@ncukondo/search-hub 0.18.0 → 0.20.0

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

@@ -58,7 +58,7 @@ export interface ReviewSummary {
     included: number;
     /** Articles with finalDecision='exclude' */
     excluded: number;
-    /** Articles without finalDecision (pending, incomplete, uncertain, agreed, conflicting) */
+    /** Articles without finalDecision (pending, incomplete, all-uncertain, agreed, divided) */
     pending: number;
 }
 /**

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

@@ -1 +1 @@
-{"version":3,"file":"register.js","sources":["../../../src/cli/commands/register.ts"],"sourcesContent":["/**\n * Register command for reference-manager integration.\n * Registers search results with reference-manager CLI.\n */\n\nimport { join } from 'node:path';\nimport { readFile, access } from 'node:fs/promises';\nimport { constants } from 'node:fs';\nimport { createInterface } from 'node:readline';\nimport { parse as parseYaml } from 'yaml';\nimport type { ProviderName, Article, Author } from '../../providers/base/types.js';\nimport { parseProviderNames } from '../utils/validation.js';\nimport { classifyStatus, type ReviewFile } from './review/types.js';\n\nexport interface RegisterCommandOptions {\n  sessionId: string;\n  providers?: ProviderName[];\n  dryRun: boolean;\n  withAbstracts: boolean;\n  /** Register only reviewed articles with finalDecision='include' */\n  reviewed?: boolean;\n  /** Register all articles, ignoring reviews */\n  all?: boolean;\n  /** Skip confirmation prompts */\n  force?: boolean;\n  /** Suppress tips and suggestions */\n  quiet?: boolean;\n}\n\nexport interface CommandLineOptions {\n  db?: string | undefined;\n  dryRun?: boolean | undefined;\n  withAbstracts?: boolean | undefined;\n  reviewed?: boolean | undefined;\n  all?: boolean | undefined;\n  force?: boolean | undefined;\n  quiet?: boolean | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\n/**\n * Parse command line options into RegisterCommandOptions.\n */\nexport function parseRegisterOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): RegisterCommandOptions {\n  const result: RegisterCommandOptions = {\n    sessionId,\n    dryRun: options.dryRun ?? false,\n    withAbstracts: options.withAbstracts ?? false,\n    reviewed: options.reviewed ?? false,\n    all: options.all ?? false,\n    force: options.force ?? false,\n    quiet: options.quiet ?? false,\n  };\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  return result;\n}\n\n/**\n * Validate register command input.\n */\nexport function validateRegisterInput(options: RegisterCommandOptions): ValidationResult {\n  if (!options.sessionId || options.sessionId.trim() === '') {\n    return {\n      valid: false,\n      error: 'A session ID is required',\n    };\n  }\n\n  return { valid: true };\n}\n\n/**\n * Format registration summary for CLI output.\n */\nexport function formatRegistrationSummary(summary: {\n  total: number;\n  added: number;\n  skipped: number;\n  failed: number;\n  noId: number;\n}): string {\n  const lines: string[] = ['Registration complete:'];\n\n  // Added\n  lines.push(`  ✓ ${summary.added} added`);\n\n  // Duplicates (skipped)\n  if (summary.skipped > 0) {\n    lines.push(`  ⚠ ${summary.skipped} duplicates (already in library)`);\n  }\n\n  // Failed\n  if (summary.failed > 0) {\n    lines.push(`  ✗ ${summary.failed} failed`);\n  }\n\n  // No ID (skipped)\n  if (summary.noId > 0) {\n    lines.push(`  - ${summary.noId} skipped (no identifier)`);\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Get registration identifier for an article.\n * PMID is preferred over DOI for better metadata quality.\n */\nfunction getRegistrationId(article: Article): string | null {\n  if (article.pmid) {\n    return `pmid:${article.pmid}`;\n  }\n  if (article.doi) {\n    return article.doi;\n  }\n  return null;\n}\n\n/**\n * Format dry run output showing what would be registered.\n */\nexport function formatDryRunOutput(articles: Article[]): string {\n  const withId: Array<{ article: Article; id: string }> = [];\n  const withoutId: Article[] = [];\n\n  for (const article of articles) {\n    const id = getRegistrationId(article);\n    if (id) {\n      withId.push({ article, id });\n    } else {\n      withoutId.push(article);\n    }\n  }\n\n  const lines: string[] = [];\n\n  // Summary\n  lines.push(\n    `Would register ${withId.length} reference${withId.length !== 1 ? 's' : ''}:`\n  );\n\n  // List articles with IDs\n  for (const { id, article } of withId) {\n    const title = article.title.length > 60\n      ? article.title.substring(0, 57) + '...'\n      : article.title;\n    lines.push(`  - ${id}: ${title}`);\n  }\n\n  // Details about articles without DOI/PMID\n  if (withoutId.length > 0) {\n    lines.push('');\n    lines.push(\n      `${withoutId.length} article${withoutId.length !== 1 ? 's' : ''} will be skipped (no DOI or PMID):`\n    );\n\n    const maxDisplay = 10;\n    const displayed = withoutId.slice(0, maxDisplay);\n\n    for (const article of displayed) {\n      const truncatedTitle = article.title.length > 50\n        ? article.title.substring(0, 50) + '...'\n        : article.title;\n\n      const altIds = getAlternativeIds(article);\n      const hasAltIds = altIds.length > 0 ? `, has: ${altIds.join(', ')}` : '';\n\n      lines.push(`  - \"${truncatedTitle}\" (source: ${article.source}${hasAltIds})`);\n    }\n\n    if (withoutId.length > maxDisplay) {\n      lines.push(`  ... and ${withoutId.length - maxDisplay} more`);\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Get alternative (non-DOI/PMID) identifiers for an article.\n */\nfunction getAlternativeIds(article: Article): string[] {\n  const ids: string[] = [];\n  if (article.arxivId) ids.push(`arxiv:${article.arxivId}`);\n  if (article.ericId) ids.push(`eric:${article.ericId}`);\n  if (article.scopusId) ids.push(`scopus:${article.scopusId}`);\n  return ids;\n}\n\n/**\n * Summary of review decisions for a session.\n */\nexport interface ReviewSummary {\n  /** Total articles in review file */\n  total: number;\n  /** Articles with finalDecision='include' */\n  included: number;\n  /** Articles with finalDecision='exclude' */\n  excluded: number;\n  /** Articles without finalDecision (pending, incomplete, uncertain, agreed, conflicting) */\n  pending: number;\n}\n\n/**\n * Check if a session has a reviews.yaml file.\n */\nexport async function hasReviewFile(sessionId: string, sessionsDir: string): Promise<boolean> {\n  const reviewsPath = join(sessionsDir, sessionId, '.internal', 'reviews.yaml');\n  try {\n    await access(reviewsPath, constants.R_OK);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Load and parse the review file for a session.\n */\nasync function loadReviewFile(sessionId: string, sessionsDir: string): Promise<ReviewFile> {\n  const reviewsPath = join(sessionsDir, sessionId, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Get review summary (counts) for a session.\n * Throws if reviews.yaml does not exist.\n */\nexport async function getReviewSummary(sessionId: string, sessionsDir: string): Promise<ReviewSummary> {\n  const reviewFile = await loadReviewFile(sessionId, sessionsDir);\n  const articles = reviewFile.articles ?? [];\n\n  const summary: ReviewSummary = {\n    total: articles.length,\n    included: 0,\n    excluded: 0,\n    pending: 0,\n  };\n\n  for (const article of articles) {\n    const status = classifyStatus(article);\n\n    if (status === 'finalized') {\n      if (article.finalDecision === 'include') {\n        summary.included++;\n      } else {\n        summary.excluded++;\n      }\n    } else {\n      // pending, incomplete, uncertain, agreed, conflicting all count as pending for registration\n      summary.pending++;\n    }\n  }\n\n  return summary;\n}\n\n/**\n * Parse author name string into Author object.\n * Simple heuristic: last word is family name, rest is given name.\n */\nfunction parseAuthorName(name: string): Author {\n  const parts = name.trim().split(/\\s+/);\n  if (parts.length === 1) {\n    return { family: parts[0] ?? '' };\n  }\n  // Last part is family name (most common pattern in scientific citations)\n  const family = parts.pop() ?? 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[];\n\n  return articles\n    .filter((entry) => entry.finalDecision === 'include')\n    .map((entry): Article => {\n      // Validate mergedFrom exists\n      if (!entry.mergedFrom) {\n        throw new Error(\n          `Article \"${entry.title}\" has mergedFrom missing. ` +\n            `This may be a legacy review file created before source tracking was fixed. ` +\n            `Please re-run 'review init' to regenerate the review file with source tracking.`\n        );\n      }\n      if (entry.mergedFrom.length === 0) {\n        throw new Error(\n          `Article \"${entry.title}\" has empty mergedFrom array. ` +\n            `This is an invalid state - please re-run 'review init' to regenerate.`\n        );\n      }\n\n      const authors: Author[] = entry.authors\n        ? entry.authors.split(/,\\s*/).map(parseAuthorName)\n        : [];\n\n      // Get source from the first entry in mergedFrom\n      const source = entry.mergedFrom[0]!.source as ProviderName;\n\n      const article: Article = {\n        title: entry.title,\n        authors,\n        source,\n        retrievedAt: new Date().toISOString(),\n      };\n      // Only set optional fields if they have values\n      if (entry.doi) article.doi = entry.doi;\n      if (entry.pmid) article.pmid = entry.pmid;\n      if (entry.scopusId) article.scopusId = entry.scopusId;\n      if (entry.arxivId) article.arxivId = entry.arxivId;\n      if (entry.ericId) article.ericId = entry.ericId;\n      if (entry.abstract) article.abstract = entry.abstract;\n      if (entry.year) article.publicationDate = entry.year;\n      return article;\n    });\n}\n\n/**\n * Format message when reviews exist but no flag specified.\n */\nexport function formatReviewRequiredMessage(summary: ReviewSummary, sessionId: string): string {\n  return `This session has a review file.\n  Status: ${summary.included} include / ${summary.excluded} exclude / ${summary.pending} pending\n\nPlease specify which articles to register:\n  --reviewed   Register ${summary.included} included articles\n  --all        Register all ${summary.total} articles (ignore reviews)\n\nExample:\n  search-hub register ${sessionId} --reviewed`;\n}\n\n/**\n * Format error when --reviewed used but no articles are included.\n */\nexport function formatNoIncludedArticlesError(summary: ReviewSummary, sessionId: string): string {\n  return `Error: No articles marked as 'include' in reviews.\n  Status: ${summary.included} include / ${summary.excluded} exclude / ${summary.pending} pending\n\nRun 'search-hub review status ${sessionId}' for details.`;\n}\n\n/**\n * Format warning when pending articles exist with --reviewed.\n */\nexport function formatPendingWarning(summary: ReviewSummary): string {\n  const articleWord = summary.pending === 1 ? 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+{"version":3,"file":"register.js","sources":["../../../src/cli/commands/register.ts"],"sourcesContent":["/**\n * Register command for reference-manager integration.\n * Registers search results with reference-manager CLI.\n */\n\nimport { join } from 'node:path';\nimport { readFile, access } from 'node:fs/promises';\nimport { constants } from 'node:fs';\nimport { createInterface } from 'node:readline';\nimport { parse as parseYaml } from 'yaml';\nimport type { ProviderName, Article, Author } from '../../providers/base/types.js';\nimport { parseProviderNames } from '../utils/validation.js';\nimport { classifyStatus, type ReviewFile } from './review/types.js';\n\nexport interface RegisterCommandOptions {\n  sessionId: string;\n  providers?: ProviderName[];\n  dryRun: boolean;\n  withAbstracts: boolean;\n  /** Register only reviewed articles with finalDecision='include' */\n  reviewed?: boolean;\n  /** Register all articles, ignoring reviews */\n  all?: boolean;\n  /** Skip confirmation prompts */\n  force?: boolean;\n  /** Suppress tips and suggestions */\n  quiet?: boolean;\n}\n\nexport interface CommandLineOptions {\n  db?: string | undefined;\n  dryRun?: boolean | undefined;\n  withAbstracts?: boolean | undefined;\n  reviewed?: boolean | undefined;\n  all?: boolean | undefined;\n  force?: boolean | undefined;\n  quiet?: boolean | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\n/**\n * Parse command line options into RegisterCommandOptions.\n */\nexport function parseRegisterOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): RegisterCommandOptions {\n  const result: RegisterCommandOptions = {\n    sessionId,\n    dryRun: options.dryRun ?? false,\n    withAbstracts: options.withAbstracts ?? false,\n    reviewed: options.reviewed ?? false,\n    all: options.all ?? false,\n    force: options.force ?? false,\n    quiet: options.quiet ?? false,\n  };\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  return result;\n}\n\n/**\n * Validate register command input.\n */\nexport function validateRegisterInput(options: RegisterCommandOptions): ValidationResult {\n  if (!options.sessionId || options.sessionId.trim() === '') {\n    return {\n      valid: false,\n      error: 'A session ID is required',\n    };\n  }\n\n  return { valid: true };\n}\n\n/**\n * Format registration summary for CLI output.\n */\nexport function formatRegistrationSummary(summary: {\n  total: number;\n  added: number;\n  skipped: number;\n  failed: number;\n  noId: number;\n}): string {\n  const lines: string[] = ['Registration complete:'];\n\n  // Added\n  lines.push(`  ✓ ${summary.added} added`);\n\n  // Duplicates (skipped)\n  if (summary.skipped > 0) {\n    lines.push(`  ⚠ ${summary.skipped} duplicates (already in library)`);\n  }\n\n  // Failed\n  if (summary.failed > 0) {\n    lines.push(`  ✗ ${summary.failed} failed`);\n  }\n\n  // No ID (skipped)\n  if (summary.noId > 0) {\n    lines.push(`  - ${summary.noId} skipped (no identifier)`);\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Get registration identifier for an article.\n * PMID is preferred over DOI for better metadata quality.\n */\nfunction getRegistrationId(article: Article): string | null {\n  if (article.pmid) {\n    return `pmid:${article.pmid}`;\n  }\n  if (article.doi) {\n    return article.doi;\n  }\n  return null;\n}\n\n/**\n * Format dry run output showing what would be registered.\n */\nexport function formatDryRunOutput(articles: Article[]): string {\n  const withId: Array<{ article: Article; id: string }> = [];\n  const withoutId: Article[] = [];\n\n  for (const article of articles) {\n    const id = getRegistrationId(article);\n    if (id) {\n      withId.push({ article, id });\n    } else {\n      withoutId.push(article);\n    }\n  }\n\n  const lines: string[] = [];\n\n  // Summary\n  lines.push(\n    `Would register ${withId.length} reference${withId.length !== 1 ? 's' : ''}:`\n  );\n\n  // List articles with IDs\n  for (const { id, article } of withId) {\n    const title = article.title.length > 60\n      ? article.title.substring(0, 57) + '...'\n      : article.title;\n    lines.push(`  - ${id}: ${title}`);\n  }\n\n  // Details about articles without DOI/PMID\n  if (withoutId.length > 0) {\n    lines.push('');\n    lines.push(\n      `${withoutId.length} article${withoutId.length !== 1 ? 's' : ''} will be skipped (no DOI or PMID):`\n    );\n\n    const maxDisplay = 10;\n    const displayed = withoutId.slice(0, maxDisplay);\n\n    for (const article of displayed) {\n      const truncatedTitle = article.title.length > 50\n        ? article.title.substring(0, 50) + '...'\n        : article.title;\n\n      const altIds = getAlternativeIds(article);\n      const hasAltIds = altIds.length > 0 ? `, has: ${altIds.join(', ')}` : '';\n\n      lines.push(`  - \"${truncatedTitle}\" (source: ${article.source}${hasAltIds})`);\n    }\n\n    if (withoutId.length > maxDisplay) {\n      lines.push(`  ... and ${withoutId.length - maxDisplay} more`);\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Get alternative (non-DOI/PMID) identifiers for an article.\n */\nfunction getAlternativeIds(article: Article): string[] {\n  const ids: string[] = [];\n  if (article.arxivId) ids.push(`arxiv:${article.arxivId}`);\n  if (article.ericId) ids.push(`eric:${article.ericId}`);\n  if (article.scopusId) ids.push(`scopus:${article.scopusId}`);\n  return ids;\n}\n\n/**\n * Summary of review decisions for a session.\n */\nexport interface ReviewSummary {\n  /** Total articles in review file */\n  total: number;\n  /** Articles with finalDecision='include' */\n  included: number;\n  /** Articles with finalDecision='exclude' */\n  excluded: number;\n  /** Articles without finalDecision (pending, incomplete, all-uncertain, agreed, divided) */\n  pending: number;\n}\n\n/**\n * Check if a session has a reviews.yaml file.\n */\nexport async function hasReviewFile(sessionId: string, sessionsDir: string): Promise<boolean> {\n  const reviewsPath = join(sessionsDir, sessionId, '.internal', 'reviews.yaml');\n  try {\n    await access(reviewsPath, constants.R_OK);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Load and parse the review file for a session.\n */\nasync function loadReviewFile(sessionId: string, sessionsDir: string): Promise<ReviewFile> {\n  const reviewsPath = join(sessionsDir, sessionId, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Get review summary (counts) for a session.\n * Throws if reviews.yaml does not exist.\n */\nexport async function getReviewSummary(sessionId: string, sessionsDir: string): Promise<ReviewSummary> {\n  const reviewFile = await loadReviewFile(sessionId, sessionsDir);\n  const articles = reviewFile.articles ?? 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package/dist/cli/commands/related.d.ts

@@ -0,0 +1,66 @@
+import { Article } from '../../providers/base/types.js';
+import { SessionFile, SessionSeeds } from '../../session/types.js';
+/**
+ * Parsed options for the related command.
+ */
+export interface RelatedCommandOptions {
+    pmids: string[];
+    name?: string;
+    maxResults: number;
+    fromSession?: string;
+    term?: string;
+}
+/**
+ * CLI option types from Commander.js.
+ */
+export interface CommandLineOptions {
+    name?: string;
+    maxResults?: string;
+    fromSession?: string;
+    pmid?: string | string[];
+    term?: string;
+}
+export interface ValidationResult {
+    valid: boolean;
+    error?: string;
+}
+/**
+ * Options for creating a related session.
+ */
+export interface CreateRelatedSessionOptions {
+    name: string;
+    seeds: SessionSeeds;
+    articles: Article[];
+    sessionsDir: string;
+}
+/**
+ * Data for formatting related output.
+ */
+export interface RelatedOutputData {
+    sessionId: string;
+    seedCount: number;
+    totalRelated: number;
+    retrievedCount: number;
+    articles: Article[];
+}
+/**
+ * Parse command line options into RelatedCommandOptions.
+ */
+export declare function parseRelatedOptions(pmidArgs: string[], options: CommandLineOptions): RelatedCommandOptions;
+/**
+ * Validate related command input.
+ */
+export declare function validateRelatedInput(options: RelatedCommandOptions): ValidationResult;
+/**
+ * Resolve seed PMIDs from options and/or existing session.
+ */
+export declare function resolveSeeds(options: RelatedCommandOptions, sessionsDir: string): Promise<string[]>;
+/**
+ * Create a related session on disk.
+ */
+export declare function createRelatedSession(options: CreateRelatedSessionOptions): Promise<SessionFile>;
+/**
+ * Format related search output for display.
+ */
+export declare function formatRelatedOutput(data: RelatedOutputData): string;
+//# sourceMappingURL=related.d.ts.map

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

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package/dist/cli/commands/related.js

@@ -0,0 +1,161 @@
+import { mkdir, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+import { createHash } from "node:crypto";
+import { stringify } from "yaml";
+import { loadSession, sanitizeName } from "../../session/manager.js";
+import { convertResultsToYaml } from "../../session/results-io.js";
+import { loadSessionArticles } from "./session-utils.js";
+function parseRelatedOptions(pmidArgs, options) {
+  const result = {
+    pmids: [...pmidArgs],
+    maxResults: 20
+  };
+  if (options.pmid) {
+    const pmidOption = Array.isArray(options.pmid) ? options.pmid : [options.pmid];
+    result.pmids = [...result.pmids, ...pmidOption];
+  }
+  if (options.name) {
+    result.name = options.name;
+  }
+  if (options.maxResults) {
+    result.maxResults = parseInt(options.maxResults, 10);
+  }
+  if (options.fromSession) {
+    result.fromSession = options.fromSession;
+  }
+  if (options.term) {
+    result.term = options.term;
+  }
+  return result;
+}
+function validateRelatedInput(options) {
+  if (options.pmids.length === 0 && !options.fromSession) {
+    return {
+      valid: false,
+      error: "At least one PMID is required. Provide PMIDs as arguments or use --from-session."
+    };
+  }
+  for (const pmid of options.pmids) {
+    if (!/^\d+$/.test(pmid)) {
+      return {
+        valid: false,
+        error: `Invalid PMID format: "${pmid}". PMIDs must be numeric.`
+      };
+    }
+  }
+  if (options.maxResults <= 0) {
+    return {
+      valid: false,
+      error: "--max-results must be a positive number."
+    };
+  }
+  return { valid: true };
+}
+async function resolveSeeds(options, sessionsDir) {
+  if (!options.fromSession) {
+    return options.pmids;
+  }
+  const session = await loadSession(options.fromSession, sessionsDir);
+  const articles = await loadSessionArticles(session, options.fromSession, sessionsDir);
+  const sessionPmids = /* @__PURE__ */ new Set();
+  for (const article of articles) {
+    if (article.pmid) {
+      sessionPmids.add(article.pmid);
+    }
+  }
+  if (options.pmids.length === 0) {
+    return [...sessionPmids];
+  }
+  const missing = options.pmids.filter((pmid) => !sessionPmids.has(pmid));
+  if (missing.length > 0) {
+    throw new Error(
+      `PMIDs not found in session "${options.fromSession}": ${missing.join(", ")}`
+    );
+  }
+  return options.pmids;
+}
+function generateRelatedSessionId(name, seeds) {
+  const date = (/* @__PURE__ */ new Date()).toISOString().slice(0, 10).replace(/-/g, "");
+  const sanitized = sanitizeName(name);
+  const hash = createHash("sha256").update(seeds.join(",")).digest("hex").slice(0, 6);
+  return `${date}_${sanitized}_${hash}`;
+}
+async function createRelatedSession(options) {
+  const { name, seeds, articles, sessionsDir } = options;
+  const id = generateRelatedSessionId(name, seeds.ids);
+  const sessionDir = join(sessionsDir, id);
+  const now = (/* @__PURE__ */ new Date()).toISOString();
+  await mkdir(sessionDir, { recursive: true });
+  const jsonlFilename = "pubmed_results.jsonl";
+  const yamlFilename = "pubmed_results.yaml";
+  const jsonlPath = join(sessionDir, jsonlFilename);
+  const jsonlContent = articles.map((a) => JSON.stringify(a)).join("\n") + "\n";
+  await writeFile(jsonlPath, jsonlContent, "utf-8");
+  const yamlPath = join(sessionDir, yamlFilename);
+  await convertResultsToYaml(jsonlPath, yamlPath, {
+    provider: "pubmed",
+    queryName: name
+  });
+  const databases = {
+    pubmed: {
+      status: "completed",
+      retrievedCount: articles.length,
+      files: {
+        query: "",
+        results: jsonlFilename,
+        resultsYaml: yamlFilename
+      }
+    }
+  };
+  const sessionFile = {
+    version: 1,
+    id,
+    name,
+    type: "related",
+    createdAt: now,
+    updatedAt: now,
+    seeds,
+    databases,
+    summary: {
+      totalHits: 0,
+      totalRetrieved: articles.length,
+      status: "completed"
+    }
+  };
+  await writeFile(
+    join(sessionDir, "session.yaml"),
+    stringify(sessionFile),
+    "utf-8"
+  );
+  return sessionFile;
+}
+function formatRelatedOutput(data) {
+  const lines = [];
+  lines.push(`Related session: ${data.sessionId}`);
+  lines.push("");
+  lines.push(`Seeds: ${data.seedCount} PMIDs`);
+  lines.push(`Related found: ${data.totalRelated}`);
+  lines.push(`Retrieved: ${data.retrievedCount}`);
+  if (data.articles.length > 0) {
+    lines.push("");
+    lines.push("Top results:");
+    const maxDisplay = Math.min(data.articles.length, 10);
+    for (let i = 0; i < maxDisplay; i++) {
+      const article = data.articles[i];
+      const title = article.title.length > 70 ? article.title.substring(0, 67) + "..." : article.title;
+      lines.push(`  ${i + 1}. ${title}`);
+    }
+    if (data.articles.length > maxDisplay) {
+      lines.push(`  ... and ${data.articles.length - maxDisplay} more`);
+    }
+  }
+  return lines.join("\n");
+}
+export {
+  createRelatedSession,
+  formatRelatedOutput,
+  parseRelatedOptions,
+  resolveSeeds,
+  validateRelatedInput
+};
+//# sourceMappingURL=related.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"related.js","sources":["../../../src/cli/commands/related.ts"],"sourcesContent":["/**\n * Related command for finding related articles via PubMed ELink.\n */\n\nimport { mkdir, writeFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { createHash } from 'node:crypto';\nimport { stringify as stringifyYaml } from 'yaml';\nimport type { Article } from '../../providers/base/types.js';\nimport type { SessionFile, SessionSeeds } from '../../session/types.js';\nimport type { DatabaseStatus } from '../../session/types.js';\nimport { loadSession } from '../../session/manager.js';\nimport { sanitizeName } from '../../session/manager.js';\nimport { convertResultsToYaml } from '../../session/results-io.js';\nimport { loadSessionArticles } from './session-utils.js';\n\n/**\n * Parsed options for the related command.\n */\nexport interface RelatedCommandOptions {\n  pmids: string[];\n  name?: string;\n  maxResults: number;\n  fromSession?: string;\n  term?: string;\n}\n\n/**\n * CLI option types from Commander.js.\n */\nexport interface CommandLineOptions {\n  name?: string;\n  maxResults?: string;\n  fromSession?: string;\n  pmid?: string | string[];\n  term?: string;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\n/**\n * Options for creating a related session.\n */\nexport interface CreateRelatedSessionOptions {\n  name: string;\n  seeds: SessionSeeds;\n  articles: Article[];\n  sessionsDir: string;\n}\n\n/**\n * Data for formatting related output.\n */\nexport interface RelatedOutputData {\n  sessionId: string;\n  seedCount: number;\n  totalRelated: number;\n  retrievedCount: number;\n  articles: Article[];\n}\n\n/**\n * Parse command line options into RelatedCommandOptions.\n */\nexport function parseRelatedOptions(\n  pmidArgs: string[],\n  options: CommandLineOptions,\n): RelatedCommandOptions {\n  const result: RelatedCommandOptions = {\n    pmids: [...pmidArgs],\n    maxResults: 20,\n  };\n\n  // --pmid option (alternative to positional args, required with --from-session)\n  if (options.pmid) {\n    const pmidOption = Array.isArray(options.pmid) ? options.pmid : [options.pmid];\n    result.pmids = [...result.pmids, ...pmidOption];\n  }\n\n  if (options.name) {\n    result.name = options.name;\n  }\n\n  if (options.maxResults) {\n    result.maxResults = parseInt(options.maxResults, 10);\n  }\n\n  if (options.fromSession) {\n    result.fromSession = options.fromSession;\n  }\n\n  if (options.term) {\n    result.term = options.term;\n  }\n\n  return result;\n}\n\n/**\n * Validate related command input.\n */\nexport function validateRelatedInput(options: RelatedCommandOptions): ValidationResult {\n  if (options.pmids.length === 0 && !options.fromSession) {\n    return {\n      valid: false,\n      error: 'At least one PMID is required. Provide PMIDs as arguments or use --from-session.',\n    };\n  }\n\n  // Validate PMID format (numeric strings)\n  for (const pmid of options.pmids) {\n    if (!/^\\d+$/.test(pmid)) {\n      return {\n        valid: false,\n        error: `Invalid PMID format: \"${pmid}\". PMIDs must be numeric.`,\n      };\n    }\n  }\n\n  if (options.maxResults <= 0) {\n    return {\n      valid: false,\n      error: '--max-results must be a positive number.',\n    };\n  }\n\n  return { valid: true };\n}\n\n/**\n * Resolve seed PMIDs from options and/or existing session.\n */\nexport async function resolveSeeds(\n  options: RelatedCommandOptions,\n  sessionsDir: string,\n): Promise<string[]> {\n  if (!options.fromSession) {\n    return options.pmids;\n  }\n\n  // Load articles from the source session\n  const session = await loadSession(options.fromSession, sessionsDir);\n  const articles = await loadSessionArticles(session, options.fromSession, sessionsDir);\n\n  // Extract PMIDs from session articles\n  const sessionPmids = new Set<string>();\n  for (const article of articles) {\n    if (article.pmid) {\n      sessionPmids.add(article.pmid);\n    }\n  }\n\n  if (options.pmids.length === 0) {\n    // No specific PMIDs requested, return all from session\n    return [...sessionPmids];\n  }\n\n  // Validate that requested PMIDs exist in the session\n  const missing = options.pmids.filter(pmid => !sessionPmids.has(pmid));\n  if (missing.length > 0) {\n    throw new Error(\n      `PMIDs not found in session \"${options.fromSession}\": ${missing.join(', ')}`\n    );\n  }\n\n  return options.pmids;\n}\n\n/**\n * Generate a session ID for a related session.\n */\nfunction generateRelatedSessionId(name: string, seeds: string[]): string {\n  const date = new Date().toISOString().slice(0, 10).replace(/-/g, '');\n  const sanitized = sanitizeName(name);\n  const hash = createHash('sha256').update(seeds.join(',')).digest('hex').slice(0, 6);\n  return `${date}_${sanitized}_${hash}`;\n}\n\n/**\n * Create a related session on disk.\n */\nexport async function createRelatedSession(\n  options: CreateRelatedSessionOptions,\n): Promise<SessionFile> {\n  const { name, seeds, articles, sessionsDir } = options;\n\n  const id = generateRelatedSessionId(name, seeds.ids);\n  const sessionDir = join(sessionsDir, id);\n  const now = new Date().toISOString();\n\n  await mkdir(sessionDir, { recursive: true });\n\n  // Write JSONL results (use {provider}_results convention for loadResults compatibility)\n  const jsonlFilename = 'pubmed_results.jsonl';\n  const yamlFilename = 'pubmed_results.yaml';\n  const jsonlPath = join(sessionDir, jsonlFilename);\n\n  const jsonlContent = articles\n    .map((a) => JSON.stringify(a))\n    .join('\\n') + '\\n';\n  await writeFile(jsonlPath, jsonlContent, 'utf-8');\n\n  // Convert to YAML\n  const yamlPath = join(sessionDir, yamlFilename);\n  await convertResultsToYaml(jsonlPath, yamlPath, {\n    provider: 'pubmed',\n    queryName: name,\n  });\n\n  // Build database status\n  const databases: Partial<Record<string, DatabaseStatus>> = {\n    pubmed: {\n      status: 'completed',\n      retrievedCount: articles.length,\n      files: {\n        query: '',\n        results: jsonlFilename,\n        resultsYaml: yamlFilename,\n      },\n    },\n  };\n\n  // Create session file\n  const sessionFile: SessionFile = {\n    version: 1,\n    id,\n    name,\n    type: 'related',\n    createdAt: now,\n    updatedAt: now,\n    seeds,\n    databases,\n    summary: {\n      totalHits: 0,\n      totalRetrieved: articles.length,\n      status: 'completed',\n    },\n  };\n\n  // Write session.yaml\n  await writeFile(\n    join(sessionDir, 'session.yaml'),\n    stringifyYaml(sessionFile),\n    'utf-8',\n  );\n\n  return sessionFile;\n}\n\n/**\n * Format related search output for display.\n */\nexport function formatRelatedOutput(data: RelatedOutputData): string {\n  const lines: string[] = [];\n\n  lines.push(`Related session: ${data.sessionId}`);\n  lines.push('');\n  lines.push(`Seeds: ${data.seedCount} PMIDs`);\n  lines.push(`Related found: ${data.totalRelated}`);\n  lines.push(`Retrieved: ${data.retrievedCount}`);\n\n  if (data.articles.length > 0) {\n    lines.push('');\n    lines.push('Top results:');\n    const maxDisplay = Math.min(data.articles.length, 10);\n    for (let i = 0; i < maxDisplay; i++) {\n      const article = data.articles[i]!;\n      const title = article.title.length > 70\n        ? article.title.substring(0, 67) + '...'\n        : article.title;\n      lines.push(`  ${i + 1}. ${title}`);\n    }\n    if (data.articles.length > maxDisplay) {\n      lines.push(`  ... and ${data.articles.length - maxDisplay} more`);\n    }\n  }\n\n  return lines.join('\\n');\n}\n"],"names":["stringifyYaml"],"mappings":";;;;;;;AAmEO,SAAS,oBACd,UACA,SACuB;AACvB,QAAM,SAAgC;AAAA,IACpC,OAAO,CAAC,GAAG,QAAQ;AAAA,IACnB,YAAY;AAAA,EAAA;AAId,MAAI,QAAQ,MAAM;AAChB,UAAM,aAAa,MAAM,QAAQ,QAAQ,IAAI,IAAI,QAAQ,OAAO,CAAC,QAAQ,IAAI;AAC7E,WAAO,QAAQ,CAAC,GAAG,OAAO,OAAO,GAAG,UAAU;AAAA,EAChD;AAEA,MAAI,QAAQ,MAAM;AAChB,WAAO,OAAO,QAAQ;AAAA,EACxB;AAEA,MAAI,QAAQ,YAAY;AACtB,WAAO,aAAa,SAAS,QAAQ,YAAY,EAAE;AAAA,EACrD;AAEA,MAAI,QAAQ,aAAa;AACvB,WAAO,cAAc,QAAQ;AAAA,EAC/B;AAEA,MAAI,QAAQ,MAAM;AAChB,WAAO,OAAO,QAAQ;AAAA,EACxB;AAEA,SAAO;AACT;AAKO,SAAS,qBAAqB,SAAkD;AACrF,MAAI,QAAQ,MAAM,WAAW,KAAK,CAAC,QAAQ,aAAa;AACtD,WAAO;AAAA,MACL,OAAO;AAAA,MACP,OAAO;AAAA,IAAA;AAAA,EAEX;AAGA,aAAW,QAAQ,QAAQ,OAAO;AAChC,QAAI,CAAC,QAAQ,KAAK,IAAI,GAAG;AACvB,aAAO;AAAA,QACL,OAAO;AAAA,QACP,OAAO,yBAAyB,IAAI;AAAA,MAAA;AAAA,IAExC;AAAA,EACF;AAEA,MAAI,QAAQ,cAAc,GAAG;AAC3B,WAAO;AAAA,MACL,OAAO;AAAA,MACP,OAAO;AAAA,IAAA;AAAA,EAEX;AAEA,SAAO,EAAE,OAAO,KAAA;AAClB;AAKA,eAAsB,aACpB,SACA,aACmB;AACnB,MAAI,CAAC,QAAQ,aAAa;AACxB,WAAO,QAAQ;AAAA,EACjB;AAGA,QAAM,UAAU,MAAM,YAAY,QAAQ,aAAa,WAAW;AAClE,QAAM,WAAW,MAAM,oBAAoB,SAAS,QAAQ,aAAa,WAAW;AAGpF,QAAM,mCAAmB,IAAA;AACzB,aAAW,WAAW,UAAU;AAC9B,QAAI,QAAQ,MAAM;AAChB,mBAAa,IAAI,QAAQ,IAAI;AAAA,IAC/B;AAAA,EACF;AAEA,MAAI,QAAQ,MAAM,WAAW,GAAG;AAE9B,WAAO,CAAC,GAAG,YAAY;AAAA,EACzB;AAGA,QAAM,UAAU,QAAQ,MAAM,OAAO,UAAQ,CAAC,aAAa,IAAI,IAAI,CAAC;AACpE,MAAI,QAAQ,SAAS,GAAG;AACtB,UAAM,IAAI;AAAA,MACR,+BAA+B,QAAQ,WAAW,MAAM,QAAQ,KAAK,IAAI,CAAC;AAAA,IAAA;AAAA,EAE9E;AAEA,SAAO,QAAQ;AACjB;AAKA,SAAS,yBAAyB,MAAc,OAAyB;AACvE,QAAM,QAAO,oBAAI,KAAA,GAAO,YAAA,EAAc,MAAM,GAAG,EAAE,EAAE,QAAQ,MAAM,EAAE;AACnE,QAAM,YAAY,aAAa,IAAI;AACnC,QAAM,OAAO,WAAW,QAAQ,EAAE,OAAO,MAAM,KAAK,GAAG,CAAC,EAAE,OAAO,KAAK,EAAE,MAAM,GAAG,CAAC;AAClF,SAAO,GAAG,IAAI,IAAI,SAAS,IAAI,IAAI;AACrC;AAKA,eAAsB,qBACpB,SACsB;AACtB,QAAM,EAAE,MAAM,OAAO,UAAU,gBAAgB;AAE/C,QAAM,KAAK,yBAAyB,MAAM,MAAM,GAAG;AACnD,QAAM,aAAa,KAAK,aAAa,EAAE;AACvC,QAAM,OAAM,oBAAI,KAAA,GAAO,YAAA;AAEvB,QAAM,MAAM,YAAY,EAAE,WAAW,MAAM;AAG3C,QAAM,gBAAgB;AACtB,QAAM,eAAe;AACrB,QAAM,YAAY,KAAK,YAAY,aAAa;AAEhD,QAAM,eAAe,SAClB,IAAI,CAAC,MAAM,KAAK,UAAU,CAAC,CAAC,EAC5B,KAAK,IAAI,IAAI;AAChB,QAAM,UAAU,WAAW,cAAc,OAAO;AAGhD,QAAM,WAAW,KAAK,YAAY,YAAY;AAC9C,QAAM,qBAAqB,WAAW,UAAU;AAAA,IAC9C,UAAU;AAAA,IACV,WAAW;AAAA,EAAA,CACZ;AAGD,QAAM,YAAqD;AAAA,IACzD,QAAQ;AAAA,MACN,QAAQ;AAAA,MACR,gBAAgB,SAAS;AAAA,MACzB,OAAO;AAAA,QACL,OAAO;AAAA,QACP,SAAS;AAAA,QACT,aAAa;AAAA,MAAA;AAAA,IACf;AAAA,EACF;AAIF,QAAM,cAA2B;AAAA,IAC/B,SAAS;AAAA,IACT;AAAA,IACA;AAAA,IACA,MAAM;AAAA,IACN,WAAW;AAAA,IACX,WAAW;AAAA,IACX;AAAA,IACA;AAAA,IACA,SAAS;AAAA,MACP,WAAW;AAAA,MACX,gBAAgB,SAAS;AAAA,MACzB,QAAQ;AAAA,IAAA;AAAA,EACV;AAIF,QAAM;AAAA,IACJ,KAAK,YAAY,cAAc;AAAA,IAC/BA,UAAc,WAAW;AAAA,IACzB;AAAA,EAAA;AAGF,SAAO;AACT;AAKO,SAAS,oBAAoB,MAAiC;AACnE,QAAM,QAAkB,CAAA;AAExB,QAAM,KAAK,oBAAoB,KAAK,SAAS,EAAE;AAC/C,QAAM,KAAK,EAAE;AACb,QAAM,KAAK,UAAU,KAAK,SAAS,QAAQ;AAC3C,QAAM,KAAK,kBAAkB,KAAK,YAAY,EAAE;AAChD,QAAM,KAAK,cAAc,KAAK,cAAc,EAAE;AAE9C,MAAI,KAAK,SAAS,SAAS,GAAG;AAC5B,UAAM,KAAK,EAAE;AACb,UAAM,KAAK,cAAc;AACzB,UAAM,aAAa,KAAK,IAAI,KAAK,SAAS,QAAQ,EAAE;AACpD,aAAS,IAAI,GAAG,IAAI,YAAY,KAAK;AACnC,YAAM,UAAU,KAAK,SAAS,CAAC;AAC/B,YAAM,QAAQ,QAAQ,MAAM,SAAS,KACjC,QAAQ,MAAM,UAAU,GAAG,EAAE,IAAI,QACjC,QAAQ;AACZ,YAAM,KAAK,KAAK,IAAI,CAAC,KAAK,KAAK,EAAE;AAAA,IACnC;AACA,QAAI,KAAK,SAAS,SAAS,YAAY;AACrC,YAAM,KAAK,aAAa,KAAK,SAAS,SAAS,UAAU,OAAO;AAAA,IAClE;AAAA,EACF;AAEA,SAAO,MAAM,KAAK,IAAI;AACxB;"}

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

@@ -1 +1 @@
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package/dist/cli/commands/review/extract.js

@@ -20,10 +20,19 @@ function seededShuffle(array, seed) {
   }
   return result;
 }
-function getBasisGuidanceComment(basis) {
+function getBasisGuidanceComment(basis, mode = "screening") {
   const schemaLine = "# yaml-language-server: $schema=./review.schema.json";
   switch (basis) {
     case "title":
+      if (mode === "picking") {
+        return [
+          schemaLine,
+          "# Review by title only.",
+          '# Mark relevant items as "include" with a comment explaining the reason.',
+          '# Leave everything else as "uncertain".',
+          ""
+        ].join("\n");
+      }
       return [
         schemaLine,
         "# Screening by title only.",
@@ -49,10 +58,10 @@ function getBasisGuidanceComment(basis) {
       ].join("\n");
   }
 }
-function getDecisionInlineComment(basis) {
+function getDecisionInlineComment(basis, mode = "screening") {
   switch (basis) {
     case "title":
-      return "# exclude / uncertain";
+      return mode === "picking" ? "# include / uncertain" : "# exclude / uncertain";
     case "abstract":
     case "fulltext":
       return "# include / exclude / uncertain";
@@ -135,6 +144,7 @@ async function executeReviewExtract(options, sessionsDir) {
   const sessionDir = join(sessionsDir, options.sessionId);
   const outputPath = join(sessionDir, "for-review", options.name, "review.yaml");
   const reviewFile = await loadReviewFile(sessionDir);
+  const mode = reviewFile.mode ?? "screening";
   const reviewers = reviewFile.reviewers;
   let filtered;
   if (options.filter && options.filter.length > 0) {
@@ -166,7 +176,7 @@ async function executeReviewExtract(options, sessionsDir) {
       articles: paginated.map((article) => buildScreeningArticle(article, options.basis))
     };
     const yamlContent = stringify(outputFile, { lineWidth: 0 });
-    const decisionComment = getDecisionInlineComment(options.basis);
+    const decisionComment = getDecisionInlineComment(options.basis, mode);
     let yamlWithComments = yamlContent.replace(
       /^(\s*-?\s*)decision: uncertain$/gm,
       `$1decision: uncertain          ${decisionComment}`
@@ -175,7 +185,7 @@ async function executeReviewExtract(options, sessionsDir) {
       /^(\s*)comment: ""$/gm,
       '$1comment: ""                  # reason for decision'
     );
-    const guidanceComment = getBasisGuidanceComment(options.basis);
+    const guidanceComment = getBasisGuidanceComment(options.basis, mode);
     finalContent = guidanceComment + yamlWithComments;
   } else {
     const outputFile = {

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          ${decisionComment}`\n    );\n\n    // Add comment field inline guidance\n    yamlWithComments = yamlWithComments.replace(\n      /^(\\s*)comment: \"\"$/gm,\n      '$1comment: \"\"                  # reason for decision'\n    );\n\n    const guidanceComment = getBasisGuidanceComment(options.basis);\n    finalContent = guidanceComment + yamlWithComments;\n  } else {\n    // Final decision mode: --finalize, or no --basis (backward compat)\n    const outputFile: ReviewFile = {\n      sessionId: options.sessionId,\n      reviewer: options.reviewer,\n      articles: paginated.map((article) => buildFinalizeArticle(article, options.basis)),\n    };\n\n    const yamlContent = stringifyYaml(outputFile, { lineWidth: 0 });\n\n    // Replace finalDecision: null with a commented placeholder for user guidance\n    let yamlWithComments = yamlContent.replace(\n      /^(\\s*)finalDecision: null$/gm,\n      '$1finalDecision: # include / exclude'\n    );\n\n    // Add reviews array inline guidance\n    yamlWithComments = yamlWithComments.replace(\n      /^(\\s*)reviews: \\[\\]$/gm,\n      '$1reviews: []                  # add new reviews here'\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  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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, mode: ReviewMode = 'screening'): string {\n  switch (basis) {\n    case 'title':\n      return mode === 'picking' ? 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'screening';\n\n  // Filter articles by status\n  const reviewers = reviewFile.reviewers;\n  let filtered: ArticleEntry[];\n  if (options.filter && options.filter.length > 0) {\n    filtered = reviewFile.articles.filter((article) => {\n      const status = classifyStatus(article, reviewers);\n      return options.filter!.includes(status);\n    });\n  } else {\n    filtered = [...reviewFile.articles];\n  }\n\n  const totalMatching = filtered.length;\n\n  // Sort articles\n  const sorted = sortArticles(filtered, options.sort ?? 'none', options.seed);\n\n  // Apply pagination\n  let paginated = sorted;\n  if (options.offset !== undefined && options.offset > 0) {\n    paginated = paginated.slice(options.offset);\n  }\n  if (options.limit !== undefined && options.limit > 0) {\n    paginated = paginated.slice(0, options.limit);\n  }\n\n  if (!options.reviewer) {\n    throw new Error('--reviewer is required for review file extract');\n  }\n\n  let finalContent: string;\n\n  if (options.basis && !options.finalize) {\n    // Screening mode: basis-scoped content with pre-populated reviews\n    const outputFile: ReviewFile = {\n      sessionId: options.sessionId,\n      basis: options.basis,\n      reviewer: options.reviewer,\n      articles: paginated.map((article) => buildScreeningArticle(article, options.basis!)),\n    };\n\n    const yamlContent = stringifyYaml(outputFile, { lineWidth: 0 });\n\n    // Add decision inline comments\n    const decisionComment = getDecisionInlineComment(options.basis, mode);\n    let 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      '$1comment: \"\"                  # reason for decision'\n    );\n\n    const guidanceComment = getBasisGuidanceComment(options.basis, mode);\n    finalContent = guidanceComment + yamlWithComments;\n  } else {\n    // Final decision mode: --finalize, or no --basis (backward compat)\n    const outputFile: ReviewFile = {\n      sessionId: options.sessionId,\n      reviewer: options.reviewer,\n      articles: paginated.map((article) => buildFinalizeArticle(article, options.basis)),\n    };\n\n    const yamlContent = stringifyYaml(outputFile, { lineWidth: 0 });\n\n    // Replace finalDecision: null with a commented placeholder for user guidance\n    let yamlWithComments = yamlContent.replace(\n      /^(\\s*)finalDecision: null$/gm,\n      '$1finalDecision: # include / exclude'\n    );\n\n    // Add reviews array inline guidance\n    yamlWithComments = yamlWithComments.replace(\n      /^(\\s*)reviews: \\[\\]$/gm,\n      '$1reviews: []                  # add new reviews here'\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  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package/dist/cli/commands/review/finalize.js

@@ -6,10 +6,10 @@ function createEmptySkippedByStatus() {
   return {
     pending: 0,
     incomplete: 0,
-    uncertain: 0,
+    "all-uncertain": 0,
     "agreed-include": 0,
     "agreed-exclude": 0,
-    conflicting: 0,
+    divided: 0,
     finalized: 0
   };
 }
@@ -74,11 +74,11 @@ function formatFinalizeOutput(result, options) {
   if (result.skippedByStatus.incomplete > 0) {
     skippedParts.push(`${result.skippedByStatus.incomplete} incomplete`);
   }
-  if (result.skippedByStatus.uncertain > 0) {
-    skippedParts.push(`${result.skippedByStatus.uncertain} uncertain`);
+  if (result.skippedByStatus["all-uncertain"] > 0) {
+    skippedParts.push(`${result.skippedByStatus["all-uncertain"]} all-uncertain`);
   }
-  if (result.skippedByStatus.conflicting > 0) {
-    skippedParts.push(`${result.skippedByStatus.conflicting} conflicting`);
+  if (result.skippedByStatus.divided > 0) {
+    skippedParts.push(`${result.skippedByStatus.divided} divided`);
   }
   if (options?.decision && result.skippedByStatus["agreed-include"] > 0) {
     skippedParts.push(`${result.skippedByStatus["agreed-include"]} agreed-include (filtered)`);

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

@@ -1 +1 @@
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+{"version":3,"file":"finalize.js","sources":["../../../../src/cli/commands/review/finalize.ts"],"sourcesContent":["/**\n * review finalize command - Auto-set finalDecision for articles with consensus\n */\n\nimport { join } from 'node:path';\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport { classifyStatus, type ReviewFile, type ReviewStatus } from './types.js';\n\nexport interface ReviewFinalizeOptions {\n  sessionId: string;\n  dryRun?: boolean;\n  minReviewers?: number;\n  decision?: 'include' | 'exclude';\n}\n\nexport interface ReviewFinalizeResult {\n  includedCount: number;\n  excludedCount: number;\n  skippedByStatus: Record<ReviewStatus, number>;\n}\n\nfunction createEmptySkippedByStatus(): Record<ReviewStatus, number> {\n  return {\n    pending: 0,\n    incomplete: 0,\n    'all-uncertain': 0,\n    'agreed-include': 0,\n    'agreed-exclude': 0,\n    divided: 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 ?? [];\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 = consensusDecision;\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; decision?: 'include' | 'exclude' }\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(`${result.skippedByStatus.incomplete} incomplete`);\n  }\n  if (result.skippedByStatus['all-uncertain'] > 0) {\n    skippedParts.push(`${result.skippedByStatus['all-uncertain']} all-uncertain`);\n  }\n  if (result.skippedByStatus.divided > 0) {\n    skippedParts.push(`${result.skippedByStatus.divided} divided`);\n  }\n\n  // Show filtered-out agreed counts when --decision is active\n  if (options?.decision && result.skippedByStatus['agreed-include'] > 0) {\n    skippedParts.push(`${result.skippedByStatus['agreed-include']} agreed-include (filtered)`);\n  }\n  if (options?.decision && result.skippedByStatus['agreed-exclude'] > 0) {\n    skippedParts.push(`${result.skippedByStatus['agreed-exclude']} agreed-exclude (filtered)`);\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":";;;;AAsBA,SAAS,6BAA2D;AAClE,SAAO;AAAA,IACL,SAAS;AAAA,IACT,YAAY;AAAA,IACZ,iBAAiB;AAAA,IACjB,kBAAkB;AAAA,IAClB,kBAAkB;AAAA,IAClB,SAAS;AAAA,IACT,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,oBAAoB,WAAW,mBAAmB,YAAY;AACpE,UAAI,QAAQ,YAAY,QAAQ,aAAa,mBAAmB;AAC9D,eAAO,gBAAgB,MAAM;AAC7B;AAAA,MACF;AAGA,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;AAAA,MAC1B;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,eAAe,IAAI,GAAG;AAC/C,iBAAa,KAAK,GAAG,OAAO,gBAAgB,eAAe,CAAC,gBAAgB;AAAA,EAC9E;AACA,MAAI,OAAO,gBAAgB,UAAU,GAAG;AACtC,iBAAa,KAAK,GAAG,OAAO,gBAAgB,OAAO,UAAU;AAAA,EAC/D;AAGA,MAAI,SAAS,YAAY,OAAO,gBAAgB,gBAAgB,IAAI,GAAG;AACrE,iBAAa,KAAK,GAAG,OAAO,gBAAgB,gBAAgB,CAAC,4BAA4B;AAAA,EAC3F;AACA,MAAI,SAAS,YAAY,OAAO,gBAAgB,gBAAgB,IAAI,GAAG;AACrE,iBAAa,KAAK,GAAG,OAAO,gBAAgB,gBAAgB,CAAC,4BAA4B;AAAA,EAC3F;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

@@ -1,8 +1,7 @@
-/**
- * review init command - Generate reviews.yaml from session results
- */
+import { ReviewMode } from './types.js';
 export interface ReviewInitOptions {
     sessionId: string;
+    mode?: ReviewMode;
     force?: boolean;
 }
 export interface ReviewInitResult {

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

@@ -1 +1 @@
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package/dist/cli/commands/review/init.js

@@ -67,6 +67,7 @@ async function executeReviewInit(options, sessionsDir) {
   const articleEntries = dedupedArticles.map(articleToEntry);
   const reviewFile = {
     sessionId: options.sessionId,
+    ...options.mode && { mode: options.mode },
     articles: articleEntries
   };
   const yamlContent = stringify(reviewFile, {