@ncukondo/search-hub 0.19.0 → 0.20.0

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

@@ -0,0 +1 @@
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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 ?? 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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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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, mode: ReviewMode = 'screening'): string {\n  const schemaLine = '# yaml-language-server: $schema=./review.schema.json';\n  switch (basis) {\n    case 'title':\n      if (mode === 'picking') {\n        return [\n          schemaLine,\n          '# Review by title only.',\n          '# Mark relevant items as \"include\" with a comment explaining the reason.',\n          '# Leave everything else as \"uncertain\".',\n          '',\n        ].join('\\n');\n      }\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, mode: ReviewMode = 'screening'): string {\n  switch (basis) {\n    case 'title':\n      return mode === 'picking' ? 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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

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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, {

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

@@ -1 +1 @@
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Use --force to overwrite.`);\n    }\n  } catch (err) {\n    if ((err as NodeJS.ErrnoException).code !== 'ENOENT') {\n      throw err;\n    }\n  }\n\n  // Create .internal/ directory\n  await mkdir(internalDir, { recursive: true });\n\n  // Load all results from session\n  const allArticles: Article[] = [];\n  const providers = Object.keys(session.databases) as ProviderName[];\n\n  for (const provider of providers) {\n    const dbStatus = session.databases[provider];\n    if (!dbStatus) continue;\n    const articles = await loadResults(sessionDir, provider);\n    allArticles.push(...articles);\n  }\n\n  // Deduplicate with mergedFrom tracking\n  const { articles: dedupedArticles, duplicatesRemoved } = deduplicateForReview(allArticles);\n\n  // Convert to ArticleEntry format\n  const articleEntries = dedupedArticles.map(articleToEntry);\n\n  // Build review file\n  const reviewFile: ReviewFile = {\n    sessionId: options.sessionId,\n    articles: articleEntries,\n  };\n\n  // Generate YAML with schema reference comment\n  const yamlContent = stringifyYaml(reviewFile, {\n    lineWidth: 0, // Disable line wrapping\n  });\n\n  // Add schema reference comment at top (local copy alongside reviews.yaml)\n  const schemaComment = `# yaml-language-server: $schema=./review.schema.json\\n`;\n\n  // Replace empty reviews arrays with commented example\n  const reviewsExample = `reviews:\n        # - reviewer: human:your-name\n        #   decision: include  # include / exclude / uncertain\n        #   comment: reason`;\n  const finalContent = schemaComment + yamlContent.replace(\n    /reviews: \\[\\]/g,\n    reviewsExample\n  );\n\n  // Write reviews.yaml\n  await writeFile(reviewsPath, finalContent, 'utf-8');\n\n  // Generate and write schema file to .internal/ alongside reviews.yaml\n  const schemaDestPath = join(internalDir, 'review.schema.json');\n  const jsonSchema = generateReviewJSONSchema();\n  await writeFile(schemaDestPath, JSON.stringify(jsonSchema, null, 2) + '\\n', 'utf-8');\n\n  return {\n    reviewsPath,\n    articleCount: articleEntries.length,\n    duplicatesRemoved,\n  };\n}\n"],"names":["stringifyYaml"],"mappings":";;;;;;;AA4BA,SAAS,cAAc,SAA2B;AAChD,SAAO,QACJ,IAAI,CAAC,MAAM;AACV,UAAM,QAAkB,CAAA;AACxB,QAAI,EAAE,OAAQ,OAAM,KAAK,EAAE,MAAM;AACjC,QAAI,EAAE,MAAO,OAAM,KAAK,EAAE,MAAM,OAAO,CAAC,CAAC;AACzC,WAAO,MAAM,KAAK,GAAG;AAAA,EACvB,CAAC,EACA,KAAK,IAAI;AACd;AAKA,SAAS,YAAY,iBAA8C;AACjE,MAAI,CAAC,gBAAiB,QAAO;AAC7B,QAAM,OAAO,gBAAgB,UAAU,GAAG,CAAC;AAC3C,SAAO,UAAU,KAAK,IAAI,IAAI,OAAO;AACvC;AAKA,SAAS,eAAe,SAAkE;AACxF,QAAM,QAAsB;AAAA,IAC1B,OAAO,QAAQ;AAAA,IACf,SAAS,CAAA;AAAA,EAAC;AAIZ,MAAI,QAAQ,IAAK,OAAM,MAAM,QAAQ;AACrC,MAAI,QAAQ,KAAM,OAAM,OAAO,QAAQ;AACvC,MAAI,QAAQ,SAAU,OAAM,WAAW,QAAQ;AAC/C,MAAI,QAAQ,QAAS,OAAM,UAAU,QAAQ;AAC7C,MAAI,QAAQ,OAAQ,OAAM,SAAS,QAAQ;AAG3C,MAAI,QAAQ,WAAW,QAAQ,QAAQ,SAAS,GAAG;AACjD,UAAM,UAAU,cAAc,QAAQ,OAAO;AAAA,EAC/C;AACA,QAAM,OAAO,YAAY,QAAQ,eAAe;AAChD,MAAI,YAAY,OAAO;AACvB,MAAI,QAAQ,SAAU,OAAM,WAAW,QAAQ;AAG/C,MAAI,QAAQ,cAAc,QAAQ,WAAW,SAAS,GAAG;AACvD,UAAM,aAAa,QAAQ;AAAA,EAC7B;AAEA,SAAO;AACT;AAKA,eAAsB,kBACpB,SACA,aAC2B;AAC3B,QAAM,aAAa,KAAK,aAAa,QAAQ,SAAS;AAGtD,QAAM,UAAU,MAAM,YAAY,QAAQ,WAAW,WAAW;AAGhE,QAAM,cAAc,KAAK,YAAY,WAAW;AAChD,QAAM,cAAc,KAAK,aAAa,cAAc;AACpD,MAAI;AACF,UAAM,OAAO,WAAW;AACxB,QAAI,CAAC,QAAQ,OAAO;AAClB,YAAM,IAAI,MAAM,wDAAwD;AAAA,IAC1E;AAAA,EACF,SAAS,KAAK;AACZ,QAAK,IAA8B,SAAS,UAAU;AACpD,YAAM;AAAA,IACR;AAAA,EACF;AAGA,QAAM,MAAM,aAAa,EAAE,WAAW,MAAM;AAG5C,QAAM,cAAyB,CAAA;AAC/B,QAAM,YAAY,OAAO,KAAK,QAAQ,SAAS;AAE/C,aAAW,YAAY,WAAW;AAChC,UAAM,WAAW,QAAQ,UAAU,QAAQ;AAC3C,QAAI,CAAC,SAAU;AACf,UAAM,WAAW,MAAM,YAAY,YAAY,QAAQ;AACvD,gBAAY,KAAK,GAAG,QAAQ;AAAA,EAC9B;AAGA,QAAM,EAAE,UAAU,iBAAiB,kBAAA,IAAsB,qBAAqB,WAAW;AAGzF,QAAM,iBAAiB,gBAAgB,IAAI,cAAc;AAGzD,QAAM,aAAyB;AAAA,IAC7B,WAAW,QAAQ;AAAA,IACnB,UAAU;AAAA,EAAA;AAIZ,QAAM,cAAcA,UAAc,YAAY;AAAA,IAC5C,WAAW;AAAA;AAAA,EAAA,CACZ;AAGD,QAAM,gBAAgB;AAAA;AAGtB,QAAM,iBAAiB;AAAA;AAAA;AAAA;AAIvB,QAAM,eAAe,gBAAgB,YAAY;AAAA,IAC/C;AAAA,IACA;AAAA,EAAA;AAIF,QAAM,UAAU,aAAa,cAAc,OAAO;AAGlD,QAAM,iBAAiB,KAAK,aAAa,oBAAoB;AAC7D,QAAM,aAAa,yBAAA;AACnB,QAAM,UAAU,gBAAgB,KAAK,UAAU,YAAY,MAAM,CAAC,IAAI,MAAM,OAAO;AAEnF,SAAO;AAAA,IACL;AAAA,IACA,cAAc,eAAe;AAAA,IAC7B;AAAA,EAAA;AAEJ;"}
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Use --force to overwrite.`);\n    }\n  } catch (err) {\n    if ((err as NodeJS.ErrnoException).code !== 'ENOENT') {\n      throw err;\n    }\n  }\n\n  // Create .internal/ directory\n  await mkdir(internalDir, { recursive: true });\n\n  // Load all results from session\n  const allArticles: Article[] = [];\n  const providers = Object.keys(session.databases) as ProviderName[];\n\n  for (const provider of providers) {\n    const dbStatus = session.databases[provider];\n    if (!dbStatus) continue;\n    const articles = await loadResults(sessionDir, provider);\n    allArticles.push(...articles);\n  }\n\n  // Deduplicate with mergedFrom tracking\n  const { articles: dedupedArticles, duplicatesRemoved } = deduplicateForReview(allArticles);\n\n  // Convert to ArticleEntry format\n  const articleEntries = dedupedArticles.map(articleToEntry);\n\n  // Build review file\n  const reviewFile: ReviewFile = {\n    sessionId: options.sessionId,\n    ...(options.mode && { mode: options.mode }),\n    articles: articleEntries,\n  };\n\n  // Generate YAML with schema reference comment\n  const yamlContent = stringifyYaml(reviewFile, {\n    lineWidth: 0, // Disable line wrapping\n  });\n\n  // Add schema reference comment at top (local copy alongside reviews.yaml)\n  const schemaComment = `# yaml-language-server: $schema=./review.schema.json\\n`;\n\n  // Replace empty reviews arrays with commented example\n  const reviewsExample = `reviews:\n        # - reviewer: human:your-name\n        #   decision: include  # include / exclude / uncertain\n        #   comment: reason`;\n  const finalContent = schemaComment + yamlContent.replace(\n    /reviews: \\[\\]/g,\n    reviewsExample\n  );\n\n  // Write reviews.yaml\n  await writeFile(reviewsPath, finalContent, 'utf-8');\n\n  // Generate and write schema file to .internal/ alongside reviews.yaml\n  const schemaDestPath = join(internalDir, 'review.schema.json');\n  const jsonSchema = generateReviewJSONSchema();\n  await writeFile(schemaDestPath, JSON.stringify(jsonSchema, null, 2) + '\\n', 'utf-8');\n\n  return {\n    reviewsPath,\n    articleCount: articleEntries.length,\n    duplicatesRemoved,\n  };\n}\n"],"names":["stringifyYaml"],"mappings":";;;;;;;AA6BA,SAAS,cAAc,SAA2B;AAChD,SAAO,QACJ,IAAI,CAAC,MAAM;AACV,UAAM,QAAkB,CAAA;AACxB,QAAI,EAAE,OAAQ,OAAM,KAAK,EAAE,MAAM;AACjC,QAAI,EAAE,MAAO,OAAM,KAAK,EAAE,MAAM,OAAO,CAAC,CAAC;AACzC,WAAO,MAAM,KAAK,GAAG;AAAA,EACvB,CAAC,EACA,KAAK,IAAI;AACd;AAKA,SAAS,YAAY,iBAA8C;AACjE,MAAI,CAAC,gBAAiB,QAAO;AAC7B,QAAM,OAAO,gBAAgB,UAAU,GAAG,CAAC;AAC3C,SAAO,UAAU,KAAK,IAAI,IAAI,OAAO;AACvC;AAKA,SAAS,eAAe,SAAkE;AACxF,QAAM,QAAsB;AAAA,IAC1B,OAAO,QAAQ;AAAA,IACf,SAAS,CAAA;AAAA,EAAC;AAIZ,MAAI,QAAQ,IAAK,OAAM,MAAM,QAAQ;AACrC,MAAI,QAAQ,KAAM,OAAM,OAAO,QAAQ;AACvC,MAAI,QAAQ,SAAU,OAAM,WAAW,QAAQ;AAC/C,MAAI,QAAQ,QAAS,OAAM,UAAU,QAAQ;AAC7C,MAAI,QAAQ,OAAQ,OAAM,SAAS,QAAQ;AAG3C,MAAI,QAAQ,WAAW,QAAQ,QAAQ,SAAS,GAAG;AACjD,UAAM,UAAU,cAAc,QAAQ,OAAO;AAAA,EAC/C;AACA,QAAM,OAAO,YAAY,QAAQ,eAAe;AAChD,MAAI,YAAY,OAAO;AACvB,MAAI,QAAQ,SAAU,OAAM,WAAW,QAAQ;AAG/C,MAAI,QAAQ,cAAc,QAAQ,WAAW,SAAS,GAAG;AACvD,UAAM,aAAa,QAAQ;AAAA,EAC7B;AAEA,SAAO;AACT;AAKA,eAAsB,kBACpB,SACA,aAC2B;AAC3B,QAAM,aAAa,KAAK,aAAa,QAAQ,SAAS;AAGtD,QAAM,UAAU,MAAM,YAAY,QAAQ,WAAW,WAAW;AAGhE,QAAM,cAAc,KAAK,YAAY,WAAW;AAChD,QAAM,cAAc,KAAK,aAAa,cAAc;AACpD,MAAI;AACF,UAAM,OAAO,WAAW;AACxB,QAAI,CAAC,QAAQ,OAAO;AAClB,YAAM,IAAI,MAAM,wDAAwD;AAAA,IAC1E;AAAA,EACF,SAAS,KAAK;AACZ,QAAK,IAA8B,SAAS,UAAU;AACpD,YAAM;AAAA,IACR;AAAA,EACF;AAGA,QAAM,MAAM,aAAa,EAAE,WAAW,MAAM;AAG5C,QAAM,cAAyB,CAAA;AAC/B,QAAM,YAAY,OAAO,KAAK,QAAQ,SAAS;AAE/C,aAAW,YAAY,WAAW;AAChC,UAAM,WAAW,QAAQ,UAAU,QAAQ;AAC3C,QAAI,CAAC,SAAU;AACf,UAAM,WAAW,MAAM,YAAY,YAAY,QAAQ;AACvD,gBAAY,KAAK,GAAG,QAAQ;AAAA,EAC9B;AAGA,QAAM,EAAE,UAAU,iBAAiB,kBAAA,IAAsB,qBAAqB,WAAW;AAGzF,QAAM,iBAAiB,gBAAgB,IAAI,cAAc;AAGzD,QAAM,aAAyB;AAAA,IAC7B,WAAW,QAAQ;AAAA,IACnB,GAAI,QAAQ,QAAQ,EAAE,MAAM,QAAQ,KAAA;AAAA,IACpC,UAAU;AAAA,EAAA;AAIZ,QAAM,cAAcA,UAAc,YAAY;AAAA,IAC5C,WAAW;AAAA;AAAA,EAAA,CACZ;AAGD,QAAM,gBAAgB;AAAA;AAGtB,QAAM,iBAAiB;AAAA;AAAA;AAAA;AAIvB,QAAM,eAAe,gBAAgB,YAAY;AAAA,IAC/C;AAAA,IACA;AAAA,EAAA;AAIF,QAAM,UAAU,aAAa,cAAc,OAAO;AAGlD,QAAM,iBAAiB,KAAK,aAAa,oBAAoB;AAC7D,QAAM,aAAa,yBAAA;AACnB,QAAM,UAAU,gBAAgB,KAAK,UAAU,YAAY,MAAM,CAAC,IAAI,MAAM,OAAO;AAEnF,SAAO;AAAA,IACL;AAAA,IACA,cAAc,eAAe;AAAA,IAC7B;AAAA,EAAA;AAEJ;"}

package/dist/cli/commands/review/next-steps.d.ts

@@ -1,8 +1,11 @@
 import { ReviewStatusResult } from './status.js';
+import { ReviewMode } from './types.js';
 import { Suggestion, SuggestionResult } from '../../suggestions/types.js';
 export interface ReviewNextStepsContext {
     sessionId: string;
     statusResult: ReviewStatusResult;
+    /** Review mode: screening (default) or picking */
+    mode?: ReviewMode;
     /** Extract name for batch continuation */
     extractName?: string;
     /** Number of articles extracted in current batch */

package/dist/cli/commands/review/next-steps.d.ts.map

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package/dist/cli/commands/review/next-steps.js

@@ -15,35 +15,69 @@ function detectNextBasis(reviewers) {
   return "fulltext";
 }
 function generateReviewNextSteps(ctx) {
-  const { sessionId, statusResult: rs } = ctx;
+  const { sessionId, statusResult: rs, mode = "screening" } = ctx;
   if (rs.total === 0) return null;
   const result = { next: [], seeAlso: [] };
-  if (rs.pending > 0) {
-    result.next.push({
-      command: `search-hub review extract --session ${sessionId} --basis title --filter pending --reviewer "<name>" --name title-screening`,
-      description: `Extract ${rs.pending} pending articles for title screening`
-    });
-  } else {
-    const agreed = rs.agreedInclude + rs.agreedExclude;
-    if (agreed > 0) {
+  if (mode === "picking") {
+    if (rs.pending > 0) {
       result.next.push({
-        command: `search-hub review finalize --session ${sessionId}`,
-        description: `Finalize ${agreed} articles with consensus`
+        command: `search-hub review extract --session ${sessionId} --basis title --filter pending --reviewer "<name>" --name title-picking`,
+        description: `Extract ${rs.pending} pending articles for title review`
       });
-    } else if (rs.divided > 0 || rs.allUncertain > 0 || rs.incomplete > 0) {
-      const unresolved = rs.divided + rs.allUncertain + rs.incomplete;
+    } else if (rs.agreedInclude > 0 || rs.allUncertain > 0) {
       const nextBasis = detectNextBasis(rs.reviewers);
+      const parts = [];
+      if (rs.agreedInclude > 0) parts.push(`${rs.agreedInclude} picked`);
+      if (rs.allUncertain > 0) parts.push(`${rs.allUncertain} uncertain`);
+      const description = `${parts.join(" + ")} — confirm at ${nextBasis} level`;
       result.next.push({
-        command: `search-hub review extract --session ${sessionId} --filter divided,all-uncertain,incomplete --basis ${nextBasis} --reviewer "<name>" --name ${nextBasis}-screening`,
-        description: `${unresolved} articles need ${nextBasis}-level review`
+        command: `search-hub review extract --session ${sessionId} --filter agreed-include,all-uncertain --basis ${nextBasis} --reviewer "<name>" --name ${nextBasis}-screening`,
+        description
       });
-    } else if (rs.finalized > 0 && rs.finalized === rs.total) {
+    } else {
+      const agreed = rs.agreedInclude + rs.agreedExclude;
+      if (agreed > 0) {
+        result.next.push({
+          command: `search-hub review finalize --session ${sessionId}`,
+          description: `Finalize ${agreed} articles with consensus`
+        });
+      } else if (rs.finalized > 0 && rs.finalized === rs.total) {
+        result.next.push({
+          command: `search-hub review export --session ${sessionId} --only included`,
+          description: `${rs.included} articles ready for export`
+        });
+      } else {
+        return null;
+      }
+    }
+  } else {
+    if (rs.pending > 0) {
       result.next.push({
-        command: `search-hub register ${sessionId} --reviewed`,
-        description: "Register accepted articles"
+        command: `search-hub review extract --session ${sessionId} --basis title --filter pending --reviewer "<name>" --name title-screening`,
+        description: `Extract ${rs.pending} pending articles for title screening`
       });
     } else {
-      return null;
+      const agreed = rs.agreedInclude + rs.agreedExclude;
+      if (agreed > 0) {
+        result.next.push({
+          command: `search-hub review finalize --session ${sessionId}`,
+          description: `Finalize ${agreed} articles with consensus`
+        });
+      } else if (rs.divided > 0 || rs.allUncertain > 0 || rs.incomplete > 0) {
+        const unresolved = rs.divided + rs.allUncertain + rs.incomplete;
+        const nextBasis = detectNextBasis(rs.reviewers);
+        result.next.push({
+          command: `search-hub review extract --session ${sessionId} --filter divided,all-uncertain,incomplete --basis ${nextBasis} --reviewer "<name>" --name ${nextBasis}-screening`,
+          description: `${unresolved} articles need ${nextBasis}-level review`
+        });
+      } else if (rs.finalized > 0 && rs.finalized === rs.total) {
+        result.next.push({
+          command: `search-hub register ${sessionId} --reviewed`,
+          description: "Register accepted articles"
+        });
+      } else {
+        return null;
+      }
     }
   }
   if (ctx.limit !== void 0 && ctx.extractedCount !== void 0 && ctx.totalMatching !== void 0) {