CODES.NETWORK_ERROR;\n            } else if (previewHasErrors && searchOpts.strict) {\n              process.exitCode = EXIT_CODES.NETWORK_ERROR;\n            } else {\n              process.exitCode = EXIT_CODES.SUCCESS;\n            }\n            if (previewHasErrors && !previewAllFailed && !globalOpts.quiet) {\n              const failed = previews.filter((p) => p.error).map((p) => `${p.provider}: ${p.error}`);\n              console.warn(`\\nWarning: Some providers failed:\\n  ${failed.join('\\n  ')}`);\n            }\n            return;\n          }\n\n          // Handle count-only mode\n          if (searchOpts.countOnly) {\n            let countConfig;\n            try {\n              countConfig = await loadConfig(globalOpts.config ? { explicitConfigPath: globalOpts.config } : {});\n            } catch {\n              countConfig = getDefaultConfig();\n            }\n\n            const counts = await executeCountOnly(searchOpts, countConfig);\n\n            if (counts.length === 0) {\n              if (!globalOpts.quiet) {\n                console.error('Error: No providers enabled or selected');\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n\n            if (!globalOpts.quiet) {\n              console.log(formatCountOnlyOutput(counts, searchOpts.queryFile));\n              const suggestion = formatSuggestion(getSuggestion({\n                command: 'search --count-only',\n                queryFile: searchOpts.queryFile,\n              }));\n              if (suggestion) console.log(suggestion);\n            }\n\n            const countHasErrors = counts.some((c) => c.error);\n            const countAllFailed = counts.every((c) => c.error);\n            if (countAllFailed) {\n              process.exitCode = EXIT_CODES.NETWORK_ERROR;\n            } else if (countHasErrors && searchOpts.strict) {\n              process.exitCode = EXIT_CODES.NETWORK_ERROR;\n            } else {\n              process.exitCode = EXIT_CODES.SUCCESS;\n            }\n            if (countHasErrors && !countAllFailed && !globalOpts.quiet) {\n              const failed = counts.filter((c) => c.error).map((c) => `${c.provider}: ${c.error}`);\n              console.warn(`\\nWarning: Some providers failed:\\n  ${failed.join('\\n  ')}`);\n            }\n            return;\n          }\n\n          // Non-dry-run: actual search execution\n          const sessionsDir = await getSessionsDir(globalOpts);\n          let config;\n          try {\n            config = await loadConfig(\n              globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}\n            );\n          } catch {\n            config = getDefaultConfig();\n          }\n\n          const showProgress = !globalOpts.quiet && process.stdout.isTTY;\n          const result = await executeSearch(\n            searchOpts,\n            sessionsDir,\n            config,\n            showProgress\n          );\n\n          if (result.success) {\n            if (!globalOpts.quiet) {\n              console.log(`\\nSearch completed. Session: ${result.sessionId}`);\n              if (result.results) {\n                for (const [provider, stats] of Object.entries(result.results)) {\n                  if (stats.error) {\n                    console.log(`  ${provider}: FAILED - ${stats.error}`);\n                  } else {\n                    console.log(`  ${provider}: ${stats.retrieved} results`);\n                  }\n                }\n              }\n              // Show warning for partial success\n              if (result.sessionStatus === 'partial' && result.results) {\n                const failed = Object.entries(result.results)\n                  .filter(([, s]) => s.error)\n                  .map(([p, s]) => `${p}: ${s.error}`);\n                if (failed.length > 0) {\n                  console.warn(`\\nWarning: Some providers failed:\\n  ${failed.join('\\n  ')}`);\n                }\n              }\n              // Show next step suggestions\n              if (result.sessionId) {\n                const sessions = await listSessions(sessionsDir);\n                const suggestionCmd = searchOpts.directQuery ? 'search --query' : 'search';\n                const suggestion = formatSuggestion(getSuggestion({\n                  command: suggestionCmd,\n                  sessionId: result.sessionId,\n                  sessionStatus: result.sessionStatus,\n                  sessionCount: sessions.length,\n                }));\n                if (suggestion) console.log(suggestion);\n              }\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n              if (globalOpts.verbose && result.results) {\n                console.error(formatVerboseProviderDetails(result.results));\n              }\n            }\n            process.exitCode = EXIT_CODES.NETWORK_ERROR;\n          }\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n        }\n      }\n    );\n\n  // Register resume command\n  program\n    .command('resume')\n    .description('Resume an interrupted search session')\n    .argument('<session-id>', 'session ID to resume')\n    .option('--db <providers>', 'resume only specific database(s)')\n    .option('--retry-failed', 'retry failed databases')\n    .addHelpText('after', `\nExamples:\n  $ search-hub resume 20240115_diabetes-ai_a3f2   # Resume session\n  $ search-hub resume SESSION_ID --retry-failed   # Retry failed databases\n  $ search-hub resume SESSION_ID --db scopus      # Resume specific database`)\n    .action(\n      async (\n        sessionId: string,\n        options?: { db?: string; retryFailed?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const resumeOpts = parseResumeOptions(sessionId, {\n            db: options?.db,\n            retryFailed: options?.retryFailed,\n          });\n\n          const validation = validateResumeInput(resumeOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Get resumable providers\n          const result = await getResumableProvidersForCommand(\n            sessionId,\n            sessionsDir,\n            {\n              providers: resumeOpts.providers,\n              retryFailed: resumeOpts.retryFailed,\n            }\n          );\n\n          if (!result.success) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          if (!result.providers || result.providers.length === 0) {\n            if (!globalOpts.quiet) {\n              console.log('No providers need resuming for this session.');\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n            return;\n          }\n\n          // Show resumable providers\n          if (!globalOpts.quiet) {\n            console.log(`Resuming session ${sessionId} with ${result.providers.length} provider(s):`);\n            for (const p of result.providers) {\n              const details = p.cursor\n                ? `cursor: ${p.cursor}`\n                : p.pageNumber\n                  ? `page: ${p.pageNumber}`\n                  : '';\n              console.log(`  - ${p.provider}: ${p.strategy}${details ? ` (${details})` : ''}`);\n            }\n            console.log('');\n          }\n\n          // Execute resume\n          let config;\n          try {\n            config = await loadConfig(\n              globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}\n            );\n          } catch {\n            config = getDefaultConfig();\n          }\n\n          const showProgress = !globalOpts.quiet && process.stdout.isTTY;\n          const execResult = await executeResume(\n            resumeOpts,\n            sessionsDir,\n            config,\n            showProgress\n          );\n\n          if (execResult.success) {\n            if (!globalOpts.quiet) {\n              console.log(`\\nResume completed. ${execResult.resumed} provider(s) resumed.`);\n              if (execResult.results) {\n                for (const [provider, stats] of Object.entries(execResult.results)) {\n                  console.log(`  ${provider}: ${stats.retrieved} results`);\n                }\n              }\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${execResult.error}`);\n              if (globalOpts.verbose && execResult.results) {\n                console.error(formatVerboseProviderDetails(execResult.results));\n              }\n            }\n            process.exitCode = EXIT_CODES.NETWORK_ERROR;\n          }\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register export command\n  program\n    .command('export')\n    .description('Export session results to various formats')\n    .argument('<session-id>', 'session ID to export')\n    .option('--format <fmt>', 'output format: ids, json, jsonl, csl-json', 'jsonl')\n    .option('-o, --output <path>', 'output file path (default: stdout)')\n    .option('--id-type <type>', 'for ids format: doi, pmid, all')\n    .option('--no-dedup', 'disable deduplication of results')\n    .option('-q, --query <expr>', 'filter results with query expression')\n    .addHelpText('after', `\nExamples:\n  $ search-hub export SESSION_ID                             # JSONL to stdout\n  $ search-hub export SESSION_ID --format json               # JSON to stdout\n  $ search-hub export SESSION_ID -q \"year:2023\"              # Filter by query\n  $ search-hub export SESSION_ID -q \"author:smith\" --format ids  # Filtered IDs\n  $ search-hub export SESSION_ID --format json -o results.json  # JSON to file\n  $ search-hub export SESSION_ID --format ids --id-type doi  # Export DOIs to stdout\n  $ search-hub export SESSION_ID --no-dedup  # Export without deduplication\n  $ search-hub export SESSION_ID --format jsonl | jq '.title'  # Pipe to jq\n\nQuery syntax:\n  Free text        diabetes             Search title and abstract\n  title:VALUE      title:learning       Title substring\n  abstract:VALUE   abstract:randomized  Abstract substring\n  author:VALUE     author:tanaka        Author name substring\n  journal:VALUE    journal:lancet       Journal name substring\n  year:VALUE       year:2023            Exact year\n  year:FROM-TO     year:2020-2024       Year range\n  doi:VALUE        doi:10.1001/xxx      DOI exact match\n  pmid:VALUE       pmid:12345678        PMID exact match\n  source:VALUE     source:pubmed        Provider exact match\n\n  Multiple terms: different fields = AND, same field = OR`)\n    .action(\n      async (\n        sessionId: string,\n        options?: {\n          format?: string;\n          output?: string;\n          idType?: string;\n          dedup?: boolean;\n          query?: string;\n        }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const exportOpts = parseExportOptions(sessionId, {\n            format: options?.format,\n            output: options?.output,\n            idType: options?.idType,\n          });\n\n          const validation = validateExportInput(exportOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load session\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Collect articles from result files\n          const articles = await loadSessionArticles(session, sessionId, sessionsDir);\n\n          // Deduplicate articles unless --no-dedup is set\n          const shouldDedup = options?.dedup !== false;\n          let exportArticles: typeof articles;\n          let duplicatesRemoved = 0;\n\n          if (shouldDedup) {\n            const dedupResult = deduplicateArticles(articles);\n            exportArticles = dedupResult.articles;\n            duplicatesRemoved = dedupResult.duplicatesRemoved;\n          } else {\n            exportArticles = articles;\n          }\n\n          // Apply -q filter\n          const preFilterCount = exportArticles.length;\n          let hasFilter = false;\n          if (options?.query) {\n            exportArticles = filterByQuery(exportArticles, options.query);\n            hasFilter = true;\n          }\n\n          // Format output\n          let output: string;\n          if (exportOpts.format === 'ids') {\n            output = formatIds(exportArticles, exportOpts.idType ?? 'all');\n          } else if (exportOpts.format === 'json') {\n            // Build per-database article counts\n            const databases: Record<string, number> = {};\n            for (const article of exportArticles) {\n              databases[article.source] = (databases[article.source] ?? 0) + 1;\n            }\n            const metadata: JsonExportMetadata = {\n              sessionId: session.id,\n              sessionName: session.name,\n              createdAt: session.createdAt,\n              databases,\n            };\n            output = formatJson(exportArticles, metadata);\n          } else if (exportOpts.format === 'csl-json') {\n            output = formatCslJson(exportArticles);\n          } else {\n            output = formatJsonl(exportArticles);\n          }\n\n          // Write to file or stdout\n          if (exportOpts.outputPath) {\n            await writeFile(exportOpts.outputPath, output, 'utf-8');\n            if (!globalOpts.quiet) {\n              let message: string;\n              if (hasFilter) {\n                message = `Exported ${exportArticles.length} articles (filtered from ${preFilterCount}) to ${exportOpts.outputPath}`;\n              } else {\n                message = `Exported ${exportArticles.length} articles to ${exportOpts.outputPath}`;\n              }\n              if (duplicatesRemoved > 0) {\n                message += ` (${duplicatesRemoved} duplicate${duplicatesRemoved === 1 ? '' : 's'} removed)`;\n              }\n              console.error(message);\n            }\n          } else {\n            process.stdout.write(output + '\\n');\n            if (!globalOpts.quiet) {\n              const parts: string[] = [];\n              if (hasFilter) {\n                parts.push(`filtered from ${preFilterCount} to ${exportArticles.length} articles`);\n              }\n              if (duplicatesRemoved > 0) {\n                parts.push(`${duplicatesRemoved} duplicate${duplicatesRemoved === 1 ? '' : 's'} removed`);\n              }\n              if (parts.length > 0) {\n                console.error(`(${parts.join(', ')})`);\n              }\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register summary command\n  program\n    .command('summary')\n    .description('Show statistical summary of session results')\n    .argument('<session-id>', 'session ID to summarize')\n    .option('--json', 'output as JSON')\n    .addHelpText('after', `\\nExamples:\n  $ search-hub summary 20240115_diabetes-ai_a3f2       # Human-readable summary\n  $ search-hub summary 20240115_diabetes-ai_a3f2 --json # JSON output`)\n    .action(\n      async (\n        sessionId: string,\n        options?: { json?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load session\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Collect articles from result files\n          const allArticles = await loadSessionArticles(session, sessionId, sessionsDir);\n\n          // Deduplicate\n          const dedupResult = deduplicateArticles(allArticles);\n\n          // Compute summary\n          const summary = computeSummary(allArticles, dedupResult.articles, {\n            sessionId,\n            sessionName: session.name,\n          });\n\n          // Format output\n          if (options?.json) {\n            console.log(formatSummaryJson(summary));\n          } else {\n            if (!globalOpts.quiet) {\n              console.log(formatSummary(summary));\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register results command\n  program\n    .command('results')\n    .description('List articles from a session with title, year, and journal')\n    .argument('<session-id>', 'session ID to list results from')\n    .option('--limit <n>', 'maximum number of results to show')\n    .option('--offset <n>', 'skip first n results')\n    .option('--json', 'output as JSON array')\n    .option('--fields <fields>', 'fields to display (comma-separated)')\n    .option('-q, --query <expr>', 'filter results with query expression')\n    .option('--abstract', 'show abstracts with results')\n    .option('--abstract-length <n>', 'maximum abstract length in characters (default: 300)')\n    .addHelpText('after', `\nExamples:\n  $ search-hub results SESSION_ID                              # List all articles\n  $ search-hub results SESSION_ID --limit 20                   # First 20 articles\n  $ search-hub results SESSION_ID -q \"diabetes\"                # Free text filter\n  $ search-hub results SESSION_ID -q \"author:smith year:2023\"  # Combined filter\n  $ search-hub results SESSION_ID -q \"doi:10.1001/xxx\"         # Exact ID match\n  $ search-hub results SESSION_ID --json                       # JSON output\n  $ search-hub results SESSION_ID -q \"source:pubmed\"           # Only PubMed\n  $ search-hub results SESSION_ID --abstract                   # Show abstracts\n\nQuery syntax:\n  Free text        diabetes             Search title and abstract\n  title:VALUE      title:learning       Title substring\n  abstract:VALUE   abstract:randomized  Abstract substring\n  author:VALUE     author:tanaka        Author name substring\n  journal:VALUE    journal:lancet       Journal name substring\n  year:VALUE       year:2023            Exact year\n  year:FROM-TO     year:2020-2024       Year range\n  doi:VALUE        doi:10.1001/xxx      DOI exact match\n  pmid:VALUE       pmid:12345678        PMID exact match\n  source:VALUE     source:pubmed        Provider exact match\n\n  Multiple terms: different fields = AND, same field = OR`)\n    .action(\n      async (\n        sessionId: string,\n        options?: {\n          limit?: string;\n          offset?: string;\n          json?: boolean;\n          fields?: string;\n          query?: string;\n          abstract?: boolean;\n          abstractLength?: string;\n        }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const resultsOpts = parseResultsOptions(sessionId, {\n            limit: options?.limit,\n            offset: options?.offset,\n            json: options?.json,\n            fields: options?.fields,\n            query: options?.query,\n            abstract: options?.abstract,\n            abstractLength: options?.abstractLength,\n          });\n\n          const validation = validateResultsInput(resultsOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load session\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Collect articles from result files\n          const articles = await loadSessionArticles(session, sessionId, sessionsDir);\n\n          // Deduplicate articles\n          const dedupResult = deduplicateArticles(articles);\n          let displayArticles = dedupResult.articles;\n\n          // Apply -q filter\n          let filteredFrom: number | undefined;\n          if (resultsOpts.query) {\n            const preFilterCount = displayArticles.length;\n            displayArticles = filterByQuery(displayArticles, resultsOpts.query);\n            if (displayArticles.length !== preFilterCount) {\n              filteredFrom = preFilterCount;\n            }\n          }\n\n          // Apply pagination\n          const total = displayArticles.length;\n          const offset = resultsOpts.offset ?? 0;\n          if (offset > 0) {\n            displayArticles = displayArticles.slice(offset);\n          }\n          if (resultsOpts.limit !== undefined && resultsOpts.limit > 0) {\n            displayArticles = displayArticles.slice(0, resultsOpts.limit);\n          }\n\n          // Format output\n          if (resultsOpts.json) {\n            console.log(formatResultsJson(displayArticles));\n          } else {\n            if (!globalOpts.quiet) {\n              console.log(formatResultsList(displayArticles, {\n                sessionId,\n                sessionName: session.name,\n                total,\n                offset,\n                filteredFrom,\n                showAbstract: resultsOpts.showAbstract,\n                abstractLength: resultsOpts.abstractLength,\n              }));\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register diff command\n  program\n    .command('diff')\n    .description('Compare results between two sessions')\n    .argument('<session-id-1>', 'first session ID')\n    .argument('<session-id-2>', 'second session ID')\n    .option('--show <section>', 'show only specific section: added, removed, or common')\n    .option('--json', 'output as JSON')\n    .option('--no-query-diff', 'hide query changes section')\n    .addHelpText('after', `\nExamples:\n  $ search-hub diff session-v1 session-v2                # Compare two sessions\n  $ search-hub diff session-v1 session-v2 --show added   # Show only added articles\n  $ search-hub diff session-v1 session-v2 --show removed # Show only removed articles\n  $ search-hub diff session-v1 session-v2 --json         # JSON output for scripting\n  $ search-hub diff session-v1 session-v2 --no-query-diff # Hide query changes\n\nQuery Refinement Workflow:\n  1. Search with broad query:    search-hub search v1.yaml --max-results 100\n  2. Create refined query:       cp v1.yaml v2.yaml && edit v2.yaml\n  3. Search with refined query:  search-hub search v2.yaml --max-results 100\n  4. Compare results:            search-hub diff <session-v1> <session-v2> --show removed\n  5. Review excluded articles to verify refinement quality`)\n    .action(\n      async (\n        sessionId1: string,\n        sessionId2: string,\n        options?: { show?: string; json?: boolean; queryDiff?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Validate --show option\n          const validShowValues: ShowFilter[] = ['added', 'removed', 'common'];\n          let showFilter: ShowFilter | undefined;\n          if (options?.show) {\n            if (!validShowValues.includes(options.show as ShowFilter)) {\n              if (!globalOpts.quiet) {\n                console.error(`Error: Invalid --show value: ${options.show}. Valid values are: ${validShowValues.join(', ')}`);\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n            showFilter = options.show as ShowFilter;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n          const noQueryDiff = options?.queryDiff === false;\n\n          // Load both sessions\n          let session1, session2;\n          try {\n            session1 = await loadSession(sessionId1, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error loading session 1: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          try {\n            session2 = await loadSession(sessionId2, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error loading session 2: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Collect articles from both sessions\n          const articles1 = await loadSessionArticles(session1, sessionId1, sessionsDir);\n          const articles2 = await loadSessionArticles(session2, sessionId2, sessionsDir);\n\n          // Deduplicate each session's articles before diffing\n          const dedup1 = deduplicateArticles(articles1);\n          const dedup2 = deduplicateArticles(articles2);\n\n          // Compute article diff\n          const diff = computeDiff(dedup1.articles, dedup2.articles);\n\n          // Load and compute query diff (unless disabled)\n          let queryDiff;\n          let showQueryDiffPlaceholder = false;\n          if (!noQueryDiff) {\n            const query1 = await loadSessionQuery(sessionId1, sessionsDir);\n            const query2 = await loadSessionQuery(sessionId2, sessionsDir);\n            if (query1 && query2) {\n              queryDiff = computeQueryDiff(query1, query2);\n            } else {\n              // At least one query is missing - show placeholder\n              showQueryDiffPlaceholder = true;\n            }\n          }\n\n          // Format and output\n          const formatOptions = { queryDiff, noQueryDiff, showQueryDiffPlaceholder };\n          if (options?.json) {\n            console.log(formatDiffJson(diff, sessionId1, sessionId2, showFilter, formatOptions));\n          } else {\n            if (!globalOpts.quiet) {\n              console.log(formatDiff(diff, sessionId1, sessionId2, showFilter, formatOptions));\n\n              // Show suggestions\n              const suggestion = formatSuggestion(getSuggestion({\n                command: 'diff',\n                sessionId: sessionId2,\n                diffSession1Id: sessionId1,\n                diffAddedCount: diff.added.length,\n                diffRemovedCount: diff.removed.length,\n              }));\n              if (suggestion) {\n                console.log(suggestion);\n              }\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register check command\n  program\n    .command('check')\n    .description('Verify coverage of known articles against session results')\n    .argument('<session-id>', 'session ID to check against')\n    .option('--file <path>', 'file with identifiers (one per line)')\n    .option('--doi <ids>', 'comma-separated DOIs to check')\n    .option('--pmid <ids>', 'comma-separated PMIDs to check')\n    .option('--json', 'output as JSON')\n    .option('--missing-only', 'show only missing identifiers')\n    .addHelpText('after', `\nExamples:\n  $ search-hub check SESSION --file known-dois.txt              # Check from file\n  $ search-hub check SESSION --doi \"10.1001/jama.2023.12345\"    # Check single DOI\n  $ search-hub check SESSION --pmid \"37654321,36543210\"         # Check PMIDs\n  $ search-hub check SESSION --file refs.txt --json             # JSON output\n  $ search-hub check SESSION --file refs.txt --missing-only     # Only missing\n\nInput file format (one identifier per line):\n  10.1001/jama.2023.12345          DOI (starts with \"10.\")\n  37654321                          PMID (numeric only)\n  DOI:10.1038/s41586-023-xxxxx    DOI (explicit prefix)\n  PMID:36543210                    PMID (explicit prefix)\n  arxiv:2301.12345                 arXiv ID (explicit prefix)\n  # comment                        Comments and empty lines ignored`)\n    .action(\n      async (\n        sessionId: string,\n        options?: { file?: string; doi?: string; pmid?: string; json?: boolean; missingOnly?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse identifiers from input sources\n          let identifiers;\n          let source: string;\n\n          if (options?.file) {\n            const filePath = expandPath(options.file);\n            let content: string;\n            try {\n              content = await readFile(filePath, 'utf-8');\n            } catch {\n              if (!globalOpts.quiet) {\n                console.error(`Error: File not found: ${filePath}`);\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n            try {\n              identifiers = parseIdentifierFile(content);\n            } catch (error) {\n              if (!globalOpts.quiet) {\n                console.error(`Error: ${error instanceof Error ? error.message : 'Failed to parse identifier file'}`);\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n            source = options.file;\n          } else if (options?.doi || options?.pmid) {\n            const lines: string[] = [];\n            if (options.doi) {\n              lines.push(...options.doi.split(',').map(d => d.trim()).filter(Boolean));\n            }\n            if (options.pmid) {\n              lines.push(...options.pmid.split(',').map(p => `PMID:${p.trim()}`).filter(Boolean));\n            }\n            identifiers = parseIdentifierFile(lines.join('\\n'));\n            source = 'command line';\n          } else {\n            if (!globalOpts.quiet) {\n              console.error('Error: Provide --file, --doi, or --pmid');\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n\n          if (identifiers.length === 0) {\n            if (!globalOpts.quiet) {\n              console.error('Error: No identifiers found in input');\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n\n          // Load session\n          const sessionsDir = await getSessionsDir(globalOpts);\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Load articles and check coverage\n          const articles = await loadSessionArticles(session, sessionId, sessionsDir);\n          const result = checkCoverage(articles, identifiers);\n\n          // Format output\n          if (options?.json) {\n            console.log(formatCheckResultJson(result, { sessionId, source }));\n          } else {\n            if (!globalOpts.quiet) {\n              console.log(formatCheckResult(result, {\n                sessionId,\n                source,\n                missingOnly: options?.missingOnly,\n              }));\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n        }\n      }\n    );\n\n  // Register merge command\n  program\n    .command('merge')\n    .description('Merge results from multiple search sessions')\n    .argument('<session-ids...>', 'two or more session IDs to merge')\n    .option('--name <string>', 'name for merged session')\n    .option('--dry-run', 'show what would be merged without creating session')\n    .option('--json', 'output as JSON')\n    .addHelpText('after', `\nExamples:\n  $ search-hub merge session-v4 session-v9                  # Merge two sessions\n  $ search-hub merge session-v4 session-v9 --name combined  # Merge with custom name\n  $ search-hub merge session-a session-b session-c          # Merge three sessions\n  $ search-hub merge session-v4 session-v9 --dry-run        # Preview merge`)\n    .action(\n      async (\n        sessionIds: string[],\n        options?: { name?: string; dryRun?: boolean; json?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          if (sessionIds.length < 2) {\n            if (!globalOpts.quiet) {\n              console.error('Error: At least two session IDs are required for merge');\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load all source sessions\n          const sessions = new Map<string, ReturnType<typeof loadSession> extends Promise<infer T> ? T : never>();\n          for (const sessionId of sessionIds) {\n            try {\n              const session = await loadSession(sessionId, sessionsDir);\n              sessions.set(sessionId, session);\n            } catch (error) {\n              if (!globalOpts.quiet) {\n                console.error(\n                  `Error loading session '${sessionId}': ${error instanceof Error ? error.message : 'Failed to load session'}`\n                );\n              }\n              process.exitCode = EXIT_CODES.SESSION_ERROR;\n              return;\n            }\n          }\n\n          // Validate sources\n          const validation = validateMergeSources(sessions);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Load articles from all sessions\n          const sessionArticles = new Map<string, Awaited<ReturnType<typeof loadSessionArticles>>>();\n          for (const [sessionId, session] of sessions) {\n            const articles = await loadSessionArticles(session, sessionId, sessionsDir);\n            sessionArticles.set(sessionId, articles);\n          }\n\n          // Merge articles\n          const mergeResult = mergeArticles(sessionArticles);\n\n          // Build output data\n          const sources = [...sessions.entries()].map(([id, session]) => ({\n            id,\n            name: session.name,\n            count: mergeResult.perSession.get(id) ?? 0,\n          }));\n\n          const byProviderCounts = new Map<string, number>();\n          for (const [provider, articles] of mergeResult.byProvider) {\n            byProviderCounts.set(provider, articles.length);\n          }\n\n          // Auto-generate name if not provided\n          const firstSession = sessions.values().next().value;\n          const mergeName = options?.name ?? (firstSession ? firstSession.name + '-merged' : 'merged');\n\n          if (options?.dryRun) {\n            // Dry run - show preview without creating session\n            const outputData = {\n              sessionId: '(dry-run)',\n              totalBefore: mergeResult.totalBefore,\n              totalAfter: mergeResult.totalAfter,\n              duplicatesRemoved: mergeResult.duplicatesRemoved,\n              sources,\n              byProvider: byProviderCounts,\n            };\n            if (options.json) {\n              console.log(formatSessionMergeJson(outputData));\n            } else if (!globalOpts.quiet) {\n              console.log(formatSessionMergeOutput(outputData));\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n            return;\n          }\n\n          // Create merged session\n          const sessionSources = [...sessions.entries()].map(([id, session]) => ({\n            id,\n            name: session.name,\n          }));\n\n          const mergedSession = await createMergedSession({\n            name: mergeName,\n            sources: sessionSources,\n            byProvider: mergeResult.byProvider,\n            totalRetrieved: mergeResult.totalAfter,\n            sessionsDir,\n            sourceSessionIds: sessionIds,\n          });\n\n          // Format output\n          const outputData = {\n            sessionId: mergedSession.id,\n            totalBefore: mergeResult.totalBefore,\n            totalAfter: mergeResult.totalAfter,\n            duplicatesRemoved: mergeResult.duplicatesRemoved,\n            sources,\n            byProvider: byProviderCounts,\n          };\n\n          if (options?.json) {\n            console.log(formatSessionMergeJson(outputData));\n          } else if (!globalOpts.quiet) {\n            console.log(formatSessionMergeOutput(outputData));\n\n            // Show suggestions\n            const suggestion = getSuggestion({\n              command: 'merge',\n              sessionId: mergedSession.id,\n            });\n            const suggestionText = formatSuggestion(suggestion);\n            if (suggestionText) {\n              console.log(suggestionText);\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register register command\n  program\n    .command('register')\n    .description('Register results with reference-manager')\n    .argument('<session-id>', 'session ID to register')\n    .option('--db <providers>', 'register only specific database(s)')\n    .option('--dry-run', 'show what would be registered without executing', false)\n    .option('--with-abstracts', 'also update abstracts via ref update', false)\n    .option('--reviewed', 'register only articles with finalDecision=include', false)\n    .option('--all', 'register all articles (ignore reviews)', false)\n    .option('--force', 'skip confirmation prompts', false)\n    .option('--no-attach-fulltext', 'skip automatic fulltext attachment')\n    .addHelpText('after', `\nExamples:\n  $ search-hub register SESSION_ID                # Register all results\n  $ search-hub register SESSION_ID --with-abstracts\n  $ search-hub register SESSION_ID --dry-run      # Preview only\n  $ search-hub register SESSION_ID --no-attach-fulltext  # Skip fulltext attachment\n\nWith review workflow:\n  $ search-hub register SESSION_ID --reviewed     # Register only included articles\n  $ search-hub register SESSION_ID --all          # Register all (ignore reviews)`)\n    .action(\n      async (\n        sessionId: string,\n        options?: {\n          db?: string;\n          dryRun?: boolean;\n          withAbstracts?: boolean;\n          reviewed?: boolean;\n          all?: boolean;\n          force?: boolean;\n          attachFulltext?: boolean;\n        }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const registerOpts = parseRegisterOptions(sessionId, {\n            db: options?.db,\n            dryRun: options?.dryRun,\n            withAbstracts: options?.withAbstracts,\n            reviewed: options?.reviewed,\n            all: options?.all,\n            force: options?.force,\n          });\n\n          const validation = validateRegisterInput(registerOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Check if ref command is available\n          const refAvailable = await checkRefAvailable();\n          if (!refAvailable && !registerOpts.dryRun) {\n            if (!globalOpts.quiet) {\n              console.error('Error: reference-manager (ref) command not found.\\n');\n              console.error('reference-manager is required to register search results.');\n              console.error('Would you like to install it now? (npm i -g @ncukondo/reference-manager) [Y/n]: ');\n            }\n\n            // For non-interactive mode, suggest installation\n            const npmAvailable = await checkNpmAvailable();\n            if (!npmAvailable) {\n              if (!globalOpts.quiet) {\n                console.error('\\nError: npm command not found.');\n                console.error('Please install Node.js first: https://nodejs.org/');\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n\n            // Try to install\n            try {\n              if (!globalOpts.quiet) {\n                console.log('\\nInstalling reference-manager...');\n              }\n              await installRefManager();\n              if (!globalOpts.quiet) {\n                console.log('✓ reference-manager installed successfully.\\n');\n              }\n            } catch (installError) {\n              if (!globalOpts.quiet) {\n                console.error(\n                  `\\nFailed to install reference-manager: ${installError instanceof Error ? installError.message : 'Unknown error'}`\n                );\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load session\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Check for review file and handle --reviewed/--all flags\n          const reviewExists = await hasReviewFile(sessionId, sessionsDir);\n          let articles: import('../providers/base/types.js').Article[];\n\n          if (registerOpts.reviewed) {\n            // --reviewed: only include reviewed articles\n            if (!reviewExists) {\n              if (!globalOpts.quiet) {\n                console.error('Error: No reviews.yaml found for this session.');\n                console.error('Run \"search-hub review init --session ' + sessionId + '\" first.');\n              }\n              process.exitCode = EXIT_CODES.SESSION_ERROR;\n              return;\n            }\n\n            const summary = await getReviewSummary(sessionId, sessionsDir);\n            if (summary.included === 0) {\n              if (!globalOpts.quiet) {\n                console.error(formatNoIncludedArticlesError(summary, sessionId));\n              }\n              process.exitCode = EXIT_CODES.SESSION_ERROR;\n              return;\n            }\n\n            // Warn about pending articles (unless --force or --dry-run)\n            if (summary.pending > 0 && !registerOpts.force && !registerOpts.dryRun) {\n              if (!globalOpts.quiet) {\n                console.log(formatPendingWarning(summary));\n              }\n              // Wait for user confirmation\n              const confirmed = await confirmPrompt();\n              if (!confirmed) {\n                process.exitCode = EXIT_CODES.SUCCESS;\n                return;\n              }\n            }\n\n            articles = await getIncludedArticles(sessionId, sessionsDir);\n          } else if (reviewExists && !registerOpts.all) {\n            // reviews.yaml exists but no flag specified\n            const summary = await getReviewSummary(sessionId, sessionsDir);\n            if (!globalOpts.quiet) {\n              console.log(formatReviewRequiredMessage(summary, sessionId));\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          } else {\n            // --all or no reviews.yaml: collect all articles from result files\n            if (reviewExists && !globalOpts.quiet) {\n              const summary = await getReviewSummary(sessionId, sessionsDir);\n              console.log(formatIgnoringReviewsNote(summary.total));\n            }\n            articles = await loadSessionArticles(session, sessionId, sessionsDir, registerOpts.providers);\n          }\n\n          // Dry run mode\n          if (registerOpts.dryRun) {\n            if (!globalOpts.quiet) {\n              console.log(formatRegisterDryRunOutput(articles));\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n            return;\n          }\n\n          // Register articles\n          if (!globalOpts.quiet) {\n            console.log(`Registering ${articles.length} references to reference-manager...`);\n          }\n\n          const sessionDir = join(sessionsDir, sessionId);\n          const registerOptions: import('../integration/register.js').RegisterOptions = {\n            sessionId,\n            sessionDir,\n            withAbstracts: registerOpts.withAbstracts,\n            ...(options?.attachFulltext === false ? { noAttachFulltext: true } : {}),\n          };\n          if (!globalOpts.quiet) {\n            registerOptions.onProgress = (current, total) => {\n              process.stdout.write(`\\rProgress: ${current}/${total}`);\n            };\n          }\n          const record = await registerArticles(articles, registerOptions);\n\n          // Save registration record\n          await saveRegistrationRecord(sessionDir, record);\n\n          if (!globalOpts.quiet) {\n            console.log('\\n');\n            console.log(formatRegistrationSummary(record.summary));\n\n            // Show fulltext attach summary\n            if (record.fulltext) {\n              const ft = record.fulltext.summary;\n              console.log('\\nFulltext attachment results:');\n              if (ft.attached > 0) {\n                const totalFiles = record.fulltext.attached.reduce((sum, a) => sum + a.files.length, 0);\n                console.log(`  ✓ ${ft.attached} articles attached (${totalFiles} files)`);\n              }\n              if (ft.skipped > 0) {\n                console.log(`  ⚠ ${ft.skipped} skipped`);\n              }\n              if (ft.failed > 0) {\n                console.log(`  ✗ ${ft.failed} failed`);\n              }\n            }\n\n            console.log(`\\nResults saved to: ${join(sessionDir, 'registration.json')}`);\n\n            // Show next step suggestions\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'register',\n              sessionId,\n              hasReviews: reviewExists,\n            }));\n            if (suggestion) console.log(suggestion);\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register review command group\n  const reviewCommand = program\n    .command('review')\n    .description('Article review workflow for systematic literature review')\n    .addHelpText('after', `\nExamples:\n  $ search-hub review init --session SESSION_ID           # Initialize reviews.yaml\n  $ search-hub review status --session SESSION_ID         # Show review progress\n  $ search-hub review list --session SESSION_ID --filter pending  # List articles\n  $ search-hub review extract --session SESSION_ID --name title-screening  # Extract for review\n  $ search-hub review merge --session SESSION_ID --name title-screening   # Merge reviews\n  $ search-hub review export --session SESSION_ID --only included -o included.yaml`);\n\n  reviewCommand\n    .command('init')\n    .description('Generate reviews.yaml from deduplicated search results')\n    .requiredOption('--session <id>', 'session ID')\n    .option('-f, --force', 'overwrite existing reviews.yaml', false)\n    .action(async (options: { session: string; force: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const initOptions: ReviewInitOptions = {\n          sessionId: options.session,\n          ...(options.force && { force: options.force }),\n        };\n        const result = await executeReviewInit(initOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(`Created ${result.reviewsPath}`);\n          console.log(`  Articles: ${result.articleCount}`);\n          if (result.duplicatesRemoved > 0) {\n            console.log(`  Duplicates removed: ${result.duplicatesRemoved}`);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('status')\n    .description('Show review progress summary')\n    .requiredOption('--session <id>', 'session ID')\n    .option('--json', 'output as JSON')\n    .action(async (options: { session: string; json?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const statusOptions: ReviewStatusOptions = {\n          sessionId: options.session,\n        };\n        const result = await executeReviewStatus(statusOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          if (options.json) {\n            console.log(JSON.stringify(result, null, 2));\n          } else {\n            console.log(formatStatusOutput(result));\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'review status',\n              sessionId: options.session,\n              reviewStatus: result,\n            }));\n            if (suggestion) console.log(suggestion);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('list')\n    .description('List articles with optional filtering')\n    .requiredOption('--session <id>', 'session ID')\n    .option('--filter <type>', 'filter by status: pending, incomplete, uncertain, agreed-include, agreed-exclude, conflicting, finalized, all', 'all')\n    .option('--json', 'output as JSON')\n    .action(async (options: { session: string; filter?: string; json?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const validFilters: ListFilter[] = ['pending', 'incomplete', 'uncertain', 'agreed-include', 'agreed-exclude', 'conflicting', 'finalized', 'all'];\n        const filter = (options.filter ?? 'all') as ListFilter;\n        if (!validFilters.includes(filter)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid filter '${options.filter}'. Valid values: ${validFilters.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const listOptions: ReviewListOptions = {\n          sessionId: options.session,\n          filter,\n        };\n        const result = await executeReviewList(listOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          if (options.json) {\n            console.log(JSON.stringify(result, null, 2));\n          } else {\n            console.log(formatListOutput(result));\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('extract')\n    .description('Extract subset to for-review/<name>/review.yaml for distributed review')\n    .requiredOption('--session <id>', 'session ID')\n    .requiredOption('--name <name>', 'name for the review subset (output: for-review/<name>/review.yaml)')\n    .option('--filter <types>', 'filter by status (comma-separated): pending, incomplete, uncertain, agreed-include, agreed-exclude, conflicting, finalized')\n    .option('--sort <method>', 'sort method: year, title, random, none', 'none')\n    .option('--limit <n>', 'limit number of articles')\n    .option('--offset <n>', 'skip first n articles')\n    .option('--seed <n>', 'random seed for reproducible sorting')\n    .option('--basis <type>', 'basis for review: title, abstract, or fulltext')\n    .option('--reviewer <id>', 'reviewer identifier (e.g., \"ai:claude\")')\n    .option('--finalize', 'extract for final decision (includes reviewHistory and finalDecision)')\n    .action(async (options: {\n      session: string;\n      name: string;\n      filter?: string;\n      sort?: string;\n      limit?: string;\n      offset?: string;\n      seed?: string;\n      basis?: string;\n      reviewer?: string;\n      finalize?: boolean;\n    }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const validSorts: SortOption[] = ['year', 'title', 'random', 'none'];\n        const sort = (options.sort ?? 'none') as SortOption;\n        if (!validSorts.includes(sort)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid sort '${options.sort}'. Valid values: ${validSorts.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const extractOptions: ReviewExtractOptions = {\n          sessionId: options.session,\n          name: options.name,\n          sort,\n        };\n\n        if (options.filter) {\n          extractOptions.filter = options.filter.split(',').map(s => s.trim()) as ReviewStatus[];\n        }\n        if (options.limit) {\n          extractOptions.limit = parseInt(options.limit, 10);\n        }\n        if (options.offset) {\n          extractOptions.offset = parseInt(options.offset, 10);\n        }\n        if (options.seed) {\n          extractOptions.seed = parseInt(options.seed, 10);\n        }\n\n        // Reviewer is required for all extract modes\n        if (!options.reviewer) {\n          if (!globalOpts.quiet) {\n            console.error('Error: --reviewer is required');\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n        extractOptions.reviewer = options.reviewer;\n\n        // Handle basis option\n        if (options.basis) {\n          const validBasis = ['title', 'abstract', 'fulltext'];\n          if (!validBasis.includes(options.basis)) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: Invalid basis '${options.basis}'. Valid values: ${validBasis.join(', ')}`);\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n          extractOptions.basis = options.basis as 'title' | 'abstract' | 'fulltext';\n        }\n\n        if (options.finalize) {\n          extractOptions.finalize = true;\n        }\n\n        const result = await executeReviewExtract(extractOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(`Extracted ${result.extractedCount} of ${result.totalMatching} articles to ${result.outputPath}`);\n          const suggestion = formatSuggestion(getSuggestion({\n            command: 'review extract',\n            sessionId: options.session,\n            extractName: options.name,\n            extractedCount: result.extractedCount,\n            totalMatching: result.totalMatching,\n            extractLimit: extractOptions.limit,\n            extractOffset: extractOptions.offset,\n          }));\n          if (suggestion) console.log(suggestion);\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('merge')\n    .description('Merge edited file back into main reviews.yaml')\n    .requiredOption('--session <id>', 'session ID')\n    .requiredOption('--name <name>', 'name of the review subset to merge (reads from for-review/<name>/review.yaml)')\n    .option('--dry-run', 'show changes without applying', false)\n    .action(async (options: { session: string; name: string; dryRun: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const mergeOptions: ReviewMergeOptions = {\n          sessionId: options.session,\n          name: options.name,\n          ...(options.dryRun && { dryRun: options.dryRun }),\n        };\n        const result = await executeReviewMerge(mergeOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(formatMergeOutput(result, options.dryRun));\n          if (!options.dryRun) {\n            const statusResult = await executeReviewStatus({ sessionId: options.session }, sessionsDir);\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'review merge',\n              sessionId: options.session,\n              reviewStatus: statusResult,\n            }));\n            if (suggestion) console.log(suggestion);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('mark')\n    .description('Mark decisions in work files')\n    .requiredOption('--file <path>', 'path to work file')\n    .option('--id <id>', 'article ID to mark')\n    .option('--decision <decision>', 'decision: include, exclude, or uncertain')\n    .option('--comment <text>', 'optional comment')\n    .action(async (options: {\n      file: string;\n      id?: string;\n      decision?: string;\n      comment?: string;\n    }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        // Validate decision if provided\n        const validDecisions = ['include', 'exclude', 'uncertain'];\n        if (options.decision && !validDecisions.includes(options.decision)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid decision '${options.decision}'. Valid values: ${validDecisions.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        // Validate required options\n        if (!options.id || !options.decision) {\n          if (!globalOpts.quiet) {\n            console.error('Error: --id and --decision must be specified');\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const markOptions: ReviewMarkOptions = {\n          file: options.file,\n          id: options.id,\n          decision: options.decision as 'include' | 'exclude' | 'uncertain',\n        };\n\n        if (options.comment) markOptions.comment = options.comment;\n\n        const result = await executeReviewMark(markOptions);\n        if (!globalOpts.quiet) {\n          console.log(`Marked ${result.marked} article(s)`);\n          for (const warning of result.warnings) {\n            console.warn(`Warning: ${warning}`);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('export')\n    .description('Export articles based on final decision')\n    .requiredOption('--session <id>', 'session ID')\n    .requiredOption('--only <filter>', 'export filter: included or excluded')\n    .requiredOption('-o, --output <path>', 'output file path')\n    .option('--format <fmt>', 'output format: yaml, json, jsonl', 'yaml')\n    .action(async (options: {\n      session: string;\n      only: string;\n      output: string;\n      format?: string;\n    }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const validOnlyValues: ReviewExportFilter[] = ['included', 'excluded'];\n        const only = options.only as ReviewExportFilter;\n        if (!validOnlyValues.includes(only)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid --only value '${options.only}'. Valid values: ${validOnlyValues.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const validFormats: ReviewExportFormat[] = ['yaml', 'json', 'jsonl'];\n        const format = (options.format ?? 'yaml') as ReviewExportFormat;\n        if (!validFormats.includes(format)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid format '${options.format}'. Valid values: ${validFormats.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const exportOptions: ReviewExportOptions = {\n          sessionId: options.session,\n          only,\n          output: options.output,\n          format,\n        };\n        const result = await executeReviewExport(exportOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(formatExportOutput(result));\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('finalize')\n    .description('Auto-set finalDecision for articles with reviewer consensus')\n    .requiredOption('--session <id>', 'session ID')\n    .option('--dry-run', 'preview without changes', false)\n    .option('--min-reviewers <n>', 'minimum agreeing reviewers needed', '1')\n    .action(async (options: { session: string; dryRun: boolean; minReviewers: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const finalizeOptions: ReviewFinalizeOptions = {\n          sessionId: options.session,\n          ...(options.dryRun && { dryRun: options.dryRun }),\n        };\n        const minReviewers = parseInt(options.minReviewers, 10);\n        if (!Number.isNaN(minReviewers) && minReviewers > 1) {\n          finalizeOptions.minReviewers = minReviewers;\n        }\n        const result = await executeReviewFinalize(finalizeOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(formatFinalizeOutput(result, { dryRun: options.dryRun }));\n          if (!options.dryRun) {\n            const statusResult = await executeReviewStatus({ sessionId: options.session }, sessionsDir);\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'review finalize',\n              sessionId: options.session,\n              reviewStatus: statusResult,\n            }));\n            if (suggestion) console.log(suggestion);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  // Register notes command group\n  const notesCommand = program\n    .command('notes')\n    .description('Manage session notes and assessments')\n    .addHelpText('after', `\nExamples:\n  $ search-hub notes list SESSION_ID             # List notes for a session\n  $ search-hub notes add SESSION_ID \"my note\"    # Add a note\n  $ search-hub notes add SESSION_ID --file assessment.md  # Add from file\n  $ search-hub notes assess SESSION_ID --precision \"~54%\" --verdict good --comment \"Good results\"\n  $ search-hub notes list --all                  # Show notes from all sessions`);\n\n  notesCommand\n    .command('list')\n    .description('List notes for a session or all sessions')\n    .argument('[session-id]', 'session ID')\n    .option('--all', 'show notes from all sessions')\n    .option('--json', 'output as JSON')\n    .action(async (sessionId?: string, options?: { all?: boolean; json?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const formatOpts = { json: options?.json ?? false };\n\n        if (options?.all) {\n          // Cross-session notes view\n          const summaries = await listSessions(sessionsDir);\n          const allNotes: SessionNotes[] = [];\n\n          for (const summary of summaries) {\n            const sessionNotesDir = join(sessionsDir, summary.id);\n            const notes = await loadNotes(sessionNotesDir);\n            allNotes.push({\n              sessionId: summary.id,\n              sessionName: summary.name,\n              notes,\n            });\n          }\n\n          if (!globalOpts.quiet) {\n            console.log(formatAllSessionNotes(allNotes, formatOpts));\n          }\n          process.exitCode = EXIT_CODES.SUCCESS;\n          return;\n        }\n\n        if (!sessionId) {\n          if (!globalOpts.quiet) {\n            console.error('Error: session-id is required (or use --all)');\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        if (!(await sessionExists(sessionId, sessionsDir))) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: session '${sessionId}' not found`);\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        // List notes for a specific session\n        const sessionDir = join(sessionsDir, sessionId);\n        const notes = await loadNotes(sessionDir);\n        if (!globalOpts.quiet) {\n          console.log(formatNotesList(notes, formatOpts));\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  notesCommand\n    .command('add')\n    .description('Add a note to a session')\n    .argument('<session-id>', 'session ID')\n    .argument('[text]', 'note text')\n    .option('--file <path>', 'read note text from a file instead')\n    .action(async (sessionId: string, text?: string, options?: { file?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const sessionDir = join(sessionsDir, sessionId);\n\n        if (!(await sessionExists(sessionId, sessionsDir))) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: session '${sessionId}' not found`);\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        let noteText: string;\n        if (options?.file) {\n          noteText = (await readFile(options.file, 'utf-8')).trim();\n        } else if (text) {\n          noteText = text;\n        } else {\n          if (!globalOpts.quiet) {\n            console.error('Error: note text or --file is required');\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        await addNote(sessionDir, noteText);\n\n        if (!globalOpts.quiet) {\n          console.log('Note added.');\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  notesCommand\n    .command('assess')\n    .description('Add a structured assessment to a session')\n    .argument('<session-id>', 'session ID')\n    .option('--precision <value>', 'estimated precision (e.g., \"~54%\", \"15/28\")')\n    .option('--verdict <value>', 'quality judgment: good, refine, reject')\n    .option('--comment <text>', 'free text explanation')\n    .action(async (sessionId: string, options?: { precision?: string; verdict?: string; comment?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        if (!options?.precision && !options?.verdict && !options?.comment) {\n          if (!globalOpts.quiet) {\n            console.error('Error: at least one of --precision, --verdict, or --comment is required');\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const sessionDir = join(sessionsDir, sessionId);\n\n        if (!(await sessionExists(sessionId, sessionsDir))) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: session '${sessionId}' not found`);\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        await addAssessment(sessionDir, {\n          precision: options?.precision,\n          verdict: options?.verdict,\n          comment: options?.comment,\n        });\n\n        if (!globalOpts.quiet) {\n          console.log('Assessment added.');\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  // Register fulltext command group (init, sync, convert, check)\n  registerFulltextCommands(program, getSessionsDir);\n\n  return program;\n}\n\n/**\n * Main entry point for CLI execution.\n */\nexport async function main(): Promise<void> {\n  const program = createProgram();\n  await program.parseAsync(process.argv);\n}\n\n// Run main if executed directly\nconst currentFile = fileURLToPath(import.meta.url);\nconst executedFile = process.argv[1];\nif (executedFile) {\n  if (realpathSync(executedFile) === realpathSync(currentFile)) {\n    main().catch((error) => {\n      console.error('Fatal error:', error);\n      process.exit(EXIT_CODES.GENERAL_ERROR);\n    });\n  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executeReviewMark,\n  type ReviewMarkOptions,\n} from './commands/review/mark.js';\nimport {\n  executeReviewExport,\n  formatExportOutput,\n  type ReviewExportOptions,\n  type ExportFormat as ReviewExportFormat,\n  type ExportFilter as ReviewExportFilter,\n} from './commands/review/export.js';\nimport {\n  executeReviewFinalize,\n  formatFinalizeOutput,\n  type ReviewFinalizeOptions,\n} from './commands/review/finalize.js';\nimport { type ReviewStatus } from './commands/review/types.js';\nimport { registerFulltextCommands } from './commands/fulltext/index.js';\n\nimport {\n  parseRegisterOptions,\n  validateRegisterInput,\n  formatRegistrationSummary,\n  formatDryRunOutput as formatRegisterDryRunOutput,\n  hasReviewFile,\n  getReviewSummary,\n  getIncludedArticles,\n  formatReviewRequiredMessage,\n  formatNoIncludedArticlesError,\n  formatPendingWarning,\n  formatIgnoringReviewsNote,\n  confirmPrompt,\n} from './commands/register.js';\nimport { formatSuggestion } from './suggestions/index.js';\nimport { getSuggestion } from './suggestions/rules.js';\nimport { registerArticles, saveRegistrationRecord } from '../integration/register.js';\nimport { checkRefAvailable, checkNpmAvailable, installRefManager } from '../integration/ref-cli.js';\nimport { loadSession, sessionExists, listSessions } from '../session/manager.js';\nimport { parseQueryFile, detectShortKeywords } from '../query/parser.js';\nimport { writeFile, readFile } from 'node:fs/promises';\nimport { realpathSync } from 'node:fs';\nimport { join } from 'node:path';\nimport { fileURLToPath } from 'node:url';\nimport { getSessionsDir } from './utils/sessions-dir.js';\nimport { expandPath } from '../utils/path.js';\nimport { loadSessionArticles, loadSessionQuery } from './commands/session-utils.js';\nimport { parseIdentifierFile, checkCoverage, formatCheckResult, formatCheckResultJson } from './commands/check.js';\n\n/**\n * Global CLI options available to all commands.\n */\nexport interface GlobalOptions {\n  /** Path to config file */\n  config?: string;\n  /** Path to session directory */\n  sessionDir?: string;\n  /** Enable verbose output */\n  verbose: boolean;\n  /** Suppress all output except errors */\n  quiet: boolean;\n  /** Enable color output (default: true, use --no-color to disable) */\n  color: boolean;\n}\n\n/**\n * Create and configure the CLI program.\n */\nexport function createProgram(): Command {\n  const program = new Command();\n\n  program\n    .name('search-hub')\n    .version(VERSION)\n    .description(\n      'CLI tool for systematic literature searching across multiple academic databases'\n    )\n    .option('-c, --config <path>', 'path to config file')\n    .option('--session-dir <path>', 'path to session directory')\n    .option('-v, --verbose', 'enable verbose output', false)\n    .option('--quiet', 'suppress all output except errors', false)\n    .option('--no-color', 'disable color output')\n    .addHelpText('after', `\nWorkflow:\n  1. query init → edit → validate / --dry-run        Query preparation\n  2. search --preview → search                       Preview & execute\n  3. results / summary / diff / check                Inspect & verify\n  4. review init → extract → merge → status          Systematic review\n  5. register / export                               Output\n\n  Iterate: search → results -q → check → diff       Query refinement\n\nQuick Start:\n  $ search-hub query init -o search.yaml        # Create query template\n  $ search-hub search search.yaml --count-only  # Check hit counts\n  $ search-hub search search.yaml               # Execute search\n  $ search-hub results <session>                # Review titles`);\n\n  // Register init command\n  program\n    .command('init')\n    .description('Initialize configuration directory')\n    .option('-f, --force', 'overwrite existing configuration', false)\n    .addHelpText('after', `\nExamples:\n  $ search-hub init                 # Initialize with default settings\n  $ search-hub init --force         # Overwrite existing configuration`)\n    .action(async (options: { force: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const result = await init({ force: options.force });\n        if (!globalOpts.quiet) {\n          if (result.success) {\n            console.log(result.message);\n          } else {\n            console.error(result.message);\n          }\n        }\n        process.exitCode = result.success ? EXIT_CODES.SUCCESS : EXIT_CODES.CONFIG_ERROR;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.GENERAL_ERROR;\n      }\n    });\n\n  // Register config command\n  program\n    .command('config')\n    .description('View and edit configuration')\n    .argument('[key]', 'configuration key to view or set')\n    .argument('[value]', 'value to set for the key')\n    .addHelpText('after', `\nExamples:\n  $ search-hub config                              # Show all config\n  $ search-hub config providers.pubmed             # Show PubMed config\n  $ search-hub config providers.pubmed.api_key KEY # Set API key`)\n    .action(async (key?: string, value?: string) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        // Load config - use default if no config file exists\n        let config;\n        try {\n          config = await loadConfig(\n            globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}\n          );\n        } catch {\n          config = getDefaultConfig();\n        }\n\n        if (!key) {\n          // View all config\n          if (!globalOpts.quiet) {\n            console.log(viewConfig(config));\n          }\n        } else if (!value) {\n          // View specific key\n          const result = viewConfigKey(config, key);\n          if (result.success) {\n            if (!globalOpts.quiet) {\n              console.log(result.value);\n            }\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n            }\n            process.exitCode = EXIT_CODES.CONFIG_ERROR;\n            return;\n          }\n        } else {\n          // Set key value\n          const result = setConfigKey(config, key, value);\n          if (result.success) {\n            // Save the modified config to file\n            const configPath = globalOpts.config ? expandPath(globalOpts.config) : getDefaultConfigPath();\n            try {\n              await saveConfig(config, { path: configPath });\n              if (!globalOpts.quiet) {\n                console.log(`Set ${key} = ${result.value}`);\n                console.log(`Saved to ${configPath}`);\n              }\n            } catch (saveError) {\n              if (!globalOpts.quiet) {\n                console.error(\n                  `Error saving config: ${saveError instanceof Error ? saveError.message : saveError}`\n                );\n              }\n              process.exitCode = EXIT_CODES.CONFIG_ERROR;\n              return;\n            }\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n            }\n            process.exitCode = EXIT_CODES.CONFIG_ERROR;\n            return;\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.CONFIG_ERROR;\n      }\n    });\n\n  // Register query command group\n  const queryCommand = program\n    .command('query')\n    .description('Query file utilities')\n    .addHelpText('after', `\nQuery YAML format (minimal):\n  name: my_search\n  query:\n    - field: title_abstract\n      terms:\n        keywords: [\"term1\", \"term2\"]\n      operator: OR\n\nUse \"search-hub query init\" to generate a template.`);\n\n  queryCommand\n    .command('validate')\n    .description('Validate query YAML file (auto-checks controlled vocabulary)')\n    .argument('<file>', 'path to query YAML file')\n    .option('--no-vocab', 'skip controlled vocabulary validation')\n    .option('--no-cache', 'skip vocabulary lookup cache')\n    .addHelpText('after', `\nExamples:\n  $ search-hub query validate ./diabetes-ai.yaml\n  $ search-hub query validate ./diabetes-ai.yaml --no-vocab   # Skip MeSH check\n  $ search-hub query validate ./diabetes-ai.yaml --no-cache   # Ignore cache`)\n    .action(async (file: string, opts: { vocab?: boolean; cache?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const noVocab = opts.vocab === false;\n        const noCache = opts.cache === false;\n\n        let cache: VocabCache | undefined;\n        if (!noVocab && !noCache) {\n          cache = new VocabCache();\n          await cache.load();\n        }\n\n        const hasSchema = await detectSchemaLink(file);\n\n        if (noVocab) {\n          const result = await validateQueryCommand(file, { noVocab });\n\n          if (!globalOpts.quiet) {\n            let output = formatValidateResult(result, file);\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'query validate',\n              queryFile: file,\n              validationSuccess: result.success,\n              hasSchemaLink: hasSchema,\n            }));\n            if (suggestion) output += '\\n' + suggestion;\n            console.log(output);\n          }\n          process.exitCode = !result.success\n            ? EXIT_CODES.QUERY_ERROR\n            : EXIT_CODES.SUCCESS;\n          return;\n        }\n\n        const rateLimiter = new RateLimiter({ tokensPerSecond: 3 });\n        const meshClient = new MeSHLookupClient({\n          rateLimiter,\n          ...(cache ? { cache } : {}),\n        });\n\n        // Create count validators for ERIC/Emtree\n        const countValidators: CountVocabValidator[] = [];\n        let config: Config | undefined;\n        try {\n          config = await loadConfig(\n            globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}\n          );\n        } catch {\n          // Config not available — skip count validators\n        }\n\n        if (config) {\n          const ericProvider = createProviderInstance('eric', config);\n          if (ericProvider) {\n            countValidators.push(\n              createEricCountValidator(ericProvider, cache ? { cache } : undefined)\n            );\n          }\n\n          const scopusProvider = createProviderInstance('scopus', config);\n          if (scopusProvider) {\n            countValidators.push(\n              createEmtreeCountValidator(scopusProvider, cache ? { cache } : undefined)\n            );\n          }\n        }\n\n        const result = await validateQueryCommand(file, {\n          meshClient,\n          ...(countValidators.length > 0 ? { countValidators } : {}),\n        });\n\n        if (cache) {\n          await cache.save();\n        }\n\n        if (!globalOpts.quiet) {\n          let output = formatValidateResult(result, file);\n          if (result.vocabResult) {\n            output += formatVocabValidationOutput(result.vocabResult);\n          }\n          const suggestion = formatSuggestion(getSuggestion({\n            command: 'query validate',\n            queryFile: file,\n            validationSuccess: result.success && !hasVocabErrors(result),\n            hasSchemaLink: hasSchema,\n          }));\n          if (suggestion) output += '\\n' + suggestion;\n          console.log(output);\n        }\n        process.exitCode =\n          !result.success || hasVocabErrors(result)\n            ? EXIT_CODES.QUERY_ERROR\n            : EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.QUERY_ERROR;\n      }\n    });\n\n  queryCommand\n    .command('translate')\n    .description('Show translated queries for each database')\n    .argument('<file>', 'path to query YAML file')\n    .option('--db <provider>', 'show translation for specific provider only')\n    .addHelpText('after', `\nExamples:\n  $ search-hub query translate ./diabetes-ai.yaml            # All databases\n  $ search-hub query translate ./diabetes-ai.yaml --db pubmed # PubMed only`)\n    .action(async (file: string, options: { db?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const translateOptions = options.db\n          ? { providers: [options.db as ProviderName] }\n          : {};\n        const result = await translateQueryCommand(file, translateOptions);\n        if (!globalOpts.quiet) {\n          console.log(formatTranslateResult(result, file));\n        }\n        process.exitCode = result.success\n          ? EXIT_CODES.SUCCESS\n          : EXIT_CODES.QUERY_ERROR;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.QUERY_ERROR;\n      }\n    });\n\n  queryCommand\n    .command('inspect')\n    .description('Show how a query resolves per provider (block replacements and added filters)')\n    .argument('<file>', 'path to query YAML file')\n    .option('--db <provider>', 'show resolution for specific provider only')\n    .addHelpText('after', `\nExamples:\n  $ search-hub query inspect ./diabetes-ai.yaml            # All databases\n  $ search-hub query inspect ./diabetes-ai.yaml --db pubmed # PubMed only`)\n    .action(async (file: string, options: { db?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const inspectOptions = options.db\n          ? { providers: [options.db as ProviderName] }\n          : {};\n        const result = await inspectQueryCommand(file, inspectOptions);\n        if (!result.success) {\n          if (!globalOpts.quiet) {\n            console.error(`\\u2717 Failed to inspect: ${file}\\n  Error: ${result.error}`);\n          }\n          process.exitCode = EXIT_CODES.QUERY_ERROR;\n          return;\n        }\n        if (!globalOpts.quiet) {\n          console.log(formatInspectOutput(result.result!));\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.QUERY_ERROR;\n      }\n    });\n\n  queryCommand\n    .command('init')\n    .description('Generate a template query YAML file')\n    .option('-o, --output <path>', 'write to file (default: stdout)')\n    .option('--force', 'overwrite existing file', false)\n    .action(async (options: { output?: string; force?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        if (options.output) {\n          const result = await writeQueryTemplate(options);\n          if (!globalOpts.quiet) {\n            if (result.success) {\n              console.log(result.message);\n            } else {\n              console.error(result.message);\n            }\n          }\n          process.exitCode = result.success ? EXIT_CODES.SUCCESS : EXIT_CODES.GENERAL_ERROR;\n        } else {\n          const template = generateQueryTemplate();\n          console.log(template);\n          process.exitCode = EXIT_CODES.SUCCESS;\n        }\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.GENERAL_ERROR;\n      }\n    });\n\n  // Register status command\n  program\n    .command('status')\n    .description('Show session status and statistics')\n    .argument('[session-id]', 'session ID to show details for')\n    .option('--json', 'output as JSON')\n    .option('--all', 'include completed sessions')\n    .addHelpText('after', `\nExamples:\n  $ search-hub status                           # List recent sessions\n  $ search-hub status 20240115_diabetes-ai_a3f2 # Show session details\n  $ search-hub status --json                    # JSON output for scripting`)\n    .action(async (sessionId?: string, options?: { json?: boolean; all?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const formatOpts = { json: options?.json ?? false };\n\n        if (sessionId) {\n          // Show specific session details\n          const result = await getSessionDetails(sessionId, sessionsDir);\n          if (result.success && result.session) {\n            // Compute deduplication stats\n            try {\n              const rawSession = await loadSession(sessionId, sessionsDir);\n              const dedupStats = await computeDeduplicationStats(sessionId, sessionsDir, rawSession);\n              result.session.uniqueArticles = dedupStats.uniqueArticles;\n              result.session.duplicatesRemoved = dedupStats.duplicatesRemoved;\n            } catch {\n              // Dedup stats are optional - don't fail the command\n            }\n            if (!globalOpts.quiet) {\n              console.log(formatSessionDetails(result.session, formatOpts));\n            }\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n        } else {\n          // List sessions\n          const listOpts = { all: options?.all ?? false };\n          const sessions = await listSessionsForDisplay(sessionsDir, listOpts);\n          if (!globalOpts.quiet) {\n            console.log(formatSessionList(sessions, formatOpts));\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  // Register search command\n  program\n    .command('search')\n    .description('Execute search across databases')\n    .argument('[query-file]', 'path to query YAML file')\n    .option('--db <providers>', 'target specific database(s), comma-separated')\n    .option('--query <string>', 'direct query in database-native syntax (advanced; requires --db; prefer YAML files)')\n    .option('--name <string>', 'session name')\n    .option('--max-results <n>', 'limit results per database')\n    .option('--dry-run', 'show translated queries without executing')\n    .option('--count-only', 'get hit counts without downloading results')\n    .option('--preview', 'get hit counts and first 5 titles without creating session')\n    .option('--skip-connection-test', 'skip API connection test during dry-run')\n    .option('--no-resume', 'start fresh even if session exists')\n    .option('--strict', 'require all targeted databases to succeed (exit non-zero on partial failure)')\n    .addHelpText('after', `\nWorkflow position:\n  query validate → [this command: search] → results / summary / diff\n\nExamples:\n  $ search-hub search ./diabetes-ai.yaml                # Search all databases\n  $ search-hub search ./query.yaml --db pubmed,eric     # Specific databases\n  $ search-hub search --db pubmed --query \"diabetes[tiab]\"  # Direct query\n  $ search-hub search ./query.yaml --dry-run            # Preview translations\n  $ search-hub search ./query.yaml --count-only         # Get hit counts only\n  $ search-hub search ./query.yaml --max-results 100    # Limit results\n\nQuery features (use \"query init\" to see full template):\n  filters:    year_from, year_to, language, publication_types\n  exclude:    NOT terms per block (terms.exclude)\n  mesh/eric:  controlled vocabulary (terms.mesh, terms.eric)\n  providers:  per-database block replacements and filter additions`)\n    .action(\n      async (\n        queryFile?: string,\n        options?: {\n          db?: string;\n          query?: string;\n          name?: string;\n          maxResults?: string;\n          dryRun?: boolean;\n          countOnly?: boolean;\n          preview?: boolean;\n          skipConnectionTest?: boolean;\n          resume?: boolean;\n          strict?: boolean;\n        }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const searchOpts = parseSearchOptions(queryFile, {\n            db: options?.db,\n            query: options?.query,\n            name: options?.name,\n            maxResults: options?.maxResults,\n            dryRun: options?.dryRun,\n            countOnly: options?.countOnly,\n            preview: options?.preview,\n            noResume: options?.resume === false,\n            strict: options?.strict,\n          });\n\n          const validation = validateSearchInput(searchOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n\n          // Check for short keywords and display warning\n          if (searchOpts.queryFile && !globalOpts.quiet) {\n            try {\n              const ast = await parseQueryFile(searchOpts.queryFile);\n              const shortKeywords = detectShortKeywords(ast);\n              if (shortKeywords.length > 0) {\n                console.error(formatShortKeywordWarning(shortKeywords));\n                console.error('');\n              }\n            } catch {\n              // Ignore parse errors here - they'll be caught later during execution\n            }\n          }\n\n          // Handle dry-run mode\n          if (searchOpts.dryRun) {\n            // Try to load config for provider readiness display\n            let dryRunConfig: Config | undefined;\n            try {\n              dryRunConfig = await loadConfig(globalOpts.config ? { explicitConfigPath: globalOpts.config } : {});\n            } catch {\n              // Config unavailable, readiness section will be omitted\n            }\n\n            if (searchOpts.queryFile) {\n              // Translate from file\n              const translateOpts = searchOpts.providers\n                ? { providers: searchOpts.providers }\n                : {};\n              const result = await translateQueryCommand(\n                searchOpts.queryFile,\n                translateOpts\n              );\n              if (result.success && result.translations) {\n                const translations = Object.entries(result.translations).map(\n                  ([provider, t]) => ({ provider, query: t.native })\n                );\n                const providers = translations.map(t => t.provider) as ProviderName[];\n                if (!globalOpts.quiet) {\n                  const dryRunOpts = dryRunConfig\n                    ? { config: dryRunConfig, providers, skipConnectionTest: options?.skipConnectionTest }\n                    : {};\n                  console.log(await formatDryRunOutput(translations, dryRunOpts));\n                }\n              } else {\n                if (!globalOpts.quiet) {\n                  console.error(`Error: ${result.error}`);\n                }\n                process.exitCode = EXIT_CODES.QUERY_ERROR;\n                return;\n              }\n            } else if (searchOpts.directQuery && searchOpts.providers) {\n              // Direct query\n              const translations = [\n                {\n                  provider: searchOpts.providers[0]!,\n                  query: searchOpts.directQuery,\n                },\n              ];\n              if (!globalOpts.quiet) {\n                const dryRunOpts = dryRunConfig\n                  ? { config: dryRunConfig, providers: searchOpts.providers as ProviderName[], skipConnectionTest: options?.skipConnectionTest }\n                  : {};\n                console.log(await formatDryRunOutput(translations, dryRunOpts));\n              }\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n            return;\n          }\n\n          // Handle preview mode\n          if (searchOpts.preview) {\n            let previewConfig;\n            try {\n              previewConfig = await loadConfig(globalOpts.config ? { explicitConfigPath: globalOpts.config } : {});\n            } catch {\n              previewConfig = getDefaultConfig();\n            }\n\n            const previews = await executePreview(searchOpts, previewConfig);\n\n            if (previews.length === 0) {\n              if (!globalOpts.quiet) {\n                console.error('Error: No providers enabled or selected');\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n\n            if (!globalOpts.quiet) {\n              console.log(formatPreviewOutput(previews, searchOpts.queryFile));\n            }\n\n            const previewHasErrors = previews.some((p) => p.error);\n            const previewAllFailed = previews.every((p) => p.error);\n            if (previewAllFailed) {\n              process.exitCode = EXIT_CODES.NETWORK_ERROR;\n            } else if (previewHasErrors && searchOpts.strict) {\n              process.exitCode = EXIT_CODES.NETWORK_ERROR;\n            } else {\n              process.exitCode = EXIT_CODES.SUCCESS;\n            }\n            if (previewHasErrors && !previewAllFailed && !globalOpts.quiet) {\n              const failed = previews.filter((p) => p.error).map((p) => `${p.provider}: ${p.error}`);\n              console.warn(`\\nWarning: Some providers failed:\\n  ${failed.join('\\n  ')}`);\n            }\n            return;\n          }\n\n          // Handle count-only mode\n          if (searchOpts.countOnly) {\n            let countConfig;\n            try {\n              countConfig = await loadConfig(globalOpts.config ? { explicitConfigPath: globalOpts.config } : {});\n            } catch {\n              countConfig = getDefaultConfig();\n            }\n\n            const counts = await executeCountOnly(searchOpts, countConfig);\n\n            if (counts.length === 0) {\n              if (!globalOpts.quiet) {\n                console.error('Error: No providers enabled or selected');\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n\n            if (!globalOpts.quiet) {\n              console.log(formatCountOnlyOutput(counts, searchOpts.queryFile));\n              const suggestion = formatSuggestion(getSuggestion({\n                command: 'search --count-only',\n                queryFile: searchOpts.queryFile,\n              }));\n              if (suggestion) console.log(suggestion);\n            }\n\n            const countHasErrors = counts.some((c) => c.error);\n            const countAllFailed = counts.every((c) => c.error);\n            if (countAllFailed) {\n              process.exitCode = EXIT_CODES.NETWORK_ERROR;\n            } else if (countHasErrors && searchOpts.strict) {\n              process.exitCode = EXIT_CODES.NETWORK_ERROR;\n            } else {\n              process.exitCode = EXIT_CODES.SUCCESS;\n            }\n            if (countHasErrors && !countAllFailed && !globalOpts.quiet) {\n              const failed = counts.filter((c) => c.error).map((c) => `${c.provider}: ${c.error}`);\n              console.warn(`\\nWarning: Some providers failed:\\n  ${failed.join('\\n  ')}`);\n            }\n            return;\n          }\n\n          // Non-dry-run: actual search execution\n          const sessionsDir = await getSessionsDir(globalOpts);\n          let config;\n          try {\n            config = await loadConfig(\n              globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}\n            );\n          } catch {\n            config = getDefaultConfig();\n          }\n\n          const showProgress = !globalOpts.quiet && process.stdout.isTTY;\n          const result = await executeSearch(\n            searchOpts,\n            sessionsDir,\n            config,\n            showProgress\n          );\n\n          if (result.success) {\n            if (!globalOpts.quiet) {\n              console.log(`\\nSearch completed. Session: ${result.sessionId}`);\n              if (result.results) {\n                for (const [provider, stats] of Object.entries(result.results)) {\n                  if (stats.error) {\n                    console.log(`  ${provider}: FAILED - ${stats.error}`);\n                  } else {\n                    console.log(`  ${provider}: ${stats.retrieved} results`);\n                  }\n                }\n              }\n              // Show warning for partial success\n              if (result.sessionStatus === 'partial' && result.results) {\n                const failed = Object.entries(result.results)\n                  .filter(([, s]) => s.error)\n                  .map(([p, s]) => `${p}: ${s.error}`);\n                if (failed.length > 0) {\n                  console.warn(`\\nWarning: Some providers failed:\\n  ${failed.join('\\n  ')}`);\n                }\n              }\n              // Show next step suggestions\n              if (result.sessionId) {\n                const sessions = await listSessions(sessionsDir);\n                const suggestionCmd = searchOpts.directQuery ? 'search --query' : 'search';\n                const suggestion = formatSuggestion(getSuggestion({\n                  command: suggestionCmd,\n                  sessionId: result.sessionId,\n                  sessionStatus: result.sessionStatus,\n                  sessionCount: sessions.length,\n                }));\n                if (suggestion) console.log(suggestion);\n              }\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n              if (globalOpts.verbose && result.results) {\n                console.error(formatVerboseProviderDetails(result.results));\n              }\n            }\n            process.exitCode = EXIT_CODES.NETWORK_ERROR;\n          }\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n        }\n      }\n    );\n\n  // Register resume command\n  program\n    .command('resume')\n    .description('Resume an interrupted search session')\n    .argument('<session-id>', 'session ID to resume')\n    .option('--db <providers>', 'resume only specific database(s)')\n    .option('--retry-failed', 'retry failed databases')\n    .addHelpText('after', `\nExamples:\n  $ search-hub resume 20240115_diabetes-ai_a3f2   # Resume session\n  $ search-hub resume SESSION_ID --retry-failed   # Retry failed databases\n  $ search-hub resume SESSION_ID --db scopus      # Resume specific database`)\n    .action(\n      async (\n        sessionId: string,\n        options?: { db?: string; retryFailed?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const resumeOpts = parseResumeOptions(sessionId, {\n            db: options?.db,\n            retryFailed: options?.retryFailed,\n          });\n\n          const validation = validateResumeInput(resumeOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Get resumable providers\n          const result = await getResumableProvidersForCommand(\n            sessionId,\n            sessionsDir,\n            {\n              providers: resumeOpts.providers,\n              retryFailed: resumeOpts.retryFailed,\n            }\n          );\n\n          if (!result.success) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${result.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          if (!result.providers || result.providers.length === 0) {\n            if (!globalOpts.quiet) {\n              console.log('No providers need resuming for this session.');\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n            return;\n          }\n\n          // Show resumable providers\n          if (!globalOpts.quiet) {\n            console.log(`Resuming session ${sessionId} with ${result.providers.length} provider(s):`);\n            for (const p of result.providers) {\n              const details = p.cursor\n                ? `cursor: ${p.cursor}`\n                : p.pageNumber\n                  ? `page: ${p.pageNumber}`\n                  : '';\n              console.log(`  - ${p.provider}: ${p.strategy}${details ? ` (${details})` : ''}`);\n            }\n            console.log('');\n          }\n\n          // Execute resume\n          let config;\n          try {\n            config = await loadConfig(\n              globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}\n            );\n          } catch {\n            config = getDefaultConfig();\n          }\n\n          const showProgress = !globalOpts.quiet && process.stdout.isTTY;\n          const execResult = await executeResume(\n            resumeOpts,\n            sessionsDir,\n            config,\n            showProgress\n          );\n\n          if (execResult.success) {\n            if (!globalOpts.quiet) {\n              console.log(`\\nResume completed. ${execResult.resumed} provider(s) resumed.`);\n              if (execResult.results) {\n                for (const [provider, stats] of Object.entries(execResult.results)) {\n                  console.log(`  ${provider}: ${stats.retrieved} results`);\n                }\n              }\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n          } else {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${execResult.error}`);\n              if (globalOpts.verbose && execResult.results) {\n                console.error(formatVerboseProviderDetails(execResult.results));\n              }\n            }\n            process.exitCode = EXIT_CODES.NETWORK_ERROR;\n          }\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register export command\n  program\n    .command('export')\n    .description('Export session results to various formats')\n    .argument('<session-id>', 'session ID to export')\n    .option('--format <fmt>', 'output format: ids, json, jsonl, csl-json', 'jsonl')\n    .option('-o, --output <path>', 'output file path (default: stdout)')\n    .option('--id-type <type>', 'for ids format: doi, pmid, all')\n    .option('--no-dedup', 'disable deduplication of results')\n    .option('-q, --query <expr>', 'filter results with query expression')\n    .addHelpText('after', `\nExamples:\n  $ search-hub export SESSION_ID                             # JSONL to stdout\n  $ search-hub export SESSION_ID --format json               # JSON to stdout\n  $ search-hub export SESSION_ID -q \"year:2023\"              # Filter by query\n  $ search-hub export SESSION_ID -q \"author:smith\" --format ids  # Filtered IDs\n  $ search-hub export SESSION_ID --format json -o results.json  # JSON to file\n  $ search-hub export SESSION_ID --format ids --id-type doi  # Export DOIs to stdout\n  $ search-hub export SESSION_ID --no-dedup  # Export without deduplication\n  $ search-hub export SESSION_ID --format jsonl | jq '.title'  # Pipe to jq\n\nQuery syntax:\n  Free text        diabetes             Search title and abstract\n  title:VALUE      title:learning       Title substring\n  abstract:VALUE   abstract:randomized  Abstract substring\n  author:VALUE     author:tanaka        Author name substring\n  journal:VALUE    journal:lancet       Journal name substring\n  year:VALUE       year:2023            Exact year\n  year:FROM-TO     year:2020-2024       Year range\n  doi:VALUE        doi:10.1001/xxx      DOI exact match\n  pmid:VALUE       pmid:12345678        PMID exact match\n  source:VALUE     source:pubmed        Provider exact match\n\n  Multiple terms: different fields = AND, same field = OR`)\n    .action(\n      async (\n        sessionId: string,\n        options?: {\n          format?: string;\n          output?: string;\n          idType?: string;\n          dedup?: boolean;\n          query?: string;\n        }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const exportOpts = parseExportOptions(sessionId, {\n            format: options?.format,\n            output: options?.output,\n            idType: options?.idType,\n          });\n\n          const validation = validateExportInput(exportOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load session\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Collect articles from result files\n          const articles = await loadSessionArticles(session, sessionId, sessionsDir);\n\n          // Deduplicate articles unless --no-dedup is set\n          const shouldDedup = options?.dedup !== false;\n          let exportArticles: typeof articles;\n          let duplicatesRemoved = 0;\n\n          if (shouldDedup) {\n            const dedupResult = deduplicateArticles(articles);\n            exportArticles = dedupResult.articles;\n            duplicatesRemoved = dedupResult.duplicatesRemoved;\n          } else {\n            exportArticles = articles;\n          }\n\n          // Apply -q filter\n          const preFilterCount = exportArticles.length;\n          let hasFilter = false;\n          if (options?.query) {\n            exportArticles = filterByQuery(exportArticles, options.query);\n            hasFilter = true;\n          }\n\n          // Format output\n          let output: string;\n          if (exportOpts.format === 'ids') {\n            output = formatIds(exportArticles, exportOpts.idType ?? 'all');\n          } else if (exportOpts.format === 'json') {\n            // Build per-database article counts\n            const databases: Record<string, number> = {};\n            for (const article of exportArticles) {\n              databases[article.source] = (databases[article.source] ?? 0) + 1;\n            }\n            const metadata: JsonExportMetadata = {\n              sessionId: session.id,\n              sessionName: session.name,\n              createdAt: session.createdAt,\n              databases,\n            };\n            output = formatJson(exportArticles, metadata);\n          } else if (exportOpts.format === 'csl-json') {\n            output = formatCslJson(exportArticles);\n          } else {\n            output = formatJsonl(exportArticles);\n          }\n\n          // Write to file or stdout\n          if (exportOpts.outputPath) {\n            await writeFile(exportOpts.outputPath, output, 'utf-8');\n            if (!globalOpts.quiet) {\n              let message: string;\n              if (hasFilter) {\n                message = `Exported ${exportArticles.length} articles (filtered from ${preFilterCount}) to ${exportOpts.outputPath}`;\n              } else {\n                message = `Exported ${exportArticles.length} articles to ${exportOpts.outputPath}`;\n              }\n              if (duplicatesRemoved > 0) {\n                message += ` (${duplicatesRemoved} duplicate${duplicatesRemoved === 1 ? '' : 's'} removed)`;\n              }\n              console.error(message);\n            }\n          } else {\n            process.stdout.write(output + '\\n');\n            if (!globalOpts.quiet) {\n              const parts: string[] = [];\n              if (hasFilter) {\n                parts.push(`filtered from ${preFilterCount} to ${exportArticles.length} articles`);\n              }\n              if (duplicatesRemoved > 0) {\n                parts.push(`${duplicatesRemoved} duplicate${duplicatesRemoved === 1 ? '' : 's'} removed`);\n              }\n              if (parts.length > 0) {\n                console.error(`(${parts.join(', ')})`);\n              }\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register summary command\n  program\n    .command('summary')\n    .description('Show statistical summary of session results')\n    .argument('<session-id>', 'session ID to summarize')\n    .option('--json', 'output as JSON')\n    .addHelpText('after', `\\nExamples:\n  $ search-hub summary 20240115_diabetes-ai_a3f2       # Human-readable summary\n  $ search-hub summary 20240115_diabetes-ai_a3f2 --json # JSON output`)\n    .action(\n      async (\n        sessionId: string,\n        options?: { json?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load session\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Collect articles from result files\n          const allArticles = await loadSessionArticles(session, sessionId, sessionsDir);\n\n          // Deduplicate\n          const dedupResult = deduplicateArticles(allArticles);\n\n          // Compute summary\n          const summary = computeSummary(allArticles, dedupResult.articles, {\n            sessionId,\n            sessionName: session.name,\n          });\n\n          // Format output\n          if (options?.json) {\n            console.log(formatSummaryJson(summary));\n          } else {\n            if (!globalOpts.quiet) {\n              console.log(formatSummary(summary));\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register results command\n  program\n    .command('results')\n    .description('List articles from a session with title, year, and journal')\n    .argument('<session-id>', 'session ID to list results from')\n    .option('--limit <n>', 'maximum number of results to show')\n    .option('--offset <n>', 'skip first n results')\n    .option('--json', 'output as JSON array')\n    .option('--fields <fields>', 'fields to display (comma-separated)')\n    .option('-q, --query <expr>', 'filter results with query expression')\n    .option('--abstract', 'show abstracts with results')\n    .option('--abstract-length <n>', 'maximum abstract length in characters (default: 300)')\n    .addHelpText('after', `\nExamples:\n  $ search-hub results SESSION_ID                              # List all articles\n  $ search-hub results SESSION_ID --limit 20                   # First 20 articles\n  $ search-hub results SESSION_ID -q \"diabetes\"                # Free text filter\n  $ search-hub results SESSION_ID -q \"author:smith year:2023\"  # Combined filter\n  $ search-hub results SESSION_ID -q \"doi:10.1001/xxx\"         # Exact ID match\n  $ search-hub results SESSION_ID --json                       # JSON output\n  $ search-hub results SESSION_ID -q \"source:pubmed\"           # Only PubMed\n  $ search-hub results SESSION_ID --abstract                   # Show abstracts\n\nQuery syntax:\n  Free text        diabetes             Search title and abstract\n  title:VALUE      title:learning       Title substring\n  abstract:VALUE   abstract:randomized  Abstract substring\n  author:VALUE     author:tanaka        Author name substring\n  journal:VALUE    journal:lancet       Journal name substring\n  year:VALUE       year:2023            Exact year\n  year:FROM-TO     year:2020-2024       Year range\n  doi:VALUE        doi:10.1001/xxx      DOI exact match\n  pmid:VALUE       pmid:12345678        PMID exact match\n  source:VALUE     source:pubmed        Provider exact match\n\n  Multiple terms: different fields = AND, same field = OR`)\n    .action(\n      async (\n        sessionId: string,\n        options?: {\n          limit?: string;\n          offset?: string;\n          json?: boolean;\n          fields?: string;\n          query?: string;\n          abstract?: boolean;\n          abstractLength?: string;\n        }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const resultsOpts = parseResultsOptions(sessionId, {\n            limit: options?.limit,\n            offset: options?.offset,\n            json: options?.json,\n            fields: options?.fields,\n            query: options?.query,\n            abstract: options?.abstract,\n            abstractLength: options?.abstractLength,\n          });\n\n          const validation = validateResultsInput(resultsOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load session\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Collect articles from result files\n          const articles = await loadSessionArticles(session, sessionId, sessionsDir);\n\n          // Deduplicate articles\n          const dedupResult = deduplicateArticles(articles);\n          let displayArticles = dedupResult.articles;\n\n          // Apply -q filter\n          let filteredFrom: number | undefined;\n          if (resultsOpts.query) {\n            const preFilterCount = displayArticles.length;\n            displayArticles = filterByQuery(displayArticles, resultsOpts.query);\n            if (displayArticles.length !== preFilterCount) {\n              filteredFrom = preFilterCount;\n            }\n          }\n\n          // Apply pagination\n          const total = displayArticles.length;\n          const offset = resultsOpts.offset ?? 0;\n          if (offset > 0) {\n            displayArticles = displayArticles.slice(offset);\n          }\n          if (resultsOpts.limit !== undefined && resultsOpts.limit > 0) {\n            displayArticles = displayArticles.slice(0, resultsOpts.limit);\n          }\n\n          // Format output\n          if (resultsOpts.json) {\n            console.log(formatResultsJson(displayArticles));\n          } else {\n            if (!globalOpts.quiet) {\n              console.log(formatResultsList(displayArticles, {\n                sessionId,\n                sessionName: session.name,\n                total,\n                offset,\n                filteredFrom,\n                showAbstract: resultsOpts.showAbstract,\n                abstractLength: resultsOpts.abstractLength,\n              }));\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register diff command\n  program\n    .command('diff')\n    .description('Compare results between two sessions')\n    .argument('<session-id-1>', 'first session ID')\n    .argument('<session-id-2>', 'second session ID')\n    .option('--show <section>', 'show only specific section: added, removed, or common')\n    .option('--json', 'output as JSON')\n    .option('--no-query-diff', 'hide query changes section')\n    .addHelpText('after', `\nExamples:\n  $ search-hub diff session-v1 session-v2                # Compare two sessions\n  $ search-hub diff session-v1 session-v2 --show added   # Show only added articles\n  $ search-hub diff session-v1 session-v2 --show removed # Show only removed articles\n  $ search-hub diff session-v1 session-v2 --json         # JSON output for scripting\n  $ search-hub diff session-v1 session-v2 --no-query-diff # Hide query changes\n\nQuery Refinement Workflow:\n  1. Search with broad query:    search-hub search v1.yaml --max-results 100\n  2. Create refined query:       cp v1.yaml v2.yaml && edit v2.yaml\n  3. Search with refined query:  search-hub search v2.yaml --max-results 100\n  4. Compare results:            search-hub diff <session-v1> <session-v2> --show removed\n  5. Review excluded articles to verify refinement quality`)\n    .action(\n      async (\n        sessionId1: string,\n        sessionId2: string,\n        options?: { show?: string; json?: boolean; queryDiff?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Validate --show option\n          const validShowValues: ShowFilter[] = ['added', 'removed', 'common'];\n          let showFilter: ShowFilter | undefined;\n          if (options?.show) {\n            if (!validShowValues.includes(options.show as ShowFilter)) {\n              if (!globalOpts.quiet) {\n                console.error(`Error: Invalid --show value: ${options.show}. Valid values are: ${validShowValues.join(', ')}`);\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n            showFilter = options.show as ShowFilter;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n          const noQueryDiff = options?.queryDiff === false;\n\n          // Load both sessions\n          let session1, session2;\n          try {\n            session1 = await loadSession(sessionId1, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error loading session 1: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          try {\n            session2 = await loadSession(sessionId2, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error loading session 2: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Collect articles from both sessions\n          const articles1 = await loadSessionArticles(session1, sessionId1, sessionsDir);\n          const articles2 = await loadSessionArticles(session2, sessionId2, sessionsDir);\n\n          // Deduplicate each session's articles before diffing\n          const dedup1 = deduplicateArticles(articles1);\n          const dedup2 = deduplicateArticles(articles2);\n\n          // Compute article diff\n          const diff = computeDiff(dedup1.articles, dedup2.articles);\n\n          // Load and compute query diff (unless disabled)\n          let queryDiff;\n          let showQueryDiffPlaceholder = false;\n          if (!noQueryDiff) {\n            const query1 = await loadSessionQuery(sessionId1, sessionsDir);\n            const query2 = await loadSessionQuery(sessionId2, sessionsDir);\n            if (query1 && query2) {\n              queryDiff = computeQueryDiff(query1, query2);\n            } else {\n              // At least one query is missing - show placeholder\n              showQueryDiffPlaceholder = true;\n            }\n          }\n\n          // Format and output\n          const formatOptions = { queryDiff, noQueryDiff, showQueryDiffPlaceholder };\n          if (options?.json) {\n            console.log(formatDiffJson(diff, sessionId1, sessionId2, showFilter, formatOptions));\n          } else {\n            if (!globalOpts.quiet) {\n              console.log(formatDiff(diff, sessionId1, sessionId2, showFilter, formatOptions));\n\n              // Show suggestions\n              const suggestion = formatSuggestion(getSuggestion({\n                command: 'diff',\n                sessionId: sessionId2,\n                diffSession1Id: sessionId1,\n                diffAddedCount: diff.added.length,\n                diffRemovedCount: diff.removed.length,\n              }));\n              if (suggestion) {\n                console.log(suggestion);\n              }\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register check command\n  program\n    .command('check')\n    .description('Verify coverage of known articles against session results')\n    .argument('<session-id>', 'session ID to check against')\n    .option('--file <path>', 'file with identifiers (one per line)')\n    .option('--doi <ids>', 'comma-separated DOIs to check')\n    .option('--pmid <ids>', 'comma-separated PMIDs to check')\n    .option('--json', 'output as JSON')\n    .option('--missing-only', 'show only missing identifiers')\n    .addHelpText('after', `\nExamples:\n  $ search-hub check SESSION --file known-dois.txt              # Check from file\n  $ search-hub check SESSION --doi \"10.1001/jama.2023.12345\"    # Check single DOI\n  $ search-hub check SESSION --pmid \"37654321,36543210\"         # Check PMIDs\n  $ search-hub check SESSION --file refs.txt --json             # JSON output\n  $ search-hub check SESSION --file refs.txt --missing-only     # Only missing\n\nInput file format (one identifier per line):\n  10.1001/jama.2023.12345          DOI (starts with \"10.\")\n  37654321                          PMID (numeric only)\n  DOI:10.1038/s41586-023-xxxxx    DOI (explicit prefix)\n  PMID:36543210                    PMID (explicit prefix)\n  arxiv:2301.12345                 arXiv ID (explicit prefix)\n  # comment                        Comments and empty lines ignored`)\n    .action(\n      async (\n        sessionId: string,\n        options?: { file?: string; doi?: string; pmid?: string; json?: boolean; missingOnly?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse identifiers from input sources\n          let identifiers;\n          let source: string;\n\n          if (options?.file) {\n            const filePath = expandPath(options.file);\n            let content: string;\n            try {\n              content = await readFile(filePath, 'utf-8');\n            } catch {\n              if (!globalOpts.quiet) {\n                console.error(`Error: File not found: ${filePath}`);\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n            try {\n              identifiers = parseIdentifierFile(content);\n            } catch (error) {\n              if (!globalOpts.quiet) {\n                console.error(`Error: ${error instanceof Error ? error.message : 'Failed to parse identifier file'}`);\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n            source = options.file;\n          } else if (options?.doi || options?.pmid) {\n            const lines: string[] = [];\n            if (options.doi) {\n              lines.push(...options.doi.split(',').map(d => d.trim()).filter(Boolean));\n            }\n            if (options.pmid) {\n              lines.push(...options.pmid.split(',').map(p => `PMID:${p.trim()}`).filter(Boolean));\n            }\n            identifiers = parseIdentifierFile(lines.join('\\n'));\n            source = 'command line';\n          } else {\n            if (!globalOpts.quiet) {\n              console.error('Error: Provide --file, --doi, or --pmid');\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n\n          if (identifiers.length === 0) {\n            if (!globalOpts.quiet) {\n              console.error('Error: No identifiers found in input');\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n\n          // Load session\n          const sessionsDir = await getSessionsDir(globalOpts);\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Load articles and check coverage\n          const articles = await loadSessionArticles(session, sessionId, sessionsDir);\n          const result = checkCoverage(articles, identifiers);\n\n          // Format output\n          if (options?.json) {\n            console.log(formatCheckResultJson(result, { sessionId, source }));\n          } else {\n            if (!globalOpts.quiet) {\n              console.log(formatCheckResult(result, {\n                sessionId,\n                source,\n                missingOnly: options?.missingOnly,\n              }));\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n        }\n      }\n    );\n\n  // Register merge command\n  program\n    .command('merge')\n    .description('Merge results from multiple search sessions')\n    .argument('<session-ids...>', 'two or more session IDs to merge')\n    .option('--name <string>', 'name for merged session')\n    .option('--dry-run', 'show what would be merged without creating session')\n    .option('--json', 'output as JSON')\n    .addHelpText('after', `\nExamples:\n  $ search-hub merge session-v4 session-v9                  # Merge two sessions\n  $ search-hub merge session-v4 session-v9 --name combined  # Merge with custom name\n  $ search-hub merge session-a session-b session-c          # Merge three sessions\n  $ search-hub merge session-v4 session-v9 --dry-run        # Preview merge`)\n    .action(\n      async (\n        sessionIds: string[],\n        options?: { name?: string; dryRun?: boolean; json?: boolean }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          if (sessionIds.length < 2) {\n            if (!globalOpts.quiet) {\n              console.error('Error: At least two session IDs are required for merge');\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load all source sessions\n          const sessions = new Map<string, ReturnType<typeof loadSession> extends Promise<infer T> ? T : never>();\n          for (const sessionId of sessionIds) {\n            try {\n              const session = await loadSession(sessionId, sessionsDir);\n              sessions.set(sessionId, session);\n            } catch (error) {\n              if (!globalOpts.quiet) {\n                console.error(\n                  `Error loading session '${sessionId}': ${error instanceof Error ? error.message : 'Failed to load session'}`\n                );\n              }\n              process.exitCode = EXIT_CODES.SESSION_ERROR;\n              return;\n            }\n          }\n\n          // Validate sources\n          const validation = validateMergeSources(sessions);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Load articles from all sessions\n          const sessionArticles = new Map<string, Awaited<ReturnType<typeof loadSessionArticles>>>();\n          for (const [sessionId, session] of sessions) {\n            const articles = await loadSessionArticles(session, sessionId, sessionsDir);\n            sessionArticles.set(sessionId, articles);\n          }\n\n          // Merge articles\n          const mergeResult = mergeArticles(sessionArticles);\n\n          // Build output data\n          const sources = [...sessions.entries()].map(([id, session]) => ({\n            id,\n            name: session.name,\n            count: mergeResult.perSession.get(id) ?? 0,\n          }));\n\n          const byProviderCounts = new Map<string, number>();\n          for (const [provider, articles] of mergeResult.byProvider) {\n            byProviderCounts.set(provider, articles.length);\n          }\n\n          // Auto-generate name if not provided\n          const firstSession = sessions.values().next().value;\n          const mergeName = options?.name ?? (firstSession ? firstSession.name + '-merged' : 'merged');\n\n          if (options?.dryRun) {\n            // Dry run - show preview without creating session\n            const outputData = {\n              sessionId: '(dry-run)',\n              totalBefore: mergeResult.totalBefore,\n              totalAfter: mergeResult.totalAfter,\n              duplicatesRemoved: mergeResult.duplicatesRemoved,\n              sources,\n              byProvider: byProviderCounts,\n            };\n            if (options.json) {\n              console.log(formatSessionMergeJson(outputData));\n            } else if (!globalOpts.quiet) {\n              console.log(formatSessionMergeOutput(outputData));\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n            return;\n          }\n\n          // Create merged session\n          const sessionSources = [...sessions.entries()].map(([id, session]) => ({\n            id,\n            name: session.name,\n          }));\n\n          const mergedSession = await createMergedSession({\n            name: mergeName,\n            sources: sessionSources,\n            byProvider: mergeResult.byProvider,\n            totalRetrieved: mergeResult.totalAfter,\n            sessionsDir,\n            sourceSessionIds: sessionIds,\n          });\n\n          // Format output\n          const outputData = {\n            sessionId: mergedSession.id,\n            totalBefore: mergeResult.totalBefore,\n            totalAfter: mergeResult.totalAfter,\n            duplicatesRemoved: mergeResult.duplicatesRemoved,\n            sources,\n            byProvider: byProviderCounts,\n          };\n\n          if (options?.json) {\n            console.log(formatSessionMergeJson(outputData));\n          } else if (!globalOpts.quiet) {\n            console.log(formatSessionMergeOutput(outputData));\n\n            // Show suggestions\n            const suggestion = getSuggestion({\n              command: 'merge',\n              sessionId: mergedSession.id,\n            });\n            const suggestionText = formatSuggestion(suggestion);\n            if (suggestionText) {\n              console.log(suggestionText);\n            }\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register register command\n  program\n    .command('register')\n    .description('Register results with reference-manager')\n    .argument('<session-id>', 'session ID to register')\n    .option('--db <providers>', 'register only specific database(s)')\n    .option('--dry-run', 'show what would be registered without executing', false)\n    .option('--with-abstracts', 'also update abstracts via ref update', false)\n    .option('--reviewed', 'register only articles with finalDecision=include', false)\n    .option('--all', 'register all articles (ignore reviews)', false)\n    .option('--force', 'skip confirmation prompts', false)\n    .option('--no-attach-fulltext', 'skip automatic fulltext attachment')\n    .addHelpText('after', `\nExamples:\n  $ search-hub register SESSION_ID                # Register all results\n  $ search-hub register SESSION_ID --with-abstracts\n  $ search-hub register SESSION_ID --dry-run      # Preview only\n  $ search-hub register SESSION_ID --no-attach-fulltext  # Skip fulltext attachment\n\nWith review workflow:\n  $ search-hub register SESSION_ID --reviewed     # Register only included articles\n  $ search-hub register SESSION_ID --all          # Register all (ignore reviews)`)\n    .action(\n      async (\n        sessionId: string,\n        options?: {\n          db?: string;\n          dryRun?: boolean;\n          withAbstracts?: boolean;\n          reviewed?: boolean;\n          all?: boolean;\n          force?: boolean;\n          attachFulltext?: boolean;\n        }\n      ) => {\n        const globalOpts = program.opts() as GlobalOptions;\n        try {\n          // Parse and validate options\n          const registerOpts = parseRegisterOptions(sessionId, {\n            db: options?.db,\n            dryRun: options?.dryRun,\n            withAbstracts: options?.withAbstracts,\n            reviewed: options?.reviewed,\n            all: options?.all,\n            force: options?.force,\n          });\n\n          const validation = validateRegisterInput(registerOpts);\n          if (!validation.valid) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: ${validation.error}`);\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Check if ref command is available\n          const refAvailable = await checkRefAvailable();\n          if (!refAvailable && !registerOpts.dryRun) {\n            if (!globalOpts.quiet) {\n              console.error('Error: reference-manager (ref) command not found.\\n');\n              console.error('reference-manager is required to register search results.');\n              console.error('Would you like to install it now? (npm i -g @ncukondo/reference-manager) [Y/n]: ');\n            }\n\n            // For non-interactive mode, suggest installation\n            const npmAvailable = await checkNpmAvailable();\n            if (!npmAvailable) {\n              if (!globalOpts.quiet) {\n                console.error('\\nError: npm command not found.');\n                console.error('Please install Node.js first: https://nodejs.org/');\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n\n            // Try to install\n            try {\n              if (!globalOpts.quiet) {\n                console.log('\\nInstalling reference-manager...');\n              }\n              await installRefManager();\n              if (!globalOpts.quiet) {\n                console.log('✓ reference-manager installed successfully.\\n');\n              }\n            } catch (installError) {\n              if (!globalOpts.quiet) {\n                console.error(\n                  `\\nFailed to install reference-manager: ${installError instanceof Error ? installError.message : 'Unknown error'}`\n                );\n              }\n              process.exitCode = EXIT_CODES.GENERAL_ERROR;\n              return;\n            }\n          }\n\n          const sessionsDir = await getSessionsDir(globalOpts);\n\n          // Load session\n          let session;\n          try {\n            session = await loadSession(sessionId, sessionsDir);\n          } catch (error) {\n            if (!globalOpts.quiet) {\n              console.error(\n                `Error: ${error instanceof Error ? error.message : 'Failed to load session'}`\n              );\n            }\n            process.exitCode = EXIT_CODES.SESSION_ERROR;\n            return;\n          }\n\n          // Check for review file and handle --reviewed/--all flags\n          const reviewExists = await hasReviewFile(sessionId, sessionsDir);\n          let articles: import('../providers/base/types.js').Article[];\n\n          if (registerOpts.reviewed) {\n            // --reviewed: only include reviewed articles\n            if (!reviewExists) {\n              if (!globalOpts.quiet) {\n                console.error('Error: No reviews.yaml found for this session.');\n                console.error('Run \"search-hub review init --session ' + sessionId + '\" first.');\n              }\n              process.exitCode = EXIT_CODES.SESSION_ERROR;\n              return;\n            }\n\n            const summary = await getReviewSummary(sessionId, sessionsDir);\n            if (summary.included === 0) {\n              if (!globalOpts.quiet) {\n                console.error(formatNoIncludedArticlesError(summary, sessionId));\n              }\n              process.exitCode = EXIT_CODES.SESSION_ERROR;\n              return;\n            }\n\n            // Warn about pending articles (unless --force or --dry-run)\n            if (summary.pending > 0 && !registerOpts.force && !registerOpts.dryRun) {\n              if (!globalOpts.quiet) {\n                console.log(formatPendingWarning(summary));\n              }\n              // Wait for user confirmation\n              const confirmed = await confirmPrompt();\n              if (!confirmed) {\n                process.exitCode = EXIT_CODES.SUCCESS;\n                return;\n              }\n            }\n\n            articles = await getIncludedArticles(sessionId, sessionsDir);\n          } else if (reviewExists && !registerOpts.all) {\n            // reviews.yaml exists but no flag specified\n            const summary = await getReviewSummary(sessionId, sessionsDir);\n            if (!globalOpts.quiet) {\n              console.log(formatReviewRequiredMessage(summary, sessionId));\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          } else {\n            // --all or no reviews.yaml: collect all articles from result files\n            if (reviewExists && !globalOpts.quiet) {\n              const summary = await getReviewSummary(sessionId, sessionsDir);\n              console.log(formatIgnoringReviewsNote(summary.total));\n            }\n            articles = await loadSessionArticles(session, sessionId, sessionsDir, registerOpts.providers);\n          }\n\n          // Dry run mode\n          if (registerOpts.dryRun) {\n            if (!globalOpts.quiet) {\n              console.log(formatRegisterDryRunOutput(articles));\n            }\n            process.exitCode = EXIT_CODES.SUCCESS;\n            return;\n          }\n\n          // Register articles\n          if (!globalOpts.quiet) {\n            console.log(`Registering ${articles.length} references to reference-manager...`);\n          }\n\n          const sessionDir = join(sessionsDir, sessionId);\n          const registerOptions: import('../integration/register.js').RegisterOptions = {\n            sessionId,\n            sessionDir,\n            withAbstracts: registerOpts.withAbstracts,\n            ...(options?.attachFulltext === false ? { noAttachFulltext: true } : {}),\n          };\n          if (!globalOpts.quiet) {\n            registerOptions.onProgress = (current, total) => {\n              process.stdout.write(`\\rProgress: ${current}/${total}`);\n            };\n          }\n          const record = await registerArticles(articles, registerOptions);\n\n          // Save registration record\n          await saveRegistrationRecord(sessionDir, record);\n\n          if (!globalOpts.quiet) {\n            console.log('\\n');\n            console.log(formatRegistrationSummary(record.summary));\n\n            // Show fulltext attach summary\n            if (record.fulltext) {\n              const ft = record.fulltext.summary;\n              console.log('\\nFulltext attachment results:');\n              if (ft.attached > 0) {\n                const totalFiles = record.fulltext.attached.reduce((sum, a) => sum + a.files.length, 0);\n                console.log(`  ✓ ${ft.attached} articles attached (${totalFiles} files)`);\n              }\n              if (ft.skipped > 0) {\n                console.log(`  ⚠ ${ft.skipped} skipped`);\n              }\n              if (ft.failed > 0) {\n                console.log(`  ✗ ${ft.failed} failed`);\n              }\n            }\n\n            console.log(`\\nResults saved to: ${join(sessionDir, 'registration.json')}`);\n\n            // Show next step suggestions\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'register',\n              sessionId,\n              hasReviews: reviewExists,\n            }));\n            if (suggestion) console.log(suggestion);\n          }\n\n          process.exitCode = EXIT_CODES.SUCCESS;\n        } catch (error) {\n          if (!globalOpts.quiet) {\n            console.error(\n              'Error:',\n              error instanceof Error ? error.message : error\n            );\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n        }\n      }\n    );\n\n  // Register review command group\n  const reviewCommand = program\n    .command('review')\n    .description('Article review workflow for systematic literature review')\n    .addHelpText('after', `\nExamples:\n  $ search-hub review init --session SESSION_ID           # Initialize reviews.yaml\n  $ search-hub review status --session SESSION_ID         # Show review progress\n  $ search-hub review list --session SESSION_ID --filter pending  # List articles\n  $ search-hub review extract --session SESSION_ID --name title-screening  # Extract for review\n  $ search-hub review merge --session SESSION_ID --name title-screening   # Merge reviews\n  $ search-hub review export --session SESSION_ID --only included -o included.yaml`);\n\n  reviewCommand\n    .command('init')\n    .description('Generate reviews.yaml from deduplicated search results')\n    .requiredOption('--session <id>', 'session ID')\n    .option('-f, --force', 'overwrite existing reviews.yaml', false)\n    .action(async (options: { session: string; force: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const initOptions: ReviewInitOptions = {\n          sessionId: options.session,\n          ...(options.force && { force: options.force }),\n        };\n        const result = await executeReviewInit(initOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(`Created ${result.reviewsPath}`);\n          console.log(`  Articles: ${result.articleCount}`);\n          if (result.duplicatesRemoved > 0) {\n            console.log(`  Duplicates removed: ${result.duplicatesRemoved}`);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('status')\n    .description('Show review progress summary')\n    .requiredOption('--session <id>', 'session ID')\n    .option('--json', 'output as JSON')\n    .action(async (options: { session: string; json?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const statusOptions: ReviewStatusOptions = {\n          sessionId: options.session,\n        };\n        const result = await executeReviewStatus(statusOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          if (options.json) {\n            console.log(JSON.stringify(result, null, 2));\n          } else {\n            console.log(formatStatusOutput(result));\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'review status',\n              sessionId: options.session,\n              reviewStatus: result,\n            }));\n            if (suggestion) console.log(suggestion);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('list')\n    .description('List articles with optional filtering')\n    .requiredOption('--session <id>', 'session ID')\n    .option('--filter <type>', 'filter by status: pending, incomplete, uncertain, agreed-include, agreed-exclude, conflicting, finalized, all', 'all')\n    .option('--json', 'output as JSON')\n    .action(async (options: { session: string; filter?: string; json?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const validFilters: ListFilter[] = ['pending', 'incomplete', 'uncertain', 'agreed-include', 'agreed-exclude', 'conflicting', 'finalized', 'all'];\n        const filter = (options.filter ?? 'all') as ListFilter;\n        if (!validFilters.includes(filter)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid filter '${options.filter}'. Valid values: ${validFilters.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const listOptions: ReviewListOptions = {\n          sessionId: options.session,\n          filter,\n        };\n        const result = await executeReviewList(listOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          if (options.json) {\n            console.log(JSON.stringify(result, null, 2));\n          } else {\n            console.log(formatListOutput(result));\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('extract')\n    .description('Extract subset to for-review/<name>/review.yaml for distributed review')\n    .requiredOption('--session <id>', 'session ID')\n    .requiredOption('--name <name>', 'name for the review subset (output: for-review/<name>/review.yaml)')\n    .option('--filter <types>', 'filter by status (comma-separated): pending, incomplete, uncertain, agreed-include, agreed-exclude, conflicting, finalized')\n    .option('--sort <method>', 'sort method: year, title, random, none', 'none')\n    .option('--limit <n>', 'limit number of articles')\n    .option('--offset <n>', 'skip first n articles')\n    .option('--seed <n>', 'random seed for reproducible sorting')\n    .option('--basis <type>', 'basis for review: title, abstract, or fulltext')\n    .option('--reviewer <id>', 'reviewer identifier (e.g., \"ai:claude\")')\n    .option('--finalize', 'extract for final decision (includes reviewHistory and finalDecision)')\n    .action(async (options: {\n      session: string;\n      name: string;\n      filter?: string;\n      sort?: string;\n      limit?: string;\n      offset?: string;\n      seed?: string;\n      basis?: string;\n      reviewer?: string;\n      finalize?: boolean;\n    }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const validSorts: SortOption[] = ['year', 'title', 'random', 'none'];\n        const sort = (options.sort ?? 'none') as SortOption;\n        if (!validSorts.includes(sort)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid sort '${options.sort}'. Valid values: ${validSorts.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const extractOptions: ReviewExtractOptions = {\n          sessionId: options.session,\n          name: options.name,\n          sort,\n        };\n\n        if (options.filter) {\n          extractOptions.filter = options.filter.split(',').map(s => s.trim()) as ReviewStatus[];\n        }\n        if (options.limit) {\n          extractOptions.limit = parseInt(options.limit, 10);\n        }\n        if (options.offset) {\n          extractOptions.offset = parseInt(options.offset, 10);\n        }\n        if (options.seed) {\n          extractOptions.seed = parseInt(options.seed, 10);\n        }\n\n        // Reviewer is required for all extract modes\n        if (!options.reviewer) {\n          if (!globalOpts.quiet) {\n            console.error('Error: --reviewer is required');\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n        extractOptions.reviewer = options.reviewer;\n\n        // Handle basis option\n        if (options.basis) {\n          const validBasis = ['title', 'abstract', 'fulltext'];\n          if (!validBasis.includes(options.basis)) {\n            if (!globalOpts.quiet) {\n              console.error(`Error: Invalid basis '${options.basis}'. Valid values: ${validBasis.join(', ')}`);\n            }\n            process.exitCode = EXIT_CODES.GENERAL_ERROR;\n            return;\n          }\n          extractOptions.basis = options.basis as 'title' | 'abstract' | 'fulltext';\n        }\n\n        if (options.finalize) {\n          extractOptions.finalize = true;\n        }\n\n        const result = await executeReviewExtract(extractOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(`Extracted ${result.extractedCount} of ${result.totalMatching} articles to ${result.outputPath}`);\n          const suggestion = formatSuggestion(getSuggestion({\n            command: 'review extract',\n            sessionId: options.session,\n            extractName: options.name,\n            extractedCount: result.extractedCount,\n            totalMatching: result.totalMatching,\n            extractLimit: extractOptions.limit,\n            extractOffset: extractOptions.offset,\n          }));\n          if (suggestion) console.log(suggestion);\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('merge')\n    .description('Merge edited file back into main reviews.yaml')\n    .requiredOption('--session <id>', 'session ID')\n    .requiredOption('--name <name>', 'name of the review subset to merge (reads from for-review/<name>/review.yaml)')\n    .option('--dry-run', 'show changes without applying', false)\n    .action(async (options: { session: string; name: string; dryRun: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const mergeOptions: ReviewMergeOptions = {\n          sessionId: options.session,\n          name: options.name,\n          ...(options.dryRun && { dryRun: options.dryRun }),\n        };\n        const result = await executeReviewMerge(mergeOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(formatMergeOutput(result, options.dryRun));\n          if (!options.dryRun) {\n            const statusResult = await executeReviewStatus({ sessionId: options.session }, sessionsDir);\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'review merge',\n              sessionId: options.session,\n              reviewStatus: statusResult,\n            }));\n            if (suggestion) console.log(suggestion);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('mark')\n    .description('Mark decisions in work files')\n    .requiredOption('--file <path>', 'path to work file')\n    .option('--id <id>', 'article ID to mark')\n    .option('--decision <decision>', 'decision: include, exclude, or uncertain')\n    .option('--comment <text>', 'optional comment')\n    .action(async (options: {\n      file: string;\n      id?: string;\n      decision?: string;\n      comment?: string;\n    }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        // Validate decision if provided\n        const validDecisions = ['include', 'exclude', 'uncertain'];\n        if (options.decision && !validDecisions.includes(options.decision)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid decision '${options.decision}'. Valid values: ${validDecisions.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        // Validate required options\n        if (!options.id || !options.decision) {\n          if (!globalOpts.quiet) {\n            console.error('Error: --id and --decision must be specified');\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const markOptions: ReviewMarkOptions = {\n          file: options.file,\n          id: options.id,\n          decision: options.decision as 'include' | 'exclude' | 'uncertain',\n        };\n\n        if (options.comment) markOptions.comment = options.comment;\n\n        const result = await executeReviewMark(markOptions);\n        if (!globalOpts.quiet) {\n          console.log(`Marked ${result.marked} article(s)`);\n          for (const warning of result.warnings) {\n            console.warn(`Warning: ${warning}`);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('export')\n    .description('Export articles based on final decision')\n    .requiredOption('--session <id>', 'session ID')\n    .requiredOption('--only <filter>', 'export filter: included or excluded')\n    .requiredOption('-o, --output <path>', 'output file path')\n    .option('--format <fmt>', 'output format: yaml, json, jsonl', 'yaml')\n    .action(async (options: {\n      session: string;\n      only: string;\n      output: string;\n      format?: string;\n    }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const validOnlyValues: ReviewExportFilter[] = ['included', 'excluded'];\n        const only = options.only as ReviewExportFilter;\n        if (!validOnlyValues.includes(only)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid --only value '${options.only}'. Valid values: ${validOnlyValues.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const validFormats: ReviewExportFormat[] = ['yaml', 'json', 'jsonl'];\n        const format = (options.format ?? 'yaml') as ReviewExportFormat;\n        if (!validFormats.includes(format)) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: Invalid format '${options.format}'. Valid values: ${validFormats.join(', ')}`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const exportOptions: ReviewExportOptions = {\n          sessionId: options.session,\n          only,\n          output: options.output,\n          format,\n        };\n        const result = await executeReviewExport(exportOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(formatExportOutput(result));\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  reviewCommand\n    .command('finalize')\n    .description('Auto-set finalDecision for articles with reviewer consensus')\n    .requiredOption('--session <id>', 'session ID')\n    .option('--dry-run', 'preview without changes', false)\n    .option('--min-reviewers <n>', 'minimum agreeing reviewers needed', '1')\n    .option('--decision <type>', 'only finalize this decision type (include or exclude)')\n    .action(async (options: { session: string; dryRun: boolean; minReviewers: string; decision?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        if (options.decision && options.decision !== 'include' && options.decision !== 'exclude') {\n          if (!globalOpts.quiet) {\n            console.error(`Error: --decision must be \"include\" or \"exclude\", got \"${options.decision}\"`);\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n        const finalizeOptions: ReviewFinalizeOptions = {\n          sessionId: options.session,\n          ...(options.dryRun && { dryRun: options.dryRun }),\n          ...(options.decision && { decision: options.decision as 'include' | 'exclude' }),\n        };\n        const minReviewers = parseInt(options.minReviewers, 10);\n        if (!Number.isNaN(minReviewers) && minReviewers > 1) {\n          finalizeOptions.minReviewers = minReviewers;\n        }\n        const result = await executeReviewFinalize(finalizeOptions, sessionsDir);\n        if (!globalOpts.quiet) {\n          console.log(formatFinalizeOutput(result, {\n            dryRun: options.dryRun,\n            ...(finalizeOptions.decision && { decision: finalizeOptions.decision }),\n          }));\n          if (!options.dryRun) {\n            const statusResult = await executeReviewStatus({ sessionId: options.session }, sessionsDir);\n            const suggestion = formatSuggestion(getSuggestion({\n              command: 'review finalize',\n              sessionId: options.session,\n              reviewStatus: statusResult,\n            }));\n            if (suggestion) console.log(suggestion);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  // Register notes command group\n  const notesCommand = program\n    .command('notes')\n    .description('Manage session notes and assessments')\n    .addHelpText('after', `\nExamples:\n  $ search-hub notes list SESSION_ID             # List notes for a session\n  $ search-hub notes add SESSION_ID \"my note\"    # Add a note\n  $ search-hub notes add SESSION_ID --file assessment.md  # Add from file\n  $ search-hub notes assess SESSION_ID --precision \"~54%\" --verdict good --comment \"Good results\"\n  $ search-hub notes list --all                  # Show notes from all sessions`);\n\n  notesCommand\n    .command('list')\n    .description('List notes for a session or all sessions')\n    .argument('[session-id]', 'session ID')\n    .option('--all', 'show notes from all sessions')\n    .option('--json', 'output as JSON')\n    .action(async (sessionId?: string, options?: { all?: boolean; json?: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const formatOpts = { json: options?.json ?? false };\n\n        if (options?.all) {\n          // Cross-session notes view\n          const summaries = await listSessions(sessionsDir);\n          const allNotes: SessionNotes[] = [];\n\n          for (const summary of summaries) {\n            const sessionNotesDir = join(sessionsDir, summary.id);\n            const notes = await loadNotes(sessionNotesDir);\n            allNotes.push({\n              sessionId: summary.id,\n              sessionName: summary.name,\n              notes,\n            });\n          }\n\n          if (!globalOpts.quiet) {\n            console.log(formatAllSessionNotes(allNotes, formatOpts));\n          }\n          process.exitCode = EXIT_CODES.SUCCESS;\n          return;\n        }\n\n        if (!sessionId) {\n          if (!globalOpts.quiet) {\n            console.error('Error: session-id is required (or use --all)');\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        if (!(await sessionExists(sessionId, sessionsDir))) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: session '${sessionId}' not found`);\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        // List notes for a specific session\n        const sessionDir = join(sessionsDir, sessionId);\n        const notes = await loadNotes(sessionDir);\n        if (!globalOpts.quiet) {\n          console.log(formatNotesList(notes, formatOpts));\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  notesCommand\n    .command('add')\n    .description('Add a note to a session')\n    .argument('<session-id>', 'session ID')\n    .argument('[text]', 'note text')\n    .option('--file <path>', 'read note text from a file instead')\n    .action(async (sessionId: string, text?: string, options?: { file?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const sessionDir = join(sessionsDir, sessionId);\n\n        if (!(await sessionExists(sessionId, sessionsDir))) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: session '${sessionId}' not found`);\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        let noteText: string;\n        if (options?.file) {\n          noteText = (await readFile(options.file, 'utf-8')).trim();\n        } else if (text) {\n          noteText = text;\n        } else {\n          if (!globalOpts.quiet) {\n            console.error('Error: note text or --file is required');\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        await addNote(sessionDir, noteText);\n\n        if (!globalOpts.quiet) {\n          console.log('Note added.');\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  notesCommand\n    .command('assess')\n    .description('Add a structured assessment to a session')\n    .argument('<session-id>', 'session ID')\n    .option('--precision <value>', 'estimated precision (e.g., \"~54%\", \"15/28\")')\n    .option('--verdict <value>', 'quality judgment: good, refine, reject')\n    .option('--comment <text>', 'free text explanation')\n    .action(async (sessionId: string, options?: { precision?: string; verdict?: string; comment?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        if (!options?.precision && !options?.verdict && !options?.comment) {\n          if (!globalOpts.quiet) {\n            console.error('Error: at least one of --precision, --verdict, or --comment is required');\n          }\n          process.exitCode = EXIT_CODES.GENERAL_ERROR;\n          return;\n        }\n\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const sessionDir = join(sessionsDir, sessionId);\n\n        if (!(await sessionExists(sessionId, sessionsDir))) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: session '${sessionId}' not found`);\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        await addAssessment(sessionDir, {\n          precision: options?.precision,\n          verdict: options?.verdict,\n          comment: options?.comment,\n        });\n\n        if (!globalOpts.quiet) {\n          console.log('Assessment added.');\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  // Register fulltext command group (init, sync, convert, check)\n  registerFulltextCommands(program, getSessionsDir);\n\n  return program;\n}\n\n/**\n * Main entry point for CLI execution.\n */\nexport async function main(): Promise<void> {\n  const program = createProgram();\n  await program.parseAsync(process.argv);\n}\n\n// Run main if executed directly\nconst currentFile = fileURLToPath(import.meta.url);\nconst executedFile = process.argv[1];\nif (executedFile) {\n  if (realpathSync(executedFile) === realpathSync(currentFile)) {\n    main().catch((error) => {\n      console.error('Fatal error:', error);\n      process.exit(EXIT_CODES.GENERAL_ERROR);\n    });\n  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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ncukondo/search-hub",
-  "version": "0.16.0",
+  "version": "0.17.0",
   "description": "A CLI tool for systematic literature searching across multiple academic databases",
   "type": "module",
   "engines": {