@ncukondo/search-hub 0.12.1 → 0.13.0

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 \"..\": \"${name}\"`);\n  }\n}\n\n/**\n * Execute review extract command\n */\nexport async function executeReviewExtract(\n  options: ReviewExtractOptions,\n  sessionsDir: string\n): Promise<ReviewExtractResult> {\n  validateName(options.name);\n\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const outputPath = join(sessionDir, 'for-review', options.name, 'review.yaml');\n  const reviewFile = await loadReviewFile(sessionDir);\n\n  // Filter articles by status\n  const reviewers = reviewFile.reviewers;\n  let filtered: ArticleEntry[];\n  if (options.filter && options.filter.length > 0) {\n    filtered = reviewFile.articles.filter((article) => {\n      const status = classifyStatus(article, reviewers);\n      return options.filter!.includes(status);\n    });\n  } else {\n    filtered = [...reviewFile.articles];\n  }\n\n  const totalMatching = filtered.length;\n\n  // Sort articles\n  const sorted = sortArticles(filtered, options.sort ?? 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yamlWithComments = yamlContent.replace(\n      /^(\\s*-?\\s*)decision: uncertain$/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  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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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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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package/dist/cli/commands/review/finalize.d.ts.map

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

@@ -48,8 +48,7 @@ async function executeReviewFinalize(options, sessionsDir) {
   }
   if (!options.dryRun) {
     const yamlContent = stringify(reviewFile, { lineWidth: 0 });
-    const schemaPath = "../../../../.search-hub/schemas/review.schema.json";
-    const schemaComment = `# yaml-language-server: $schema=${schemaPath}
+    const schemaComment = `# yaml-language-server: $schema=./review.schema.json
 `;
     await writeFile(reviewsPath, schemaComment + yamlContent, "utf-8");
   }

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

@@ -1 +1 @@
-{"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}\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 minimum reviewer count\n      const reviews = article.reviews ?? [];\n      const uniqueReviewers = new Set(reviews.map((r) => r.reviewer));\n      if (uniqueReviewers.size < minReviewers) {\n        result.skippedByStatus[status]++;\n        continue;\n      }\n\n      if (!options.dryRun) {\n        article.finalDecision = status === 'agreed-include' ? 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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}\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 minimum reviewer count\n      const reviews = article.reviews ?? [];\n      const uniqueReviewers = new Set(reviews.map((r) => r.reviewer));\n      if (uniqueReviewers.size < minReviewers) {\n        result.skippedByStatus[status]++;\n        continue;\n      }\n\n      if (!options.dryRun) {\n        article.finalDecision = status === 'agreed-include' ? 'include' : 'exclude';\n      }\n\n      if (status === 'agreed-include') {\n        result.includedCount++;\n      } else {\n        result.excludedCount++;\n      }\n    } else {\n      result.skippedByStatus[status]++;\n    }\n  }\n\n  // Write back if not dry-run\n  if (!options.dryRun) {\n    const yamlContent = stringifyYaml(reviewFile, { lineWidth: 0 });\n    const schemaComment = `# yaml-language-server: $schema=./review.schema.json\\n`;\n    await writeFile(reviewsPath, schemaComment + yamlContent, 'utf-8');\n  }\n\n  return result;\n}\n\n/**\n * Format finalize result as human-readable string\n */\nexport function formatFinalizeOutput(\n  result: ReviewFinalizeResult,\n  options?: { dryRun?: boolean }\n): string {\n  const lines: string[] = [];\n\n  if (options?.dryRun) {\n    lines.push('Dry run - no changes made');\n    lines.push('');\n  }\n\n  const total = result.includedCount + result.excludedCount;\n  lines.push(`Finalized ${total} articles (${result.includedCount} include, ${result.excludedCount} exclude)`);\n\n  // Build skipped summary (only non-zero, non-agreed statuses)\n  const skippedParts: string[] = [];\n  if (result.skippedByStatus.pending > 0) {\n    skippedParts.push(`${result.skippedByStatus.pending} pending`);\n  }\n  if (result.skippedByStatus.incomplete > 0) {\n    skippedParts.push(`${result.skippedByStatus.incomplete} incomplete`);\n  }\n  if (result.skippedByStatus.uncertain > 0) {\n    skippedParts.push(`${result.skippedByStatus.uncertain} uncertain`);\n  }\n  if (result.skippedByStatus.conflicting > 0) {\n    skippedParts.push(`${result.skippedByStatus.conflicting} conflicting`);\n  }\n\n  if (skippedParts.length > 0) {\n    lines.push(`Skipped: ${skippedParts.join(', ')}`);\n  }\n\n  return lines.join('\\n');\n}\n"],"names":["parseYaml","stringifyYaml"],"mappings":";;;;AAqBA,SAAS,6BAA2D;AAClE,SAAO;AAAA,IACL,SAAS;AAAA,IACT,YAAY;AAAA,IACZ,WAAW;AAAA,IACX,kBAAkB;AAAA,IAClB,kBAAkB;AAAA,IAClB,aAAa;AAAA,IACb,WAAW;AAAA,EAAA;AAEf;AAKA,eAAsB,sBACpB,SACA,aAC+B;AAC/B,QAAM,aAAa,KAAK,aAAa,QAAQ,SAAS;AACtD,QAAM,cAAc,KAAK,YAAY,aAAa,cAAc;AAChE,QAAM,UAAU,MAAM,SAAS,aAAa,OAAO;AACnD,QAAM,aAAaA,MAAU,OAAO;AAEpC,QAAM,YAAY,WAAW,aAAa,CAAA;AAC1C,QAAM,eAAe,QAAQ,gBAAgB;AAE7C,QAAM,SAA+B;AAAA,IACnC,eAAe;AAAA,IACf,eAAe;AAAA,IACf,iBAAiB,2BAAA;AAAA,EAA2B;AAG9C,aAAW,WAAW,WAAW,UAAU;AACzC,UAAM,SAAS,eAAe,SAAS,SAAS;AAEhD,QAAI,WAAW,oBAAoB,WAAW,kBAAkB;AAE9D,YAAM,UAAU,QAAQ,WAAW,CAAA;AACnC,YAAM,kBAAkB,IAAI,IAAI,QAAQ,IAAI,CAAC,MAAM,EAAE,QAAQ,CAAC;AAC9D,UAAI,gBAAgB,OAAO,cAAc;AACvC,eAAO,gBAAgB,MAAM;AAC7B;AAAA,MACF;AAEA,UAAI,CAAC,QAAQ,QAAQ;AACnB,gBAAQ,gBAAgB,WAAW,mBAAmB,YAAY;AAAA,MACpE;AAEA,UAAI,WAAW,kBAAkB;AAC/B,eAAO;AAAA,MACT,OAAO;AACL,eAAO;AAAA,MACT;AAAA,IACF,OAAO;AACL,aAAO,gBAAgB,MAAM;AAAA,IAC/B;AAAA,EACF;AAGA,MAAI,CAAC,QAAQ,QAAQ;AACnB,UAAM,cAAcC,UAAc,YAAY,EAAE,WAAW,GAAG;AAC9D,UAAM,gBAAgB;AAAA;AACtB,UAAM,UAAU,aAAa,gBAAgB,aAAa,OAAO;AAAA,EACnE;AAEA,SAAO;AACT;AAKO,SAAS,qBACd,QACA,SACQ;AACR,QAAM,QAAkB,CAAA;AAExB,MAAI,SAAS,QAAQ;AACnB,UAAM,KAAK,2BAA2B;AACtC,UAAM,KAAK,EAAE;AAAA,EACf;AAEA,QAAM,QAAQ,OAAO,gBAAgB,OAAO;AAC5C,QAAM,KAAK,aAAa,KAAK,cAAc,OAAO,aAAa,aAAa,OAAO,aAAa,WAAW;AAG3G,QAAM,eAAyB,CAAA;AAC/B,MAAI,OAAO,gBAAgB,UAAU,GAAG;AACtC,iBAAa,KAAK,GAAG,OAAO,gBAAgB,OAAO,UAAU;AAAA,EAC/D;AACA,MAAI,OAAO,gBAAgB,aAAa,GAAG;AACzC,iBAAa,KAAK,GAAG,OAAO,gBAAgB,UAAU,aAAa;AAAA,EACrE;AACA,MAAI,OAAO,gBAAgB,YAAY,GAAG;AACxC,iBAAa,KAAK,GAAG,OAAO,gBAAgB,SAAS,YAAY;AAAA,EACnE;AACA,MAAI,OAAO,gBAAgB,cAAc,GAAG;AAC1C,iBAAa,KAAK,GAAG,OAAO,gBAAgB,WAAW,cAAc;AAAA,EACvE;AAEA,MAAI,aAAa,SAAS,GAAG;AAC3B,UAAM,KAAK,YAAY,aAAa,KAAK,IAAI,CAAC,EAAE;AAAA,EAClD;AAEA,SAAO,MAAM,KAAK,IAAI;AACxB;"}

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

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

@@ -86,8 +86,7 @@ async function executeReviewInit(options, sessionsDir) {
     lineWidth: 0
     // Disable line wrapping
   });
-  const schemaPath = "../../../../.search-hub/schemas/review.schema.json";
-  const schemaComment = `# yaml-language-server: $schema=${schemaPath}
+  const schemaComment = `# yaml-language-server: $schema=./review.schema.json
 `;
   const reviewsExample = `reviews:
         # - reviewer: human:your-name
@@ -98,9 +97,7 @@ async function executeReviewInit(options, sessionsDir) {
     reviewsExample
   );
   await writeFile(reviewsPath, finalContent, "utf-8");
-  const schemasDir = join(dirname(sessionsDir), ".search-hub", "schemas");
-  await mkdir(schemasDir, { recursive: true });
-  const schemaDestPath = join(schemasDir, "review.schema.json");
+  const schemaDestPath = join(internalDir, "review.schema.json");
   try {
     const schemaSourcePath = await findSchemaSource();
     await copyFile(schemaSourcePath, schemaDestPath);

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

@@ -1 +1 @@
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package/dist/cli/commands/review/merge.d.ts.map

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+{"version":3,"file":"merge.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/review/merge.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,OAAO,KAAK,EAAE,UAAU,EAAkC,WAAW,EAAE,MAAM,YAAY,CAAC;AA0B1F,MAAM,WAAW,kBAAkB;IACjC,SAAS,EAAE,MAAM,CAAC;IAClB,2EAA2E;IAC3E,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,iBAAiB;IAChC,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,cAAc,EAAE,MAAM,CAAC;IACvB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,0BAA0B,EAAE,MAAM,CAAC;IACnC,0BAA0B,EAAE,MAAM,CAAC;IACnC,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAmBD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,UAAU,EAAE,UAAU,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,GAAG,IAAI,CAQ/F;AA8ND;;GAEG;AACH,wBAAsB,kBAAkB,CACtC,OAAO,EAAE,kBAAkB,EAC3B,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,iBAAiB,CAAC,CAkC5B;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,iBAAiB,EAAE,MAAM,EAAE,OAAO,GAAG,MAAM,CAgDpF"}

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

@@ -194,8 +194,7 @@ async function executeReviewMerge(options, sessionsDir) {
     const yamlContent = stringify(mainFile, {
       lineWidth: 0
     });
-    const schemaPath = "../../../../.search-hub/schemas/review.schema.json";
-    const schemaComment = `# yaml-language-server: $schema=${schemaPath}
+    const schemaComment = `# yaml-language-server: $schema=./review.schema.json
 `;
     const finalContent = schemaComment + yamlContent;
     await writeFile(mainReviewsPath, finalContent, "utf-8");

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

@@ -1 +1 @@
-{"version":3,"file":"merge.js","sources":["../../../../src/cli/commands/review/merge.ts"],"sourcesContent":["/**\n * review merge command - Merge edited file back into main reviews.yaml\n */\n\nimport { join } from 'node:path';\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport type { ReviewFile, ArticleEntry, Review, WorkFile, ReviewBasis } from './types.js';\nimport { validateName } from './extract.js';\n\n\n/**\n * Check if a file is a work file (has basis field)\n */\n/** @deprecated Detects old WorkFile format (flat id/decision fields). Kept for backward compat. */\nfunction isWorkFile(file: unknown): file is WorkFile {\n  if (\n    typeof file !== 'object' ||\n    file === null ||\n    !('basis' in file) ||\n    !('reviewer' in file) ||\n    !('articles' in file) ||\n    !Array.isArray((file as WorkFile).articles)\n  ) {\n    return false;\n  }\n  // Distinguish from new ReviewFile-with-basis: old WorkFile has articles with flat `id` + `decision` fields\n  const articles = (file as WorkFile).articles;\n  if (articles.length === 0) return false;\n  const first = articles[0]!;\n  return 'id' in first && 'decision' in first && !('reviews' in first);\n}\n\nexport interface ReviewMergeOptions {\n  sessionId: string;\n  /** Name of the review subset (reads from for-review/<name>/review.yaml) */\n  name: string;\n  dryRun?: boolean;\n}\n\nexport interface ReviewMergeResult {\n  reviewsAdded: number;\n  decisionsSet: number;\n  includeCount: number;\n  excludeCount: number;\n  uncertainCount: number;\n  finalDecisionsSet: number;\n  finalDecisionsIncludeCount: number;\n  finalDecisionsExcludeCount: number;\n  warnings: string[];\n}\n\n/**\n * Load review file from path\n */\nasync function loadReviewFile(path: string): Promise<ReviewFile> {\n  const content = await readFile(path, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Auto-detect review basis from article data: fulltext > abstract > title\n */\nfunction detectBasis(article: ArticleEntry): ReviewBasis {\n  if (article.fulltext) return 'fulltext';\n  if (article.abstract) return 'abstract';\n  return 'title';\n}\n\n/**\n * Register a reviewer in the review file's reviewers registry.\n * Deduplicates by name+basis pair.\n */\nexport function registerReviewer(reviewFile: ReviewFile, name: string, basis: ReviewBasis): void {\n  if (!reviewFile.reviewers) {\n    reviewFile.reviewers = [];\n  }\n  const exists = reviewFile.reviewers.some((r) => r.name === name && r.basis === basis);\n  if (!exists) {\n    reviewFile.reviewers.push({ name, basis });\n  }\n}\n\n/**\n * Match article from extracted file to main file\n */\nfunction findMatchingArticle(\n  extracted: ArticleEntry,\n  mainArticles: ArticleEntry[]\n): ArticleEntry | undefined {\n  // Try matching by various identifiers\n  for (const main of mainArticles) {\n    if (extracted.pmid && main.pmid && extracted.pmid === main.pmid) {\n      return main;\n    }\n    if (extracted.doi && main.doi && extracted.doi.toLowerCase() === main.doi.toLowerCase()) {\n      return main;\n    }\n    if (extracted.scopusId && main.scopusId && extracted.scopusId === main.scopusId) {\n      return main;\n    }\n    if (extracted.arxivId && main.arxivId && extracted.arxivId === main.arxivId) {\n      return main;\n    }\n    if (extracted.ericId && main.ericId && extracted.ericId === main.ericId) {\n      return main;\n    }\n  }\n  return undefined;\n}\n\n/**\n * Match work file article by id to main file\n * The id can be a DOI, PMID, ScopusId, ArxivId, EricId, or title\n */\nfunction findMatchingArticleById(\n  id: string,\n  mainArticles: ArticleEntry[]\n): ArticleEntry | undefined {\n  for (const main of mainArticles) {\n    // Match by DOI (case-insensitive)\n    if (main.doi && main.doi.toLowerCase() === id.toLowerCase()) {\n      return main;\n    }\n    // Match by PMID\n    if (main.pmid && main.pmid === id) {\n      return main;\n    }\n    // Match by ScopusId\n    if (main.scopusId && main.scopusId === id) {\n      return main;\n    }\n    // Match by ArxivId\n    if (main.arxivId && main.arxivId === id) {\n      return main;\n    }\n    // Match by EricId\n    if (main.ericId && main.ericId === id) {\n      return main;\n    }\n    // Match by title (fallback, case-insensitive)\n    if (main.title.toLowerCase() === id.toLowerCase()) {\n      return main;\n    }\n  }\n  return undefined;\n}\n\n/**\n * Process work file format (with basis/reviewer)\n */\nfunction processWorkFile(\n  workFile: WorkFile,\n  mainFile: ReviewFile,\n  options: ReviewMergeOptions\n): ReviewMergeResult {\n  const result: ReviewMergeResult = {\n    reviewsAdded: 0,\n    decisionsSet: 0,\n    includeCount: 0,\n    excludeCount: 0,\n    uncertainCount: 0,\n    finalDecisionsSet: 0,\n    finalDecisionsIncludeCount: 0,\n    finalDecisionsExcludeCount: 0,\n    warnings: [],\n  };\n\n  const timestamp = new Date().toISOString();\n\n  // Register the reviewer for this work file's basis\n  if (!options.dryRun) {\n    registerReviewer(mainFile, workFile.reviewer, workFile.basis);\n  }\n\n  for (const workArticle of workFile.articles) {\n    // Skip articles with null decision (not yet reviewed)\n    if (workArticle.decision === null) {\n      continue;\n    }\n\n    const mainArticle = findMatchingArticleById(workArticle.id, mainFile.articles);\n\n    if (!mainArticle) {\n      result.warnings.push(`Article not found in main file: id=\"${workArticle.id}\"`);\n      continue;\n    }\n\n    // Ensure mainArticle.reviews is an array\n    if (!mainArticle.reviews) {\n      mainArticle.reviews = [];\n    }\n\n    // Create review from work file article\n    const review: Review = {\n      reviewer: workFile.reviewer,\n      decision: workArticle.decision,\n      basis: workFile.basis,\n      timestamp,\n    };\n\n    // Add comment if provided\n    if (workArticle.comment) {\n      review.comment = workArticle.comment;\n    }\n\n    if (!options.dryRun) {\n      mainArticle.reviews.push(review);\n    }\n    result.reviewsAdded++;\n\n    // Count decision types\n    if (workArticle.decision === 'include') result.includeCount++;\n    else if (workArticle.decision === 'exclude') result.excludeCount++;\n    else if (workArticle.decision === 'uncertain') result.uncertainCount++;\n  }\n\n  return result;\n}\n\n/**\n * Process review file format (with reviewHistory separation)\n */\nfunction processReviewFile(\n  extractedFile: ReviewFile,\n  mainFile: ReviewFile,\n  options: ReviewMergeOptions\n): ReviewMergeResult {\n  const result: ReviewMergeResult = {\n    reviewsAdded: 0,\n    decisionsSet: 0,\n    includeCount: 0,\n    excludeCount: 0,\n    uncertainCount: 0,\n    finalDecisionsSet: 0,\n    finalDecisionsIncludeCount: 0,\n    finalDecisionsExcludeCount: 0,\n    warnings: [],\n  };\n\n  const timestamp = new Date().toISOString();\n  const topLevelReviewer = extractedFile.reviewer;\n\n  for (const extracted of extractedFile.articles) {\n    const mainArticle = findMatchingArticle(extracted, mainFile.articles);\n\n    if (!mainArticle) {\n      result.warnings.push(`Article not found in main file: \"${extracted.title}\"`);\n      continue;\n    }\n\n    // Merge only reviews[] (reviewHistory is ignored)\n    const extractedReviews = extracted.reviews ?? [];\n\n    // Ensure mainArticle.reviews is an array\n    if (!mainArticle.reviews) {\n      mainArticle.reviews = [];\n    }\n\n    for (const review of extractedReviews) {\n      // Fill in reviewer from top-level field if not on individual review\n      const reviewer = review.reviewer ?? topLevelReviewer;\n      if (!reviewer) {\n        throw new Error('reviewer is required: set reviewer on individual review or top-level ReviewFile');\n      }\n      // Fill in basis from review, top-level field, or auto-detect from article data\n      const basis = review.basis ?? extractedFile.basis ?? detectBasis(extracted);\n\n      if (!options.dryRun) {\n        const mergedReview: Review = {\n          ...review,\n          reviewer,\n          basis,\n          timestamp: review.timestamp ?? timestamp,\n        };\n        mainArticle.reviews.push(mergedReview);\n\n        // Register reviewer\n        registerReviewer(mainFile, reviewer, basis);\n      }\n      result.reviewsAdded++;\n\n      // Count decision types\n      if (review.decision === 'include') result.includeCount++;\n      else if (review.decision === 'exclude') result.excludeCount++;\n      else if (review.decision === 'uncertain') result.uncertainCount++;\n    }\n\n    // Overwrite finalDecision if set in extracted (null means unset)\n    if (extracted.finalDecision !== undefined && extracted.finalDecision !== null) {\n      if (!options.dryRun) {\n        mainArticle.finalDecision = extracted.finalDecision;\n      }\n      result.decisionsSet++;\n      result.finalDecisionsSet++;\n      if (extracted.finalDecision === 'include') result.finalDecisionsIncludeCount++;\n      else if (extracted.finalDecision === 'exclude') result.finalDecisionsExcludeCount++;\n    }\n  }\n\n  return result;\n}\n\n/**\n * Execute review merge command\n */\nexport async function executeReviewMerge(\n  options: ReviewMergeOptions,\n  sessionsDir: string\n): Promise<ReviewMergeResult> {\n  validateName(options.name);\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const mainReviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const filePath = join(sessionDir, 'for-review', options.name, 'review.yaml');\n\n  // Load both files\n  const mainFile = await loadReviewFile(mainReviewsPath);\n  const content = await readFile(filePath, 'utf-8');\n  const inputFile = parseYaml(content);\n\n  let result: ReviewMergeResult;\n\n  // Detect file format and process accordingly\n  if (isWorkFile(inputFile)) {\n    result = processWorkFile(inputFile, mainFile, options);\n  } else {\n    result = processReviewFile(inputFile as ReviewFile, mainFile, options);\n  }\n\n  // Write back if not dry-run\n  if (!options.dryRun) {\n    const yamlContent = stringifyYaml(mainFile, {\n      lineWidth: 0,\n    });\n\n    // Preserve schema reference comment\n    // Path from sessions/{id}/.internal/ to .search-hub/schemas/\n    const schemaPath = '../../../../.search-hub/schemas/review.schema.json';\n    const schemaComment = `# yaml-language-server: $schema=${schemaPath}\\n`;\n    const finalContent = schemaComment + yamlContent;\n\n    await writeFile(mainReviewsPath, finalContent, 'utf-8');\n  }\n\n  return result;\n}\n\n/**\n * Format merge result as human-readable string\n */\nexport function formatMergeOutput(result: ReviewMergeResult, dryRun: boolean): string {\n  const lines: string[] = [];\n\n  if (dryRun) {\n    lines.push('Dry run - no changes made');\n    lines.push('');\n  }\n\n  lines.push('Merge Summary:');\n\n  // Build reviews line with decision breakdown\n  if (result.reviewsAdded === 0) {\n    lines.push(`  Reviews added: 0`);\n  } else {\n    const parts: string[] = [];\n    if (result.excludeCount > 0) parts.push(`${result.excludeCount} exclude`);\n    if (result.includeCount > 0) parts.push(`${result.includeCount} include`);\n    if (result.uncertainCount > 0) parts.push(`${result.uncertainCount} uncertain`);\n\n    if (parts.length > 0) {\n      lines.push(`  Reviews added: ${result.reviewsAdded} (${parts.join(', ')})`);\n    } else {\n      lines.push(`  Reviews added: ${result.reviewsAdded}`);\n    }\n  }\n\n  // Show final decisions only when some were set\n  if (result.finalDecisionsSet > 0) {\n    const parts: string[] = [];\n    if (result.finalDecisionsIncludeCount > 0) parts.push(`${result.finalDecisionsIncludeCount} include`);\n    if (result.finalDecisionsExcludeCount > 0) parts.push(`${result.finalDecisionsExcludeCount} exclude`);\n\n    if (parts.length > 0) {\n      lines.push(`  Final decisions set: ${result.finalDecisionsSet} (${parts.join(', ')})`);\n    } else {\n      lines.push(`  Final decisions set: ${result.finalDecisionsSet}`);\n    }\n  }\n\n  if (result.warnings.length > 0) {\n    lines.push('');\n    lines.push('Warnings:');\n    for (const warning of result.warnings) {\n      lines.push(`  - ${warning}`);\n    }\n  }\n\n  return 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Kept for backward compat. */\nfunction isWorkFile(file: unknown): file is WorkFile {\n  if (\n    typeof file !== 'object' ||\n    file === null ||\n    !('basis' in file) ||\n    !('reviewer' in file) ||\n    !('articles' in file) ||\n    !Array.isArray((file as WorkFile).articles)\n  ) {\n    return false;\n  }\n  // Distinguish from new ReviewFile-with-basis: old WorkFile has articles with flat `id` + `decision` fields\n  const articles = (file as WorkFile).articles;\n  if (articles.length === 0) return false;\n  const first = articles[0]!;\n  return 'id' in first && 'decision' in first && !('reviews' in first);\n}\n\nexport interface ReviewMergeOptions {\n  sessionId: string;\n  /** Name of the review subset (reads from for-review/<name>/review.yaml) */\n  name: string;\n  dryRun?: boolean;\n}\n\nexport interface ReviewMergeResult {\n  reviewsAdded: number;\n  decisionsSet: number;\n  includeCount: number;\n  excludeCount: number;\n  uncertainCount: number;\n  finalDecisionsSet: 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reviewFile.reviewers.push({ name, basis });\n  }\n}\n\n/**\n * Match article from extracted file to main file\n */\nfunction findMatchingArticle(\n  extracted: ArticleEntry,\n  mainArticles: ArticleEntry[]\n): ArticleEntry | undefined {\n  // Try matching by various identifiers\n  for (const main of mainArticles) {\n    if (extracted.pmid && main.pmid && extracted.pmid === main.pmid) {\n      return main;\n    }\n    if (extracted.doi && main.doi && extracted.doi.toLowerCase() === main.doi.toLowerCase()) {\n      return main;\n    }\n    if (extracted.scopusId && main.scopusId && extracted.scopusId === main.scopusId) {\n      return main;\n    }\n    if (extracted.arxivId && main.arxivId && extracted.arxivId === main.arxivId) {\n      return main;\n    }\n    if (extracted.ericId && main.ericId && extracted.ericId === main.ericId) {\n      return main;\n    }\n  }\n  return undefined;\n}\n\n/**\n * Match work file article by id to main file\n * The id can be a DOI, PMID, ScopusId, 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Reviews added: ${result.reviewsAdded}`);\n    }\n  }\n\n  // Show final decisions only when some were set\n  if (result.finalDecisionsSet > 0) {\n    const parts: string[] = [];\n    if (result.finalDecisionsIncludeCount > 0) parts.push(`${result.finalDecisionsIncludeCount} include`);\n    if (result.finalDecisionsExcludeCount > 0) parts.push(`${result.finalDecisionsExcludeCount} exclude`);\n\n    if (parts.length > 0) {\n      lines.push(`  Final decisions set: ${result.finalDecisionsSet} (${parts.join(', ')})`);\n    } else {\n      lines.push(`  Final decisions set: ${result.finalDecisionsSet}`);\n    }\n  }\n\n  if (result.warnings.length > 0) {\n    lines.push('');\n    lines.push('Warnings:');\n    for (const warning of result.warnings) {\n      lines.push(`  - ${warning}`);\n    }\n  }\n\n  return 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package/dist/cli/commands/review/types.d.ts

@@ -1,4 +1,4 @@
-import { ArticleFulltextRef } from '../../../fulltext/types.js';
+import { ArticleFulltextRef } from '@ncukondo/academic-fulltext';
 export type ReviewDecision = 'include' | 'exclude' | 'uncertain';
 /**
  * Basis of the review decision (what information was used)

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

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

@@ -1 +1 @@
-{"version":3,"file":"types.js","sources":["../../../../src/cli/commands/review/types.ts"],"sourcesContent":["/**\n * Review workflow types for article assessment tracking\n */\n\nimport type { ArticleFulltextRef } from '../../../fulltext/types.js';\n\nexport type ReviewDecision = 'include' | 'exclude' | 'uncertain';\n\n/**\n * Basis of the review decision (what information was used)\n */\nexport type ReviewBasis = 'title' | 'abstract' | 'fulltext';\n\n/**\n * Individual assessment of an article by a reviewer\n */\nexport interface Review {\n  /** Reviewer identifier: \"human:name\" or \"ai:name\" */\n  reviewer: string;\n  /** Assessment decision */\n  decision?: ReviewDecision;\n  /** Basis of the decision (what information was used) */\n  basis?: ReviewBasis;\n  /** Optional comment or reason */\n  comment?: string;\n  /** ISO 8601 timestamp (optional - auto-assigned on merge if not provided) */\n  timestamp?: string;\n}\n\n/**\n * Source information for merged duplicates\n */\nexport interface MergedSource {\n  source: string;\n  pmid?: string;\n  doi?: string;\n  scopusId?: string;\n  arxivId?: string;\n  ericId?: string;\n}\n\n/**\n * Article entry with identifiers, bibliographic info, and reviews\n */\nexport interface ArticleEntry {\n  // Identifiers (at least one required for matching)\n  doi?: string;\n  pmid?: string;\n  scopusId?: string;\n  arxivId?: string;\n  ericId?: string;\n\n  // Bibliographic info (for reviewer reference)\n  title: string;\n  authors?: string;\n  year?: string;\n  abstract?: string;\n\n  // Deduplication tracking\n  mergedFrom?: MergedSource[];\n\n  // Review data\n  reviews: Review[];\n  /** Historical reviews (only in extracted ReviewFiles, never in master file) */\n  reviewHistory?: Review[];\n  finalDecision?: 'include' | 'exclude' | null;\n\n  // Fulltext reference (set by fulltext init/sync)\n  fulltext?: ArticleFulltextRef;\n}\n\n/**\n * Top-level structure of the reviews.yaml file\n */\nexport interface ReviewerRecord {\n  name: string;\n  basis: ReviewBasis;\n}\n\nexport interface ReviewFile {\n  sessionId: string;\n  /** Path to inclusion criteria file */\n  criteria?: string;\n  /** Reviewer identifier (only in extracted ReviewFiles) */\n  reviewer?: string;\n  /** Basis level for screening (only in extracted ReviewFiles) */\n  basis?: ReviewBasis;\n  articles: ArticleEntry[];\n  /** Registry of reviewers who participated at each basis level */\n  reviewers?: ReviewerRecord[];\n}\n\n/**\n * Work file article entry for AI agent workflow\n */\n/** @deprecated Use ReviewFile format with reviews[] instead. 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Kept for backward compatibility. */\nexport interface WorkFile {\n  sessionId: string;\n  basis: ReviewBasis;\n  reviewer: string;\n  articles: WorkFileArticle[];\n}\n\n/**\n * Basis priority rank: fulltext > abstract > title > undefined\n */\nconst BASIS_RANK: Record<string, number> = {\n  title: 1,\n  abstract: 2,\n  fulltext: 3,\n};\n\nexport function basisRank(basis: ReviewBasis | undefined): number {\n  if (basis === undefined) return 0;\n  return BASIS_RANK[basis] ?? 0;\n}\n\n/**\n * Review status classification (7-state model)\n */\nexport type ReviewStatus =\n  | 'pending'\n  | 'incomplete'\n  | 'uncertain'\n  | 'agreed-include'\n  | 'agreed-exclude'\n  | 'conflicting'\n  | 'finalized';\n\n/**\n * Classify the review status of an article entry\n *\n * Classification logic (in order):\n * 1. finalDecision set?           → finalized\n * 2. No reviews?                  → pending\n * 3. 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+{"version":3,"file":"types.js","sources":["../../../../src/cli/commands/review/types.ts"],"sourcesContent":["/**\n * Review workflow types for article assessment tracking\n */\n\nimport type { ArticleFulltextRef } from '@ncukondo/academic-fulltext';\n\nexport type ReviewDecision = 'include' | 'exclude' | 'uncertain';\n\n/**\n * Basis of the review decision (what information was used)\n */\nexport type ReviewBasis = 'title' | 'abstract' | 'fulltext';\n\n/**\n * Individual assessment of an article by a reviewer\n */\nexport interface Review {\n  /** Reviewer identifier: \"human:name\" or \"ai:name\" */\n  reviewer: string;\n  /** Assessment decision */\n  decision?: ReviewDecision;\n  /** Basis of the decision (what information was used) */\n  basis?: ReviewBasis;\n  /** Optional comment or reason */\n  comment?: string;\n  /** ISO 8601 timestamp (optional - auto-assigned on merge if not provided) */\n  timestamp?: string;\n}\n\n/**\n * Source information for merged duplicates\n */\nexport interface MergedSource {\n  source: string;\n  pmid?: string;\n  doi?: string;\n  scopusId?: string;\n  arxivId?: string;\n  ericId?: string;\n}\n\n/**\n * Article entry with identifiers, bibliographic info, and reviews\n */\nexport interface ArticleEntry {\n  // Identifiers (at least one required for matching)\n  doi?: string;\n  pmid?: string;\n  scopusId?: string;\n  arxivId?: string;\n  ericId?: string;\n\n  // Bibliographic info (for reviewer reference)\n  title: string;\n  authors?: string;\n  year?: string;\n  abstract?: string;\n\n  // Deduplication tracking\n  mergedFrom?: MergedSource[];\n\n  // Review data\n  reviews: Review[];\n  /** Historical reviews (only in extracted ReviewFiles, never in master file) */\n  reviewHistory?: Review[];\n  finalDecision?: 'include' | 'exclude' | null;\n\n  // Fulltext reference (set by fulltext init/sync)\n  fulltext?: ArticleFulltextRef;\n}\n\n/**\n * Top-level structure of the reviews.yaml file\n */\nexport interface ReviewerRecord {\n  name: string;\n  basis: ReviewBasis;\n}\n\nexport interface ReviewFile {\n  sessionId: string;\n  /** Path to inclusion criteria file */\n  criteria?: string;\n  /** Reviewer identifier (only in extracted ReviewFiles) */\n  reviewer?: string;\n  /** Basis level for screening (only in extracted ReviewFiles) */\n  basis?: ReviewBasis;\n  articles: ArticleEntry[];\n  /** Registry of reviewers who participated at each basis level */\n  reviewers?: ReviewerRecord[];\n}\n\n/**\n * Work file article entry for AI agent workflow\n */\n/** @deprecated Use ReviewFile format with reviews[] instead. Kept for backward compatibility. */\nexport interface WorkFileArticle {\n  id: string;\n  title: string;\n  abstract?: string;\n  /** Fulltext directory name (only for fulltext basis) */\n  fulltext?: string;\n  decision: ReviewDecision | null;\n  comment: string;\n}\n\n/**\n * Work file structure for AI agent workflow\n */\n/** @deprecated Use ReviewFile format with basis field instead. Kept for backward compatibility. */\nexport interface WorkFile {\n  sessionId: string;\n  basis: ReviewBasis;\n  reviewer: string;\n  articles: WorkFileArticle[];\n}\n\n/**\n * Basis priority rank: fulltext > abstract > title > undefined\n */\nconst BASIS_RANK: Record<string, number> = {\n  title: 1,\n  abstract: 2,\n  fulltext: 3,\n};\n\nexport function basisRank(basis: ReviewBasis | undefined): number {\n  if (basis === undefined) return 0;\n  return BASIS_RANK[basis] ?? 0;\n}\n\n/**\n * Review status classification (7-state model)\n */\nexport type ReviewStatus =\n  | 'pending'\n  | 'incomplete'\n  | 'uncertain'\n  | 'agreed-include'\n  | 'agreed-exclude'\n  | 'conflicting'\n  | 'finalized';\n\n/**\n * Classify the review status of an article entry\n *\n * Classification logic (in order):\n * 1. finalDecision set?           → finalized\n * 2. No reviews?                  → pending\n * 3. 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package/dist/cli/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAQA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAqKpC;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,0BAA0B;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,gCAAgC;IAChC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,4BAA4B;IAC5B,OAAO,EAAE,OAAO,CAAC;IACjB,wCAAwC;IACxC,KAAK,EAAE,OAAO,CAAC;IACf,qEAAqE;IACrE,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,wBAAgB,aAAa,IAAI,OAAO,CA0tEvC;AAED;;GAEG;AACH,wBAAsB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAG1C"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAQA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAiLpC;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,0BAA0B;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,gCAAgC;IAChC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,4BAA4B;IAC5B,OAAO,EAAE,OAAO,CAAC;IACjB,wCAAwC;IACxC,KAAK,EAAE,OAAO,CAAC;IACf,qEAAqE;IACrE,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,wBAAgB,aAAa,IAAI,OAAO,CAkzEvC;AAED;;GAEG;AACH,wBAAsB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAG1C"}

package/dist/cli/index.js

@@ -9,12 +9,16 @@ import "../config/schema.js";
 import { getDefaultConfig } from "../config/defaults.js";
 import { getDefaultConfigPath } from "../config/paths.js";
 import { viewConfig, viewConfigKey, setConfigKey } from "./commands/config.js";
-import { validateQueryCommand, formatValidateResult } from "./commands/query/validate.js";
+import { detectSchemaLink, validateQueryCommand, formatValidateResult, formatVocabValidationOutput, hasVocabErrors } from "./commands/query/validate.js";
+import { MeSHLookupClient } from "../query/mesh-lookup.js";
+import { RateLimiter } from "../providers/base/rate-limiter.js";
+import { VocabCache } from "../query/vocab-cache.js";
+import { createEricCountValidator, createEmtreeCountValidator } from "../query/vocab-validator.js";
+import { createProviderInstance, executePreview, executeCountOnly, executeSearch } from "./commands/search-executor.js";
 import { translateQueryCommand, formatTranslateResult } from "./commands/query/translate.js";
 import { writeQueryTemplate, generateQueryTemplate } from "./commands/query/init.js";
 import { getSessionDetails, computeDeduplicationStats, formatSessionDetails, listSessionsForDisplay, formatSessionList } from "./commands/status.js";
 import { parseSearchOptions, validateSearchInput, formatShortKeywordWarning, formatDryRunOutput, formatPreviewOutput, formatCountOnlyOutput } from "./commands/search.js";
-import { executePreview, executeCountOnly, executeSearch } from "./commands/search-executor.js";
 import { parseResumeOptions, validateResumeInput, getResumableProvidersForCommand } from "./commands/resume.js";
 import { executeResume } from "./commands/resume-executor.js";
 import { formatVerboseProviderDetails } from "./commands/search-utils.js";
@@ -172,16 +176,86 @@ Query YAML format (minimal):
       operator: OR
 
 Use "search-hub query init" to generate a template.`);
-  queryCommand.command("validate").description("Validate query YAML file").argument("<file>", "path to query YAML file").addHelpText("after", `
+  queryCommand.command("validate").description("Validate query YAML file (auto-checks controlled vocabulary)").argument("<file>", "path to query YAML file").option("--no-vocab", "skip controlled vocabulary validation").option("--no-cache", "skip vocabulary lookup cache").addHelpText("after", `
 Examples:
-  $ search-hub query validate ./diabetes-ai.yaml`).action(async (file) => {
+  $ search-hub query validate ./diabetes-ai.yaml
+  $ search-hub query validate ./diabetes-ai.yaml --no-vocab   # Skip MeSH check
+  $ search-hub query validate ./diabetes-ai.yaml --no-cache   # Ignore cache`).action(async (file, opts) => {
     const globalOpts = program.opts();
     try {
-      const result = await validateQueryCommand(file);
+      const noVocab = opts.vocab === false;
+      const noCache = opts.cache === false;
+      let cache;
+      if (!noVocab && !noCache) {
+        cache = new VocabCache();
+        await cache.load();
+      }
+      const hasSchema = await detectSchemaLink(file);
+      if (noVocab) {
+        const result2 = await validateQueryCommand(file, { noVocab });
+        if (!globalOpts.quiet) {
+          let output = formatValidateResult(result2, file);
+          const suggestion = formatSuggestion(getSuggestion({
+            command: "query validate",
+            queryFile: file,
+            validationSuccess: result2.success,
+            hasSchemaLink: hasSchema
+          }));
+          if (suggestion) output += "\n" + suggestion;
+          console.log(output);
+        }
+        process.exitCode = !result2.success ? EXIT_CODES.QUERY_ERROR : EXIT_CODES.SUCCESS;
+        return;
+      }
+      const rateLimiter = new RateLimiter({ tokensPerSecond: 3 });
+      const meshClient = new MeSHLookupClient({
+        rateLimiter,
+        ...cache ? { cache } : {}
+      });
+      const countValidators = [];
+      let config2;
+      try {
+        config2 = await loadConfig(
+          globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}
+        );
+      } catch {
+      }
+      if (config2) {
+        const ericProvider = createProviderInstance("eric", config2);
+        if (ericProvider) {
+          countValidators.push(
+            createEricCountValidator(ericProvider, cache ? { cache } : void 0)
+          );
+        }
+        const scopusProvider = createProviderInstance("scopus", config2);
+        if (scopusProvider) {
+          countValidators.push(
+            createEmtreeCountValidator(scopusProvider, cache ? { cache } : void 0)
+          );
+        }
+      }
+      const result = await validateQueryCommand(file, {
+        meshClient,
+        ...countValidators.length > 0 ? { countValidators } : {}
+      });
+      if (cache) {
+        await cache.save();
+      }
       if (!globalOpts.quiet) {
-        console.log(formatValidateResult(result, file));
+        let output = formatValidateResult(result, file);
+        if (result.vocabResult) {
+          output += formatVocabValidationOutput(result.vocabResult);
+        }
+        const suggestion = formatSuggestion(getSuggestion({
+          command: "query validate",
+          queryFile: file,
+          validationSuccess: result.success && !hasVocabErrors(result),
+          hasSchemaLink: hasSchema
+        }));
+        if (suggestion) output += "\n" + suggestion;
+        console.log(output);
       }
-      process.exitCode = result.success ? EXIT_CODES.SUCCESS : EXIT_CODES.QUERY_ERROR;
+      process.exitCode = !result.success || hasVocabErrors(result) ? EXIT_CODES.QUERY_ERROR : EXIT_CODES.SUCCESS;
     } catch (error) {
       if (!globalOpts.quiet) {
         console.error(