@ncukondo/search-hub 0.15.1 → 0.17.0

package/dist/cli/commands/export.d.ts

@@ -18,9 +18,6 @@ export interface CommandLineOptions {
     output?: string | undefined;
     idType?: string | undefined;
     query?: string | undefined;
-    filterYear?: string | undefined;
-    filterTitle?: string | undefined;
-    filterAbstract?: string | undefined;
 }
 export interface ValidationResult {
     valid: boolean;

package/dist/cli/commands/export.d.ts.map

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package/dist/cli/commands/export.js

@@ -177,37 +177,8 @@ function deduplicateArticles(articles) {
   }
   return { articles: unique, duplicatesRemoved };
 }
-function filterArticles(articles, filter) {
-  const hasYearFilter = filter.yearFrom !== void 0 || filter.yearTo !== void 0;
-  const hasTitleFilter = filter.titleKeywords !== void 0 && filter.titleKeywords.length > 0;
-  const hasAbstractFilter = filter.abstractKeywords !== void 0 && filter.abstractKeywords.length > 0;
-  if (!hasYearFilter && !hasTitleFilter && !hasAbstractFilter) {
-    return articles;
-  }
-  return articles.filter((article) => {
-    if (hasYearFilter) {
-      const year = extractYear(article.publicationDate);
-      if (year === null) return false;
-      if (filter.yearFrom !== void 0 && year < filter.yearFrom) return false;
-      if (filter.yearTo !== void 0 && year > filter.yearTo) return false;
-    }
-    if (hasTitleFilter) {
-      const titleLower = article.title.toLowerCase();
-      const matched = filter.titleKeywords.some((kw) => titleLower.includes(kw.toLowerCase()));
-      if (!matched) return false;
-    }
-    if (hasAbstractFilter) {
-      if (!article.abstract) return false;
-      const abstractLower = article.abstract.toLowerCase();
-      const matched = filter.abstractKeywords.some((kw) => abstractLower.includes(kw.toLowerCase()));
-      if (!matched) return false;
-    }
-    return true;
-  });
-}
 export {
   deduplicateArticles,
-  filterArticles,
   formatCslJson,
   formatIds,
   formatJson,

package/dist/cli/commands/export.js.map

@@ -1 +1 @@
-{"version":3,"file":"export.js","sources":["../../../src/cli/commands/export.ts"],"sourcesContent":["import type { Article } from '../../providers/base/types.js';\nimport { articlesToCslJson } from '../../integration/csl-json.js';\nimport { getArticleKeys } from './session-utils.js';\n\nexport type ExportFormat = 'ids' | 'json' | 'jsonl' | 'csl-json';\nexport type IdType = 'doi' | 'pmid' | 'all';\n\nexport interface ExportFilter {\n  yearFrom?: number;\n  yearTo?: number;\n  titleKeywords?: string[];\n  abstractKeywords?: string[];\n}\n\nexport interface ExportCommandOptions {\n  sessionId: string;\n  format: ExportFormat;\n  outputPath?: string;\n  idType?: IdType;\n}\n\nexport interface CommandLineOptions {\n  format?: string | undefined;\n  output?: string | undefined;\n  idType?: string | undefined;\n  query?: string | undefined;\n  filterYear?: string | undefined;\n  filterTitle?: string | undefined;\n  filterAbstract?: string | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\nconst VALID_FORMATS: ExportFormat[] = ['ids', 'json', 'jsonl', 'csl-json'];\nconst VALID_ID_TYPES: IdType[] = ['doi', 'pmid', 'all'];\n\nexport function parseExportOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): ExportCommandOptions {\n  const result: ExportCommandOptions = {\n    sessionId,\n    format: (options.format as ExportFormat) || 'jsonl',\n  };\n\n  if (options.output) {\n    result.outputPath = options.output;\n  }\n\n  if (options.idType) {\n    result.idType = options.idType as IdType;\n  }\n\n  return result;\n}\n\nexport function validateExportInput(options: ExportCommandOptions): ValidationResult {\n  if (!options.sessionId || options.sessionId.trim() === '') {\n    return {\n      valid: false,\n      error: 'A session ID is required',\n    };\n  }\n\n  if (!VALID_FORMATS.includes(options.format)) {\n    return {\n      valid: false,\n      error: `Invalid format: ${options.format}. Valid formats are: ${VALID_FORMATS.join(', ')}`,\n    };\n  }\n\n  if (options.idType) {\n    if (!VALID_ID_TYPES.includes(options.idType)) {\n      return {\n        valid: false,\n        error: `Invalid id-type: ${options.idType}. Valid types are: ${VALID_ID_TYPES.join(', ')}`,\n      };\n    }\n\n    if (options.format !== 'ids') {\n      return {\n        valid: false,\n        error: '--id-type can only be used with --format ids',\n      };\n    }\n  }\n\n  return { valid: true };\n}\n\nexport function formatIds(articles: Article[], idType: IdType): string {\n  if (idType === 'all') {\n    const groups: string[] = [];\n    for (const article of articles) {\n      const ids: string[] = [];\n      if (article.pmid) ids.push(`pmid:${article.pmid}`);\n      if (article.doi) ids.push(`doi:${article.doi}`);\n      if (article.arxivId) ids.push(`arxiv:${article.arxivId}`);\n      if (article.scopusId) ids.push(`scopus:${article.scopusId}`);\n      if (article.ericId) ids.push(`eric:${article.ericId}`);\n      if (ids.length > 0) {\n        groups.push(ids.join('\\n'));\n      }\n    }\n    return groups.join('\\n\\n');\n  }\n\n  const ids: string[] = [];\n  for (const article of articles) {\n    if (idType === 'doi') {\n      if (article.doi) {\n        ids.push(article.doi);\n      }\n    } else if (idType === 'pmid') {\n      if (article.pmid) {\n        ids.push(article.pmid);\n      }\n    }\n  }\n\n  return ids.join('\\n');\n}\n\nfunction extractYear(publicationDate: string | undefined): number | null {\n  if (!publicationDate) return null;\n  const year = parseInt(publicationDate.substring(0, 4), 10);\n  return Number.isNaN(year) ? null : year;\n}\n\nfunction addYearField(articles: Article[]): (Article & { year: number | null })[] {\n  return articles.map((article) => ({\n    ...article,\n    year: extractYear(article.publicationDate),\n  }));\n}\n\nexport interface JsonExportMetadata {\n  sessionId: string;\n  sessionName: string;\n  createdAt: string;\n  databases: Record<string, number>;\n}\n\nexport function formatJson(articles: Article[], metadata?: JsonExportMetadata): string {\n  const articlesWithYear = addYearField(articles);\n\n  if (!metadata) {\n    return JSON.stringify(articlesWithYear, null, 2);\n  }\n\n  return JSON.stringify(\n    {\n      session: {\n        id: metadata.sessionId,\n        name: metadata.sessionName,\n        createdAt: metadata.createdAt,\n      },\n      summary: {\n        totalResults: articles.length,\n        databases: metadata.databases,\n      },\n      results: articlesWithYear,\n    },\n    null,\n    2\n  );\n}\n\nexport function formatJsonl(articles: Article[]): string {\n  if (articles.length === 0) {\n    return '';\n  }\n  return addYearField(articles).map((article) => JSON.stringify(article)).join('\\n');\n}\n\nexport function formatCslJson(articles: Article[]): string {\n  const cslItems = articlesToCslJson(articles);\n  return JSON.stringify(cslItems, null, 2);\n}\n\n\nconst METADATA_FIELDS: (keyof Article)[] = [\n  'doi', 'pmid', 'arxivId', 'scopusId', 'ericId',\n  'abstract', 'publicationDate', 'journal', 'volume', 'issue', 'pages',\n];\n\nfunction countMetadataFields(article: Article): number {\n  let count = 0;\n  for (const field of METADATA_FIELDS) {\n    if (article[field] !== undefined && article[field] !== '') {\n      count++;\n    }\n  }\n  return count;\n}\n\nexport interface DeduplicationResult {\n  articles: Article[];\n  duplicatesRemoved: number;\n}\n\nexport function deduplicateArticles(articles: Article[]): DeduplicationResult {\n  // Map from identifier key to index in the unique array\n  const keyToIndex = new Map<string, number>();\n  const unique: Article[] = [];\n  let duplicatesRemoved = 0;\n\n  for (const article of articles) {\n    const keys = getArticleKeys(article);\n\n    if (keys.length === 0) {\n      // No identifiers - cannot deduplicate, keep the article\n      unique.push(article);\n      continue;\n    }\n\n    // Check if any identifier has been seen before\n    let existingIndex: number | undefined;\n    for (const key of keys) {\n      const idx = keyToIndex.get(key);\n      if (idx !== undefined) {\n        existingIndex = idx;\n        break;\n      }\n    }\n\n    if (existingIndex !== undefined) {\n      // Duplicate found - compare metadata richness\n      const existing = unique[existingIndex]!;\n      if (countMetadataFields(article) > countMetadataFields(existing)) {\n        // Replace with the richer record\n        unique[existingIndex] = article;\n        // Update all keys to point to the same index\n        const newKeys = getArticleKeys(article);\n        for (const key of newKeys) {\n          keyToIndex.set(key, existingIndex);\n        }\n      }\n      duplicatesRemoved++;\n    } else {\n      const index = unique.length;\n      unique.push(article);\n      // Map all identifiers to this index\n      for (const key of keys) {\n        keyToIndex.set(key, index);\n      }\n    }\n  }\n\n  return { articles: unique, duplicatesRemoved };\n}\n\nexport function filterArticles(articles: Article[], filter: ExportFilter): Article[] {\n  const hasYearFilter = filter.yearFrom !== undefined || filter.yearTo !== 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Abstract keyword filter (OR within keywords, AND with other filters)\n    if (hasAbstractFilter) {\n      if (!article.abstract) return false;\n      const abstractLower = article.abstract.toLowerCase();\n      const matched = filter.abstractKeywords!.some((kw) => abstractLower.includes(kw.toLowerCase()));\n      if (!matched) return false;\n    }\n\n    return true;\n  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+{"version":3,"file":"export.js","sources":["../../../src/cli/commands/export.ts"],"sourcesContent":["import type { Article } from '../../providers/base/types.js';\nimport { articlesToCslJson } from '../../integration/csl-json.js';\nimport { getArticleKeys } from './session-utils.js';\n\nexport type ExportFormat = 'ids' | 'json' | 'jsonl' | 'csl-json';\nexport type IdType = 'doi' | 'pmid' | 'all';\n\nexport interface ExportFilter {\n  yearFrom?: number;\n  yearTo?: number;\n  titleKeywords?: string[];\n  abstractKeywords?: string[];\n}\n\nexport interface ExportCommandOptions {\n  sessionId: string;\n  format: ExportFormat;\n  outputPath?: string;\n  idType?: IdType;\n}\n\nexport interface CommandLineOptions {\n  format?: string | undefined;\n  output?: string | undefined;\n  idType?: string | undefined;\n  query?: string | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\nconst VALID_FORMATS: ExportFormat[] = ['ids', 'json', 'jsonl', 'csl-json'];\nconst VALID_ID_TYPES: IdType[] = ['doi', 'pmid', 'all'];\n\nexport function parseExportOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): ExportCommandOptions {\n  const result: ExportCommandOptions = {\n    sessionId,\n    format: (options.format as ExportFormat) || 'jsonl',\n  };\n\n  if (options.output) {\n    result.outputPath = options.output;\n  }\n\n  if (options.idType) {\n    result.idType = options.idType as IdType;\n  }\n\n  return result;\n}\n\nexport function validateExportInput(options: ExportCommandOptions): ValidationResult {\n  if (!options.sessionId || options.sessionId.trim() === '') {\n    return {\n      valid: false,\n      error: 'A session ID is required',\n    };\n  }\n\n  if (!VALID_FORMATS.includes(options.format)) {\n    return {\n      valid: false,\n      error: `Invalid format: ${options.format}. Valid formats are: ${VALID_FORMATS.join(', ')}`,\n    };\n  }\n\n  if (options.idType) {\n    if (!VALID_ID_TYPES.includes(options.idType)) {\n      return {\n        valid: false,\n        error: `Invalid id-type: ${options.idType}. Valid types are: ${VALID_ID_TYPES.join(', ')}`,\n      };\n    }\n\n    if (options.format !== 'ids') {\n      return {\n        valid: false,\n        error: '--id-type can only be used with --format ids',\n      };\n    }\n  }\n\n  return { valid: true };\n}\n\nexport function formatIds(articles: Article[], idType: IdType): string {\n  if (idType === 'all') {\n    const groups: string[] = [];\n    for (const article of articles) {\n      const ids: string[] = [];\n      if (article.pmid) ids.push(`pmid:${article.pmid}`);\n      if (article.doi) ids.push(`doi:${article.doi}`);\n      if (article.arxivId) ids.push(`arxiv:${article.arxivId}`);\n      if (article.scopusId) ids.push(`scopus:${article.scopusId}`);\n      if (article.ericId) ids.push(`eric:${article.ericId}`);\n      if (ids.length > 0) {\n        groups.push(ids.join('\\n'));\n      }\n    }\n    return groups.join('\\n\\n');\n  }\n\n  const ids: string[] = [];\n  for (const article of articles) {\n    if (idType === 'doi') {\n      if (article.doi) {\n        ids.push(article.doi);\n      }\n    } else if (idType === 'pmid') {\n      if (article.pmid) {\n        ids.push(article.pmid);\n      }\n    }\n  }\n\n  return ids.join('\\n');\n}\n\nfunction extractYear(publicationDate: string | undefined): number | null {\n  if (!publicationDate) return null;\n  const year = parseInt(publicationDate.substring(0, 4), 10);\n  return Number.isNaN(year) ? null : year;\n}\n\nfunction addYearField(articles: Article[]): (Article & { year: number | null })[] {\n  return articles.map((article) => ({\n    ...article,\n    year: extractYear(article.publicationDate),\n  }));\n}\n\nexport interface JsonExportMetadata {\n  sessionId: string;\n  sessionName: string;\n  createdAt: string;\n  databases: Record<string, number>;\n}\n\nexport function formatJson(articles: Article[], metadata?: JsonExportMetadata): string {\n  const articlesWithYear = addYearField(articles);\n\n  if (!metadata) {\n    return JSON.stringify(articlesWithYear, null, 2);\n  }\n\n  return JSON.stringify(\n    {\n      session: {\n        id: metadata.sessionId,\n        name: metadata.sessionName,\n        createdAt: metadata.createdAt,\n      },\n      summary: {\n        totalResults: articles.length,\n        databases: metadata.databases,\n      },\n      results: articlesWithYear,\n    },\n    null,\n    2\n  );\n}\n\nexport function formatJsonl(articles: Article[]): string {\n  if (articles.length === 0) {\n    return '';\n  }\n  return addYearField(articles).map((article) => JSON.stringify(article)).join('\\n');\n}\n\nexport function formatCslJson(articles: Article[]): string {\n  const cslItems = articlesToCslJson(articles);\n  return JSON.stringify(cslItems, null, 2);\n}\n\n\nconst METADATA_FIELDS: (keyof Article)[] = [\n  'doi', 'pmid', 'arxivId', 'scopusId', 'ericId',\n  'abstract', 'publicationDate', 'journal', 'volume', 'issue', 'pages',\n];\n\nfunction countMetadataFields(article: Article): number {\n  let count = 0;\n  for (const field of METADATA_FIELDS) {\n    if (article[field] !== undefined && article[field] !== '') {\n      count++;\n    }\n  }\n  return count;\n}\n\nexport interface DeduplicationResult {\n  articles: Article[];\n  duplicatesRemoved: number;\n}\n\nexport function deduplicateArticles(articles: Article[]): DeduplicationResult {\n  // Map from identifier key to index in the unique array\n  const keyToIndex = new Map<string, number>();\n  const unique: Article[] = [];\n  let duplicatesRemoved = 0;\n\n  for (const article of articles) {\n    const keys = getArticleKeys(article);\n\n    if (keys.length === 0) {\n      // No identifiers - cannot deduplicate, keep the article\n      unique.push(article);\n      continue;\n    }\n\n    // Check if any identifier has been seen before\n    let existingIndex: number | undefined;\n    for (const key of keys) {\n      const idx = keyToIndex.get(key);\n      if (idx !== undefined) {\n        existingIndex = idx;\n        break;\n      }\n    }\n\n    if (existingIndex !== undefined) {\n      // Duplicate found - compare metadata richness\n      const existing = unique[existingIndex]!;\n      if (countMetadataFields(article) > countMetadataFields(existing)) {\n        // Replace with the richer record\n        unique[existingIndex] = article;\n        // Update all keys to point to the same index\n        const newKeys = getArticleKeys(article);\n        for (const key of newKeys) {\n          keyToIndex.set(key, existingIndex);\n        }\n      }\n      duplicatesRemoved++;\n    } else {\n      const index = unique.length;\n      unique.push(article);\n      // Map all identifiers to this index\n      for (const key of keys) {\n        keyToIndex.set(key, index);\n      }\n    }\n  }\n\n  return { articles: unique, duplicatesRemoved };\n}\n\nexport function filterArticles(articles: Article[], filter: ExportFilter): Article[] {\n  const hasYearFilter = filter.yearFrom !== undefined || filter.yearTo !== 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package/dist/cli/commands/results.d.ts

@@ -1,5 +1,4 @@
 import { Article } from '../../providers/base/types.js';
-import { ExportFilter } from './export.js';
 export interface ResultsCommandOptions {
     sessionId: string;
     limit?: number;
@@ -7,7 +6,6 @@ export interface ResultsCommandOptions {
     json: boolean;
     fields?: string[];
     query?: string;
-    filter?: ExportFilter;
     showAbstract: boolean;
     abstractLength?: number;
 }
@@ -17,9 +15,6 @@ export interface CommandLineOptions {
     json?: boolean | undefined;
     fields?: string | undefined;
     query?: string | undefined;
-    filterYear?: string | undefined;
-    filterTitle?: string | undefined;
-    filterAbstract?: string | undefined;
     abstract?: boolean | undefined;
     abstractLength?: string | undefined;
 }

package/dist/cli/commands/results.d.ts.map

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package/dist/cli/commands/results.js

@@ -19,36 +19,6 @@ function parseResultsOptions(sessionId, options) {
   if (options.query !== void 0) {
     result.query = options.query;
   }
-  const filter = {};
-  let hasFilter = false;
-  if (options.filterYear) {
-    const parts = options.filterYear.split("-");
-    if (parts.length === 2) {
-      const from = parseInt(parts[0], 10);
-      const to = parseInt(parts[1], 10);
-      if (!Number.isNaN(from)) filter.yearFrom = from;
-      if (!Number.isNaN(to)) filter.yearTo = to;
-      hasFilter = true;
-    } else if (parts.length === 1) {
-      const year = parseInt(parts[0], 10);
-      if (!Number.isNaN(year)) {
-        filter.yearFrom = year;
-        filter.yearTo = year;
-        hasFilter = true;
-      }
-    }
-  }
-  if (options.filterTitle) {
-    filter.titleKeywords = options.filterTitle.split(",").map((s) => s.trim()).filter(Boolean);
-    hasFilter = true;
-  }
-  if (options.filterAbstract) {
-    filter.abstractKeywords = options.filterAbstract.split(",").map((s) => s.trim()).filter(Boolean);
-    hasFilter = true;
-  }
-  if (hasFilter) {
-    result.filter = filter;
-  }
   return result;
 }
 function validateResultsInput(options) {
@@ -70,12 +40,6 @@ function validateResultsInput(options) {
       error: "offset must be a non-negative number"
     };
   }
-  if (options.query !== void 0 && options.query !== "" && options.filter) {
-    return {
-      valid: false,
-      error: "Cannot use -q/--query together with --filter-year, --filter-title, or --filter-abstract. Use -q only."
-    };
-  }
   return { valid: true };
 }
 const DEFAULT_TITLE_MAX_LENGTH = 70;

package/dist/cli/commands/results.js.map

@@ -1 +1 @@
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Use -q only.',\n    };\n  }\n\n  return { valid: true };\n}\n\nconst DEFAULT_TITLE_MAX_LENGTH = 70;\nconst DEFAULT_ABSTRACT_MAX_LENGTH = 300;\n\nfunction extractYear(publicationDate: string | undefined): number | null {\n  if (!publicationDate) return null;\n  const year = parseInt(publicationDate.substring(0, 4), 10);\n  return Number.isNaN(year) ? null : year;\n}\n\nfunction truncateText(text: string, maxLength: number): string {\n  if (text.length <= maxLength) return text;\n  return text.substring(0, maxLength - 3) + '...';\n}\n\nfunction truncateTitle(title: string, maxLength: number = DEFAULT_TITLE_MAX_LENGTH): string {\n  return truncateText(title, maxLength);\n}\n\nexport function formatResultsList(\n  articles: Article[],\n  options: FormatOptions\n): string {\n  const lines: string[] = [];\n\n  // Header\n  lines.push(`Results: ${options.sessionName} (${options.sessionId})`);\n\n  if (articles.length === 0) {\n    lines.push('No articles found.');\n    return lines.join('\\n');\n  }\n\n  // Pagination info\n  const offset = options.offset ?? 0;\n  const startNum = offset + 1;\n  const endNum = offset + articles.length;\n  const articleWord = options.total === 1 ? 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[${yearStr}] ${title}`);\n\n    if (article.journal) {\n      lines.push(`    ${article.journal}`);\n    }\n\n    if (article.doi) {\n      lines.push(`    DOI: ${article.doi}`);\n    }\n\n    if (options.showAbstract) {\n      lines.push('');\n      if (article.abstract && article.abstract.trim() !== '') {\n        const maxLength = options.abstractLength ?? 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package/dist/cli/commands/review/extract.d.ts.map

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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 ?? 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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          ${decisionComment}`\n    );\n\n    // Add comment field inline guidance\n    yamlWithComments = yamlWithComments.replace(\n      /^(\\s*)comment: \"\"$/gm,\n      '$1comment: \"\"                  # reason for decision'\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    let yamlWithComments = yamlContent.replace(\n      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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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[];\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  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

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAQA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAqLpC;;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,CAu9EvC;AAED;;GAEG;AACH,wBAAsB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAG1C"}

package/dist/cli/index.js

@@ -23,7 +23,7 @@ import { parseSearchOptions, validateSearchInput, formatShortKeywordWarning, for
 import { parseResumeOptions, validateResumeInput, getResumableProvidersForCommand } from "./commands/resume.js";
 import { executeResume } from "./commands/resume-executor.js";
 import { formatVerboseProviderDetails } from "./commands/search-utils.js";
-import { parseExportOptions, validateExportInput, deduplicateArticles, filterArticles, formatIds, formatJson, formatCslJson, formatJsonl } from "./commands/export.js";
+import { parseExportOptions, validateExportInput, deduplicateArticles, formatIds, formatJson, formatCslJson, formatJsonl } from "./commands/export.js";
 import { computeSummary, formatSummaryJson, formatSummary } from "./commands/summary.js";
 import { parseResultsOptions, validateResultsInput, formatResultsJson, formatResultsList } from "./commands/results.js";
 import { filterByQuery } from "./commands/query-filter.js";
@@ -728,7 +728,7 @@ Resume completed. ${execResult.resumed} provider(s) resumed.`);
       }
     }
   );
-  program.command("export").description("Export session results to various formats").argument("<session-id>", "session ID to export").option("--format <fmt>", "output format: ids, json, jsonl, csl-json", "jsonl").option("-o, --output <path>", "output file path (default: stdout)").option("--id-type <type>", "for ids format: doi, pmid, all").option("--no-dedup", "disable deduplication of results").option("-q, --query <expr>", "filter results with query expression").option("--filter-year <range>", "year range filter (deprecated, use -q)").option("--filter-title <keywords>", "title keyword filter (deprecated, use -q)").option("--filter-abstract <keywords>", "abstract keyword filter (deprecated, use -q)").addHelpText("after", `
+  program.command("export").description("Export session results to various formats").argument("<session-id>", "session ID to export").option("--format <fmt>", "output format: ids, json, jsonl, csl-json", "jsonl").option("-o, --output <path>", "output file path (default: stdout)").option("--id-type <type>", "for ids format: doi, pmid, all").option("--no-dedup", "disable deduplication of results").option("-q, --query <expr>", "filter results with query expression").addHelpText("after", `
 Examples:
   $ search-hub export SESSION_ID                             # JSONL to stdout
   $ search-hub export SESSION_ID --format json               # JSON to stdout
@@ -755,14 +755,6 @@ Query syntax:
     async (sessionId, options) => {
       const globalOpts = program.opts();
       try {
-        const hasLegacyFilter = options?.filterYear || options?.filterTitle || options?.filterAbstract;
-        if (options?.query && hasLegacyFilter) {
-          if (!globalOpts.quiet) {
-            console.error("Error: Cannot use -q/--query together with --filter-year, --filter-title, or --filter-abstract. Use -q only.");
-          }
-          process.exitCode = EXIT_CODES.SESSION_ERROR;
-          return;
-        }
         const exportOpts = parseExportOptions(sessionId, {
           format: options?.format,
           output: options?.output,
@@ -805,33 +797,6 @@ Query syntax:
         if (options?.query) {
           exportArticles = filterByQuery(exportArticles, options.query);
           hasFilter = true;
-        } else {
-          const filter = {};
-          if (options?.filterYear) {
-            const parts = options.filterYear.split("-");
-            if (parts.length === 2) {
-              const from = parseInt(parts[0], 10);
-              const to = parseInt(parts[1], 10);
-              if (!Number.isNaN(from)) filter.yearFrom = from;
-              if (!Number.isNaN(to)) filter.yearTo = to;
-            } else if (parts.length === 1) {
-              const year = parseInt(parts[0], 10);
-              if (!Number.isNaN(year)) {
-                filter.yearFrom = year;
-                filter.yearTo = year;
-              }
-            }
-          }
-          if (options?.filterTitle) {
-            filter.titleKeywords = options.filterTitle.split(",").map((s) => s.trim()).filter(Boolean);
-          }
-          if (options?.filterAbstract) {
-            filter.abstractKeywords = options.filterAbstract.split(",").map((s) => s.trim()).filter(Boolean);
-          }
-          hasFilter = !!(filter.yearFrom !== void 0 || filter.yearTo !== void 0 || filter.titleKeywords && filter.titleKeywords.length > 0 || filter.abstractKeywords && filter.abstractKeywords.length > 0);
-          if (hasFilter) {
-            exportArticles = filterArticles(exportArticles, filter);
-          }
         }
         let output;
         if (exportOpts.format === "ids") {
@@ -939,7 +904,7 @@ Examples:
       }
     }
   );
-  program.command("results").description("List articles from a session with title, year, and journal").argument("<session-id>", "session ID to list results from").option("--limit <n>", "maximum number of results to show").option("--offset <n>", "skip first n results").option("--json", "output as JSON array").option("--fields <fields>", "fields to display (comma-separated)").option("-q, --query <expr>", "filter results with query expression").option("--filter-year <range>", "year range filter (deprecated, use -q)").option("--filter-title <keywords>", "title keyword filter (deprecated, use -q)").option("--filter-abstract <keywords>", "abstract keyword filter (deprecated, use -q)").option("--abstract", "show abstracts with results").option("--abstract-length <n>", "maximum abstract length in characters (default: 300)").addHelpText("after", `
+  program.command("results").description("List articles from a session with title, year, and journal").argument("<session-id>", "session ID to list results from").option("--limit <n>", "maximum number of results to show").option("--offset <n>", "skip first n results").option("--json", "output as JSON array").option("--fields <fields>", "fields to display (comma-separated)").option("-q, --query <expr>", "filter results with query expression").option("--abstract", "show abstracts with results").option("--abstract-length <n>", "maximum abstract length in characters (default: 300)").addHelpText("after", `
 Examples:
   $ search-hub results SESSION_ID                              # List all articles
   $ search-hub results SESSION_ID --limit 20                   # First 20 articles
@@ -972,9 +937,6 @@ Query syntax:
           json: options?.json,
           fields: options?.fields,
           query: options?.query,
-          filterYear: options?.filterYear,
-          filterTitle: options?.filterTitle,
-          filterAbstract: options?.filterAbstract,
           abstract: options?.abstract,
           abstractLength: options?.abstractLength
         });
@@ -1009,12 +971,6 @@ Query syntax:
           if (displayArticles.length !== preFilterCount) {
             filteredFrom = preFilterCount;
           }
-        } else if (resultsOpts.filter) {
-          const preFilterCount = displayArticles.length;
-          displayArticles = filterArticles(displayArticles, resultsOpts.filter);
-          if (displayArticles.length !== preFilterCount) {
-            filteredFrom = preFilterCount;
-          }
         }
         const total = displayArticles.length;
         const offset = resultsOpts.offset ?? 0;
@@ -1834,13 +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) {
@@ -1848,7 +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({