@ncukondo/search-hub 0.11.0 → 0.12.1

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

@@ -0,0 +1,82 @@
+import { Article, ProviderName } from '../../providers/base/types.js';
+import { SessionFile, SessionSource } from '../../session/types.js';
+/**
+ * Result of merging articles from multiple sessions.
+ */
+export interface MergeResult {
+    /** All unique articles after deduplication */
+    articles: Article[];
+    /** Articles grouped by provider */
+    byProvider: Map<ProviderName, Article[]>;
+    /** Total article count before deduplication */
+    totalBefore: number;
+    /** Total unique article count after deduplication */
+    totalAfter: number;
+    /** Number of duplicates removed */
+    duplicatesRemoved: number;
+    /** Per-session article counts (before dedup) */
+    perSession: Map<string, number>;
+}
+/**
+ * Options for creating a merged session.
+ */
+export interface CreateMergedSessionOptions {
+    name: string;
+    sources: SessionSource[];
+    byProvider: Map<ProviderName, Article[]>;
+    totalRetrieved: number;
+    sessionsDir: string;
+    sourceSessionIds: string[];
+}
+/**
+ * Validation result for merge sources.
+ */
+export interface MergeValidationResult {
+    valid: boolean;
+    error?: string;
+    expandedCommand?: string;
+}
+/**
+ * Output data for formatting merge results.
+ */
+export interface MergeOutputData {
+    sessionId: string;
+    totalBefore: number;
+    totalAfter: number;
+    duplicatesRemoved: number;
+    sources: Array<{
+        id: string;
+        name: string;
+        count: number;
+    }>;
+    byProvider: Map<string, number>;
+}
+/**
+ * Merge articles from multiple sessions with identifier-based deduplication.
+ *
+ * When duplicates are found (same DOI, PMID, etc.), the article with
+ * richer metadata is kept.
+ */
+export declare function mergeArticles(sessionArticles: Map<string, Article[]>): MergeResult;
+/**
+ * Copy source session provenance files to sources/ subdirectory.
+ * Copies session.yaml, query_common.yaml, and query text files.
+ */
+export declare function copySourceProvenance(sourceSessionId: string, sessionsDir: string, mergedSessionDir: string): Promise<void>;
+/**
+ * Validate that all source sessions are valid for merging.
+ */
+export declare function validateMergeSources(sessions: Map<string, SessionFile>): MergeValidationResult;
+/**
+ * Create a merged session on disk.
+ */
+export declare function createMergedSession(options: CreateMergedSessionOptions): Promise<SessionFile>;
+/**
+ * Format merge result as human-readable text.
+ */
+export declare function formatMergeOutput(data: MergeOutputData): string;
+/**
+ * Format merge result as JSON.
+ */
+export declare function formatMergeJson(data: MergeOutputData): string;
+//# sourceMappingURL=merge.d.ts.map

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

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package/dist/cli/commands/merge.js

@@ -0,0 +1,221 @@
+import { mkdir, writeFile, copyFile, readdir } from "node:fs/promises";
+import { join } from "node:path";
+import { createHash } from "node:crypto";
+import { stringify } from "yaml";
+import { isMergedSession } from "../../session/types.js";
+import { sanitizeName } from "../../session/manager.js";
+import { convertResultsToYaml } from "../../session/results-io.js";
+import { getArticleKeys } from "./session-utils.js";
+function countMetadataFields(article) {
+  let count = 0;
+  if (article.doi) count++;
+  if (article.pmid) count++;
+  if (article.arxivId) count++;
+  if (article.scopusId) count++;
+  if (article.ericId) count++;
+  if (article.abstract) count++;
+  if (article.publicationDate) count++;
+  if (article.journal) count++;
+  if (article.volume) count++;
+  if (article.issue) count++;
+  if (article.pages) count++;
+  if (article.authors.length > 0) count++;
+  return count;
+}
+function mergeArticles(sessionArticles) {
+  const keyToIndex = /* @__PURE__ */ new Map();
+  const unique = [];
+  let totalBefore = 0;
+  let duplicatesRemoved = 0;
+  const perSession = /* @__PURE__ */ new Map();
+  for (const [sessionId, articles] of sessionArticles) {
+    perSession.set(sessionId, articles.length);
+    totalBefore += articles.length;
+    for (const article of articles) {
+      const keys = getArticleKeys(article);
+      if (keys.length === 0) {
+        unique.push(article);
+        continue;
+      }
+      let existingIndex;
+      for (const key of keys) {
+        const idx = keyToIndex.get(key);
+        if (idx !== void 0) {
+          existingIndex = idx;
+          break;
+        }
+      }
+      if (existingIndex !== void 0) {
+        const existing = unique[existingIndex];
+        if (countMetadataFields(article) > countMetadataFields(existing)) {
+          unique[existingIndex] = article;
+          const newKeys = getArticleKeys(article);
+          for (const key of newKeys) {
+            keyToIndex.set(key, existingIndex);
+          }
+        }
+        duplicatesRemoved++;
+      } else {
+        const index = unique.length;
+        unique.push(article);
+        for (const key of keys) {
+          keyToIndex.set(key, index);
+        }
+      }
+    }
+  }
+  const byProvider = /* @__PURE__ */ new Map();
+  for (const article of unique) {
+    const existing = byProvider.get(article.source) ?? [];
+    existing.push(article);
+    byProvider.set(article.source, existing);
+  }
+  return {
+    articles: unique,
+    byProvider,
+    totalBefore,
+    totalAfter: unique.length,
+    duplicatesRemoved,
+    perSession
+  };
+}
+async function copySourceProvenance(sourceSessionId, sessionsDir, mergedSessionDir) {
+  const sourceDir = join(sessionsDir, sourceSessionId);
+  const targetDir = join(mergedSessionDir, "sources", sourceSessionId);
+  await mkdir(targetDir, { recursive: true });
+  for (const file of ["session.yaml", "query_common.yaml"]) {
+    try {
+      await copyFile(join(sourceDir, file), join(targetDir, file));
+    } catch {
+    }
+  }
+  const entries = await readdir(sourceDir);
+  for (const entry of entries) {
+    if (entry.startsWith("query_") && entry.endsWith(".txt")) {
+      await copyFile(join(sourceDir, entry), join(targetDir, entry));
+    }
+  }
+}
+function validateMergeSources(sessions) {
+  for (const [sessionId, session] of sessions) {
+    if (isMergedSession(session)) {
+      const originalSources = session.sources?.map((s) => s.id) ?? [];
+      const otherIds = [...sessions.keys()].filter((id) => id !== sessionId);
+      const allSources = [.../* @__PURE__ */ new Set([...originalSources, ...otherIds])];
+      const expandedCommand = `search-hub merge ${allSources.join(" ")}`;
+      return {
+        valid: false,
+        error: `Session '${sessionId}' is a merged session (sources: ${originalSources.join(", ")}).
+  Merge the original sources directly:
+  ${expandedCommand}`,
+        expandedCommand
+      };
+    }
+  }
+  for (const [sessionId, session] of sessions) {
+    if (session.summary.status !== "completed") {
+      return {
+        valid: false,
+        error: `Session '${sessionId}' is not completed (status: ${session.summary.status}). Only completed sessions can be merged.`
+      };
+    }
+  }
+  return { valid: true };
+}
+function generateMergedSessionId(name, sourceIds) {
+  const date = (/* @__PURE__ */ new Date()).toISOString().slice(0, 10).replace(/-/g, "");
+  const sanitized = sanitizeName(name);
+  const hash = createHash("sha256").update(sourceIds.join(",")).digest("hex").slice(0, 6);
+  return `${date}_${sanitized}_${hash}`;
+}
+async function createMergedSession(options) {
+  const { name, sources, byProvider, totalRetrieved, sessionsDir, sourceSessionIds } = options;
+  const id = generateMergedSessionId(name, sourceSessionIds);
+  const sessionDir = join(sessionsDir, id);
+  const now = (/* @__PURE__ */ new Date()).toISOString();
+  await mkdir(sessionDir, { recursive: true });
+  const databases = {};
+  for (const [provider, articles] of byProvider) {
+    const jsonlFilename = `${provider}_results.jsonl`;
+    const yamlFilename = `${provider}_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,
+      queryName: name
+    });
+    databases[provider] = {
+      status: "completed",
+      retrievedCount: articles.length,
+      files: {
+        query: "",
+        results: jsonlFilename,
+        resultsYaml: yamlFilename
+      }
+    };
+  }
+  const sessionFile = {
+    version: 1,
+    id,
+    name,
+    type: "merge",
+    createdAt: now,
+    updatedAt: now,
+    sources,
+    databases,
+    summary: {
+      totalHits: 0,
+      totalRetrieved,
+      status: "completed"
+    }
+  };
+  await writeFile(
+    join(sessionDir, "session.yaml"),
+    stringify(sessionFile),
+    "utf-8"
+  );
+  for (const sourceId of sourceSessionIds) {
+    await copySourceProvenance(sourceId, sessionsDir, sessionDir);
+  }
+  return sessionFile;
+}
+function formatMergeOutput(data) {
+  const lines = [];
+  lines.push(`Merged session: ${data.sessionId}`);
+  lines.push("");
+  lines.push("Sources:");
+  for (const source of data.sources) {
+    lines.push(`  ${source.id} (${source.name}): ${source.count} articles`);
+  }
+  lines.push("");
+  lines.push(`Total articles: ${data.totalBefore} → ${data.totalAfter} unique (${data.duplicatesRemoved} duplicates removed)`);
+  if (data.byProvider.size > 0) {
+    lines.push("");
+    lines.push("By database:");
+    for (const [provider, count] of data.byProvider) {
+      lines.push(`  ${provider}: ${count} articles`);
+    }
+  }
+  return lines.join("\n");
+}
+function formatMergeJson(data) {
+  return JSON.stringify({
+    sessionId: data.sessionId,
+    totalBefore: data.totalBefore,
+    totalAfter: data.totalAfter,
+    duplicatesRemoved: data.duplicatesRemoved,
+    sources: data.sources,
+    byProvider: Object.fromEntries(data.byProvider)
+  }, null, 2);
+}
+export {
+  copySourceProvenance,
+  createMergedSession,
+  formatMergeJson,
+  formatMergeOutput,
+  mergeArticles,
+  validateMergeSources
+};
+//# sourceMappingURL=merge.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"merge.js","sources":["../../../src/cli/commands/merge.ts"],"sourcesContent":["import { mkdir, writeFile, readFile, readdir, copyFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { createHash } from 'node:crypto';\nimport { stringify as stringifyYaml } from 'yaml';\nimport type { Article, ProviderName } from '../../providers/base/types.js';\nimport type { SessionFile, SessionSource, DatabaseStatus } from '../../session/types.js';\nimport { isMergedSession } from '../../session/types.js';\nimport { sanitizeName } from '../../session/manager.js';\nimport { convertResultsToYaml } from '../../session/results-io.js';\nimport { getArticleKeys } from './session-utils.js';\n\n/**\n * Result of merging articles from multiple sessions.\n */\nexport interface MergeResult {\n  /** All unique articles after deduplication */\n  articles: Article[];\n  /** Articles grouped by provider */\n  byProvider: Map<ProviderName, Article[]>;\n  /** Total article count before deduplication */\n  totalBefore: number;\n  /** Total unique article count after deduplication */\n  totalAfter: number;\n  /** Number of duplicates removed */\n  duplicatesRemoved: number;\n  /** Per-session article counts (before dedup) */\n  perSession: Map<string, number>;\n}\n\n/**\n * Options for creating a merged session.\n */\nexport interface CreateMergedSessionOptions {\n  name: string;\n  sources: SessionSource[];\n  byProvider: Map<ProviderName, Article[]>;\n  totalRetrieved: number;\n  sessionsDir: string;\n  sourceSessionIds: string[];\n}\n\n/**\n * Validation result for merge sources.\n */\nexport interface MergeValidationResult {\n  valid: boolean;\n  error?: string;\n  expandedCommand?: string;\n}\n\n/**\n * Output data for formatting merge results.\n */\nexport interface MergeOutputData {\n  sessionId: string;\n  totalBefore: number;\n  totalAfter: number;\n  duplicatesRemoved: number;\n  sources: Array<{ id: string; name: string; count: number }>;\n  byProvider: Map<string, number>;\n}\n\n/**\n * Count metadata fields for comparing article richness.\n */\nfunction countMetadataFields(article: Article): number {\n  let count = 0;\n  if (article.doi) count++;\n  if (article.pmid) count++;\n  if (article.arxivId) count++;\n  if (article.scopusId) count++;\n  if (article.ericId) count++;\n  if (article.abstract) count++;\n  if (article.publicationDate) count++;\n  if (article.journal) count++;\n  if (article.volume) count++;\n  if (article.issue) count++;\n  if (article.pages) count++;\n  if (article.authors.length > 0) count++;\n  return count;\n}\n\n/**\n * Merge articles from multiple sessions with identifier-based deduplication.\n *\n * When duplicates are found (same DOI, PMID, etc.), the article with\n * richer metadata is kept.\n */\nexport function mergeArticles(\n  sessionArticles: Map<string, Article[]>,\n): MergeResult {\n  const keyToIndex = new Map<string, number>();\n  const unique: Article[] = [];\n  let totalBefore = 0;\n  let duplicatesRemoved = 0;\n  const perSession = new Map<string, number>();\n\n  for (const [sessionId, articles] of sessionArticles) {\n    perSession.set(sessionId, articles.length);\n    totalBefore += articles.length;\n\n    for (const article of articles) {\n      const keys = getArticleKeys(article);\n\n      if (keys.length === 0) {\n        unique.push(article);\n        continue;\n      }\n\n      let existingIndex: number | undefined;\n      for (const key of keys) {\n        const idx = keyToIndex.get(key);\n        if (idx !== undefined) {\n          existingIndex = idx;\n          break;\n        }\n      }\n\n      if (existingIndex !== undefined) {\n        const existing = unique[existingIndex]!;\n        if (countMetadataFields(article) > countMetadataFields(existing)) {\n          unique[existingIndex] = article;\n          const newKeys = getArticleKeys(article);\n          for (const key of newKeys) {\n            keyToIndex.set(key, existingIndex);\n          }\n        }\n        duplicatesRemoved++;\n      } else {\n        const index = unique.length;\n        unique.push(article);\n        for (const key of keys) {\n          keyToIndex.set(key, index);\n        }\n      }\n    }\n  }\n\n  // Group by provider\n  const byProvider = new Map<ProviderName, Article[]>();\n  for (const article of unique) {\n    const existing = byProvider.get(article.source) ?? [];\n    existing.push(article);\n    byProvider.set(article.source, existing);\n  }\n\n  return {\n    articles: unique,\n    byProvider,\n    totalBefore,\n    totalAfter: unique.length,\n    duplicatesRemoved,\n    perSession,\n  };\n}\n\n/**\n * Copy source session provenance files to sources/ subdirectory.\n * Copies session.yaml, query_common.yaml, and query text files.\n */\nexport async function copySourceProvenance(\n  sourceSessionId: string,\n  sessionsDir: string,\n  mergedSessionDir: string,\n): Promise<void> {\n  const sourceDir = join(sessionsDir, sourceSessionId);\n  const targetDir = join(mergedSessionDir, 'sources', sourceSessionId);\n  await mkdir(targetDir, { recursive: true });\n\n  // Copy session.yaml and query_common.yaml\n  for (const file of ['session.yaml', 'query_common.yaml']) {\n    try {\n      await copyFile(join(sourceDir, file), join(targetDir, file));\n    } catch {\n      // Skip if file doesn't exist\n    }\n  }\n\n  // Copy query text files (query_*.txt)\n  const entries = await readdir(sourceDir);\n  for (const entry of entries) {\n    if (entry.startsWith('query_') && entry.endsWith('.txt')) {\n      await copyFile(join(sourceDir, entry), join(targetDir, entry));\n    }\n  }\n}\n\n/**\n * Validate that all source sessions are valid for merging.\n */\nexport function validateMergeSources(\n  sessions: Map<string, SessionFile>,\n): MergeValidationResult {\n  // Check for merged sessions as sources\n  for (const [sessionId, session] of sessions) {\n    if (isMergedSession(session)) {\n      // Collect original sources from the merged session\n      const originalSources = session.sources?.map((s) => s.id) ?? [];\n      // Collect non-merged session IDs\n      const otherIds = [...sessions.keys()].filter((id) => id !== sessionId);\n      // Build expanded command with original sources + other sessions\n      const allSources = [...new Set([...originalSources, ...otherIds])];\n      const expandedCommand = `search-hub merge ${allSources.join(' ')}`;\n\n      return {\n        valid: false,\n        error: `Session '${sessionId}' is a merged session (sources: ${originalSources.join(', ')}).\\n  Merge the original sources directly:\\n  ${expandedCommand}`,\n        expandedCommand,\n      };\n    }\n  }\n\n  // Check that all sessions are completed\n  for (const [sessionId, session] of sessions) {\n    if (session.summary.status !== 'completed') {\n      return {\n        valid: false,\n        error: `Session '${sessionId}' is not completed (status: ${session.summary.status}). Only completed sessions can be merged.`,\n      };\n    }\n  }\n\n  return { valid: true };\n}\n\n/**\n * Generate a session ID for a merged session.\n */\nfunction generateMergedSessionId(name: string, sourceIds: string[]): string {\n  const date = new Date().toISOString().slice(0, 10).replace(/-/g, '');\n  const sanitized = sanitizeName(name);\n  const hash = createHash('sha256').update(sourceIds.join(',')).digest('hex').slice(0, 6);\n  return `${date}_${sanitized}_${hash}`;\n}\n\n/**\n * Create a merged session on disk.\n */\nexport async function createMergedSession(\n  options: CreateMergedSessionOptions,\n): Promise<SessionFile> {\n  const { name, sources, byProvider, totalRetrieved, sessionsDir, sourceSessionIds } = options;\n\n  const id = generateMergedSessionId(name, sourceSessionIds);\n  const sessionDir = join(sessionsDir, id);\n  const now = new Date().toISOString();\n\n  await mkdir(sessionDir, { recursive: true });\n\n  // Build database statuses and write result files\n  const databases: Partial<Record<ProviderName, DatabaseStatus>> = {};\n\n  for (const [provider, articles] of byProvider) {\n    const jsonlFilename = `${provider}_results.jsonl`;\n    const yamlFilename = `${provider}_results.yaml`;\n    const jsonlPath = join(sessionDir, jsonlFilename);\n\n    // Write JSONL results\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,\n      queryName: name,\n    });\n\n    databases[provider] = {\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: 'merge',\n    createdAt: now,\n    updatedAt: now,\n    sources,\n    databases,\n    summary: {\n      totalHits: 0,\n      totalRetrieved: totalRetrieved,\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  // Copy provenance from source sessions\n  for (const sourceId of sourceSessionIds) {\n    await copySourceProvenance(sourceId, sessionsDir, sessionDir);\n  }\n\n  return sessionFile;\n}\n\n/**\n * Format merge result as human-readable text.\n */\nexport function formatMergeOutput(data: MergeOutputData): string {\n  const lines: string[] = [];\n\n  lines.push(`Merged session: ${data.sessionId}`);\n  lines.push('');\n  lines.push('Sources:');\n  for (const source of data.sources) {\n    lines.push(`  ${source.id} (${source.name}): ${source.count} articles`);\n  }\n  lines.push('');\n  lines.push(`Total articles: ${data.totalBefore} → ${data.totalAfter} unique (${data.duplicatesRemoved} duplicates removed)`);\n\n  if (data.byProvider.size > 0) {\n    lines.push('');\n    lines.push('By database:');\n    for (const [provider, count] of data.byProvider) {\n      lines.push(`  ${provider}: ${count} articles`);\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Format merge result as JSON.\n */\nexport function formatMergeJson(data: MergeOutputData): string {\n  return JSON.stringify({\n    sessionId: data.sessionId,\n    totalBefore: data.totalBefore,\n    totalAfter: data.totalAfter,\n    duplicatesRemoved: data.duplicatesRemoved,\n    sources: data.sources,\n    byProvider: Object.fromEntries(data.byProvider),\n  }, null, 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package/dist/cli/commands/resume.d.ts.map

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package/dist/cli/commands/resume.js

@@ -1,4 +1,5 @@
 import { loadSession, getResumableProviders } from "../../session/manager.js";
+import { isMergedSession } from "../../session/types.js";
 import { parseProviderNames } from "../utils/validation.js";
 function parseResumeOptions(sessionId, options) {
   const result = {
@@ -24,6 +25,12 @@ function validateResumeInput(options) {
 async function getResumableProvidersForCommand(sessionId, sessionsDir, options) {
   try {
     const session = await loadSession(sessionId, sessionsDir);
+    if (isMergedSession(session)) {
+      return {
+        success: false,
+        error: `Cannot resume merged session '${sessionId}'. Merged sessions are created from other sessions and cannot be resumed.`
+      };
+    }
     let resumable = getResumableProviders(session);
     if (options.providers && options.providers.length > 0) {
       resumable = resumable.filter((r) => options.providers.includes(r.provider));

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

@@ -1 +1 @@
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+{"version":3,"file":"resume.js","sources":["../../../src/cli/commands/resume.ts"],"sourcesContent":["import { loadSession, getResumableProviders } from '../../session/manager.js';\nimport type { ProviderName, ResumableProvider } from '../../session/types.js';\nimport { isMergedSession } from '../../session/types.js';\nimport { parseProviderNames } from '../utils/validation.js';\n\nexport interface ResumeCommandOptions {\n  sessionId: string;\n  providers?: ProviderName[];\n  retryFailed?: boolean;\n}\n\nexport interface CommandLineOptions {\n  db?: string | undefined;\n  retryFailed?: boolean | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\nexport interface ResumeResult {\n  success: boolean;\n  providers?: ResumableProvider[];\n  error?: string;\n}\n\nexport function parseResumeOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): ResumeCommandOptions {\n  const result: ResumeCommandOptions = {\n    sessionId,\n  };\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  if (options.retryFailed) {\n    result.retryFailed = true;\n  }\n\n  return result;\n}\n\nexport function validateResumeInput(options: ResumeCommandOptions): 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\nexport async function getResumableProvidersForCommand(\n  sessionId: string,\n  sessionsDir: string,\n  options: { providers?: ProviderName[] | undefined; retryFailed?: boolean | undefined }\n): Promise<ResumeResult> {\n  try {\n    const session = await loadSession(sessionId, sessionsDir);\n\n    // Reject merged sessions\n    if (isMergedSession(session)) {\n      return {\n        success: false,\n        error: `Cannot resume merged session '${sessionId}'. Merged sessions are created from other sessions and cannot be resumed.`,\n      };\n    }\n\n    let resumable = getResumableProviders(session);\n\n    // Filter by specific providers if requested\n    if (options.providers && options.providers.length > 0) {\n      resumable = resumable.filter((r) => options.providers!.includes(r.provider));\n    }\n\n    // Filter to only retry strategies if retryFailed is true\n    if (options.retryFailed) {\n      resumable = resumable.filter((r) => r.strategy === 'retry');\n    }\n\n    return {\n      success: true,\n      providers: resumable,\n    };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : 'Unknown error';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n}\n"],"names":[],"mappings":";;;AA2BO,SAAS,mBACd,WACA,SACsB;AACtB,QAAM,SAA+B;AAAA,IACnC;AAAA,EAAA;AAGF,MAAI,QAAQ,IAAI;AACd,WAAO,YAAY,mBAAmB,QAAQ,EAAE;AAAA,EAClD;AAEA,MAAI,QAAQ,aAAa;AACvB,WAAO,cAAc;AAAA,EACvB;AAEA,SAAO;AACT;AAEO,SAAS,oBAAoB,SAAiD;AACnF,MAAI,CAAC,QAAQ,aAAa,QAAQ,UAAU,KAAA,MAAW,IAAI;AACzD,WAAO;AAAA,MACL,OAAO;AAAA,MACP,OAAO;AAAA,IAAA;AAAA,EAEX;AAEA,SAAO,EAAE,OAAO,KAAA;AAClB;AAEA,eAAsB,gCACpB,WACA,aACA,SACuB;AACvB,MAAI;AACF,UAAM,UAAU,MAAM,YAAY,WAAW,WAAW;AAGxD,QAAI,gBAAgB,OAAO,GAAG;AAC5B,aAAO;AAAA,QACL,SAAS;AAAA,QACT,OAAO,iCAAiC,SAAS;AAAA,MAAA;AAAA,IAErD;AAEA,QAAI,YAAY,sBAAsB,OAAO;AAG7C,QAAI,QAAQ,aAAa,QAAQ,UAAU,SAAS,GAAG;AACrD,kBAAY,UAAU,OAAO,CAAC,MAAM,QAAQ,UAAW,SAAS,EAAE,QAAQ,CAAC;AAAA,IAC7E;AAGA,QAAI,QAAQ,aAAa;AACvB,kBAAY,UAAU,OAAO,CAAC,MAAM,EAAE,aAAa,OAAO;AAAA,IAC5D;AAEA,WAAO;AAAA,MACL,SAAS;AAAA,MACT,WAAW;AAAA,IAAA;AAAA,EAEf,SAAS,OAAO;AACd,UAAM,UAAU,iBAAiB,QAAQ,MAAM,UAAU;AACzD,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO;AAAA,IAAA;AAAA,EAEX;AACF;"}

package/dist/cli/commands/status.js

@@ -43,7 +43,7 @@ async function getSessionDetails(sessionId, sessionsDir) {
       status: session.summary.status,
       createdAt: session.createdAt,
       updatedAt: session.updatedAt,
-      queryFile: session.query.file,
+      queryFile: session.query?.file ?? "",
       totalHits: session.summary.totalHits,
       totalRetrieved: session.summary.totalRetrieved,
       databases

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

@@ -1 +1 @@
-{"version":3,"file":"status.js","sources":["../../../src/cli/commands/status.ts"],"sourcesContent":["import { join } from 'node:path';\nimport { listSessions, loadSession } from '../../session/manager.js';\nimport { deduplicateArticles } from './export.js';\nimport { loadNotes, formatNotesList, type NoteEntry } from './notes.js';\nimport { loadResults } from '../../session/results-io.js';\nimport type { ProviderName } from '../../providers/base/types.js';\n\nexport interface SessionListItem {\n  id: string;\n  name: string;\n  status: string;\n  createdAt: string;\n  progress: string;\n}\n\nexport interface DatabaseDetails {\n  provider: string;\n  status: string;\n  totalHits: number;\n  retrievedCount: number;\n  error?: string;\n}\n\nexport interface SessionDetails {\n  id: string;\n  name: string;\n  description?: string;\n  status: string;\n  createdAt: string;\n  updatedAt: string;\n  queryFile: string;\n  totalHits: number;\n  totalRetrieved: number;\n  databases: DatabaseDetails[];\n  uniqueArticles?: number;\n  duplicatesRemoved?: number;\n  notes?: NoteEntry[];\n}\n\nexport interface ListOptions {\n  all: boolean;\n}\n\nexport interface FormatOptions {\n  json: boolean;\n}\n\nexport interface SessionListResult {\n  sessions: SessionListItem[];\n  totalCount: number;\n  filteredCount: number;\n  showingAll: boolean;\n}\n\nexport async function listSessionsForDisplay(\n  sessionsDir: string,\n  options: ListOptions\n): Promise<SessionListResult> {\n  const summaries = await listSessions(sessionsDir);\n\n  const filtered = options.all\n    ? summaries\n    : summaries.filter((s) => s.status !== 'completed');\n\n  const sessions = filtered.map((s) => ({\n    id: s.id,\n    name: s.name,\n    status: s.status,\n    createdAt: s.createdAt,\n    progress: `${s.totalRetrieved}/${s.totalHits}`,\n  }));\n\n  return {\n    sessions,\n    totalCount: summaries.length,\n    filteredCount: filtered.length,\n    showingAll: options.all,\n  };\n}\n\nexport async function getSessionDetails(\n  sessionId: string,\n  sessionsDir: string\n): Promise<{ success: boolean; session?: SessionDetails; error?: string }> {\n  try {\n    const session = await loadSession(sessionId, sessionsDir);\n\n    const databases: DatabaseDetails[] = [];\n    for (const [provider, dbStatus] of Object.entries(session.databases)) {\n      if (!dbStatus) continue;\n      const dbDetail: DatabaseDetails = {\n        provider,\n        status: dbStatus.status,\n        totalHits: dbStatus.totalHits ?? 0,\n        retrievedCount: dbStatus.retrievedCount ?? 0,\n      };\n      if (dbStatus.error?.message) {\n        dbDetail.error = dbStatus.error.message;\n      }\n      databases.push(dbDetail);\n    }\n\n    const sessionDetails: SessionDetails = {\n      id: session.id,\n      name: session.name,\n      status: session.summary.status,\n      createdAt: session.createdAt,\n      updatedAt: session.updatedAt,\n      queryFile: session.query.file,\n      totalHits: session.summary.totalHits,\n      totalRetrieved: session.summary.totalRetrieved,\n      databases,\n    };\n    if (session.description) {\n      sessionDetails.description = session.description;\n    }\n\n    // Load notes (optional - don't fail if notes can't be loaded)\n    try {\n      const sessionDir = join(sessionsDir, sessionId);\n      const notes = await loadNotes(sessionDir);\n      if (notes.length > 0) {\n        sessionDetails.notes = notes;\n      }\n    } catch {\n      // Notes are optional - ignore errors\n    }\n\n    return {\n      success: true,\n      session: sessionDetails,\n    };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : 'Unknown error';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n}\n\nexport async function computeDeduplicationStats(\n  sessionId: string,\n  sessionsDir: string,\n  session: { databases: Record<string, { files?: { results?: string } } | undefined> }\n): Promise<{ uniqueArticles: number; duplicatesRemoved: number }> {\n  const articles: import('../../providers/base/types.js').Article[] = [];\n  const sessionDir = join(sessionsDir, sessionId);\n\n  for (const [providerName] of Object.entries(session.databases)) {\n    const providerArticles = await loadResults(sessionDir, providerName as ProviderName);\n    articles.push(...providerArticles);\n  }\n\n  if (articles.length === 0) {\n    return { uniqueArticles: 0, duplicatesRemoved: 0 };\n  }\n\n  const result = deduplicateArticles(articles);\n  return {\n    uniqueArticles: result.articles.length,\n    duplicatesRemoved: result.duplicatesRemoved,\n  };\n}\n\nexport function formatSessionList(\n  result: SessionListResult,\n  options: FormatOptions\n): string {\n  if (options.json) {\n    return JSON.stringify(result.sessions, null, 2);\n  }\n\n  if (result.sessions.length === 0) {\n    if (result.totalCount === 0) {\n      return 'No sessions found.';\n    }\n    // Sessions exist but are filtered out (all completed)\n    const completedCount = result.totalCount - result.filteredCount;\n    return `No active sessions. ${completedCount} completed session${completedCount === 1 ? '' : 's'} hidden (use --all to show).`;\n  }\n\n  const header = `${'ID'.padEnd(35)} ${'NAME'.padEnd(20)} ${'STATUS'.padEnd(15)} ${'PROGRESS'.padEnd(12)} CREATED`;\n  const separator = '-'.repeat(100);\n\n  const rows = result.sessions.map((s) => {\n    const date = new Date(s.createdAt).toLocaleDateString();\n    return `${s.id.padEnd(35)} ${s.name.padEnd(20)} ${s.status.padEnd(15)} ${s.progress.padEnd(12)} ${date}`;\n  });\n\n  const lines = [header, separator, ...rows];\n\n  // Show hint about hidden completed sessions if not showing all\n  if (!result.showingAll && result.totalCount > result.filteredCount) {\n    const hiddenCount = result.totalCount - result.filteredCount;\n    lines.push('');\n    lines.push(`(${hiddenCount} completed session${hiddenCount === 1 ? '' : 's'} hidden, use --all to show)`);\n  }\n\n  return lines.join('\\n');\n}\n\nexport function formatSessionDetails(\n  details: SessionDetails,\n  options: FormatOptions\n): string {\n  if (options.json) {\n    return JSON.stringify(details, null, 2);\n  }\n\n  const lines: string[] = [];\n\n  lines.push(`Session: ${details.name}`);\n  lines.push(`ID: ${details.id}`);\n  if (details.description) {\n    lines.push(`Description: ${details.description}`);\n  }\n  lines.push(`Status: ${details.status}`);\n  lines.push(`Query File: ${details.queryFile}`);\n  lines.push(`Created: ${new Date(details.createdAt).toLocaleString()}`);\n  lines.push(`Updated: ${new Date(details.updatedAt).toLocaleString()}`);\n  lines.push('');\n  if (details.duplicatesRemoved !== undefined && details.duplicatesRemoved > 0) {\n    lines.push(`Total: ${details.totalRetrieved} raw / ${details.uniqueArticles} unique (${details.duplicatesRemoved} duplicates)`);\n  } else {\n    lines.push(`Total: ${details.totalRetrieved}/${details.totalHits} results`);\n  }\n  lines.push('');\n  lines.push('Databases:');\n\n  for (const db of details.databases) {\n    const statusIcon = getStatusIcon(db.status);\n    let line = `  ${statusIcon} ${db.provider.padEnd(10)} ${db.status.padEnd(12)} ${db.retrievedCount}/${db.totalHits}`;\n    if (db.error) {\n      line += ` (${db.error})`;\n    }\n    lines.push(line);\n  }\n\n  // Display notes if present\n  if (details.notes && details.notes.length > 0) {\n    lines.push('');\n    lines.push('Notes:');\n    lines.push(formatNotesList(details.notes));\n  }\n\n  return lines.join('\\n');\n}\n\nfunction getStatusIcon(status: string): string {\n  switch (status) {\n    case 'completed':\n      return '\\u2713'; 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+{"version":3,"file":"status.js","sources":["../../../src/cli/commands/status.ts"],"sourcesContent":["import { join } from 'node:path';\nimport { listSessions, loadSession } from '../../session/manager.js';\nimport { deduplicateArticles } from './export.js';\nimport { loadNotes, formatNotesList, type NoteEntry } from './notes.js';\nimport { loadResults } from '../../session/results-io.js';\nimport type { ProviderName } from '../../providers/base/types.js';\n\nexport interface SessionListItem {\n  id: string;\n  name: string;\n  status: string;\n  createdAt: string;\n  progress: string;\n}\n\nexport interface DatabaseDetails {\n  provider: string;\n  status: string;\n  totalHits: number;\n  retrievedCount: number;\n  error?: string;\n}\n\nexport interface SessionDetails {\n  id: string;\n  name: string;\n  description?: string;\n  status: string;\n  createdAt: string;\n  updatedAt: string;\n  queryFile: string;\n  totalHits: number;\n  totalRetrieved: number;\n  databases: DatabaseDetails[];\n  uniqueArticles?: number;\n  duplicatesRemoved?: number;\n  notes?: NoteEntry[];\n}\n\nexport interface ListOptions {\n  all: boolean;\n}\n\nexport interface FormatOptions {\n  json: boolean;\n}\n\nexport interface SessionListResult {\n  sessions: SessionListItem[];\n  totalCount: number;\n  filteredCount: number;\n  showingAll: boolean;\n}\n\nexport async function listSessionsForDisplay(\n  sessionsDir: string,\n  options: ListOptions\n): Promise<SessionListResult> {\n  const summaries = await listSessions(sessionsDir);\n\n  const filtered = options.all\n    ? summaries\n    : summaries.filter((s) => s.status !== 'completed');\n\n  const sessions = filtered.map((s) => ({\n    id: s.id,\n    name: s.name,\n    status: s.status,\n    createdAt: s.createdAt,\n    progress: `${s.totalRetrieved}/${s.totalHits}`,\n  }));\n\n  return {\n    sessions,\n    totalCount: summaries.length,\n    filteredCount: filtered.length,\n    showingAll: options.all,\n  };\n}\n\nexport async function getSessionDetails(\n  sessionId: string,\n  sessionsDir: string\n): Promise<{ success: boolean; session?: SessionDetails; error?: string }> {\n  try {\n    const session = await loadSession(sessionId, sessionsDir);\n\n    const databases: DatabaseDetails[] = [];\n    for (const [provider, dbStatus] of Object.entries(session.databases)) {\n      if (!dbStatus) continue;\n      const dbDetail: DatabaseDetails = {\n        provider,\n        status: dbStatus.status,\n        totalHits: dbStatus.totalHits ?? 0,\n        retrievedCount: dbStatus.retrievedCount ?? 0,\n      };\n      if (dbStatus.error?.message) {\n        dbDetail.error = dbStatus.error.message;\n      }\n      databases.push(dbDetail);\n    }\n\n    const sessionDetails: SessionDetails = {\n      id: session.id,\n      name: session.name,\n      status: session.summary.status,\n      createdAt: session.createdAt,\n      updatedAt: session.updatedAt,\n      queryFile: session.query?.file ?? '',\n      totalHits: session.summary.totalHits,\n      totalRetrieved: session.summary.totalRetrieved,\n      databases,\n    };\n    if (session.description) {\n      sessionDetails.description = session.description;\n    }\n\n    // Load notes (optional - don't fail if notes can't be loaded)\n    try {\n      const sessionDir = join(sessionsDir, sessionId);\n      const notes = await loadNotes(sessionDir);\n      if (notes.length > 0) {\n        sessionDetails.notes = notes;\n      }\n    } catch {\n      // Notes are optional - ignore errors\n    }\n\n    return {\n      success: true,\n      session: sessionDetails,\n    };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : 'Unknown error';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n}\n\nexport async function computeDeduplicationStats(\n  sessionId: string,\n  sessionsDir: string,\n  session: { databases: Record<string, { files?: { results?: string } } | undefined> }\n): Promise<{ uniqueArticles: number; duplicatesRemoved: number }> {\n  const articles: import('../../providers/base/types.js').Article[] = [];\n  const sessionDir = join(sessionsDir, sessionId);\n\n  for (const [providerName] of Object.entries(session.databases)) {\n    const providerArticles = await loadResults(sessionDir, providerName as ProviderName);\n    articles.push(...providerArticles);\n  }\n\n  if (articles.length === 0) {\n    return { uniqueArticles: 0, duplicatesRemoved: 0 };\n  }\n\n  const result = deduplicateArticles(articles);\n  return {\n    uniqueArticles: result.articles.length,\n    duplicatesRemoved: result.duplicatesRemoved,\n  };\n}\n\nexport function formatSessionList(\n  result: SessionListResult,\n  options: FormatOptions\n): string {\n  if (options.json) {\n    return JSON.stringify(result.sessions, null, 2);\n  }\n\n  if (result.sessions.length === 0) {\n    if (result.totalCount === 0) {\n      return 'No sessions found.';\n    }\n    // Sessions exist but are filtered out (all completed)\n    const completedCount = result.totalCount - result.filteredCount;\n    return `No active sessions. ${completedCount} completed session${completedCount === 1 ? '' : 's'} hidden (use --all to show).`;\n  }\n\n  const header = `${'ID'.padEnd(35)} ${'NAME'.padEnd(20)} ${'STATUS'.padEnd(15)} ${'PROGRESS'.padEnd(12)} CREATED`;\n  const separator = '-'.repeat(100);\n\n  const rows = result.sessions.map((s) => {\n    const date = new Date(s.createdAt).toLocaleDateString();\n    return `${s.id.padEnd(35)} ${s.name.padEnd(20)} ${s.status.padEnd(15)} ${s.progress.padEnd(12)} ${date}`;\n  });\n\n  const lines = [header, separator, ...rows];\n\n  // Show hint about hidden completed sessions if not showing all\n  if (!result.showingAll && result.totalCount > result.filteredCount) {\n    const hiddenCount = result.totalCount - result.filteredCount;\n    lines.push('');\n    lines.push(`(${hiddenCount} completed session${hiddenCount === 1 ? '' : 's'} hidden, use --all to show)`);\n  }\n\n  return lines.join('\\n');\n}\n\nexport function formatSessionDetails(\n  details: SessionDetails,\n  options: FormatOptions\n): string {\n  if (options.json) {\n    return JSON.stringify(details, null, 2);\n  }\n\n  const lines: string[] = [];\n\n  lines.push(`Session: ${details.name}`);\n  lines.push(`ID: ${details.id}`);\n  if (details.description) {\n    lines.push(`Description: ${details.description}`);\n  }\n  lines.push(`Status: ${details.status}`);\n  lines.push(`Query File: ${details.queryFile}`);\n  lines.push(`Created: ${new Date(details.createdAt).toLocaleString()}`);\n  lines.push(`Updated: ${new Date(details.updatedAt).toLocaleString()}`);\n  lines.push('');\n  if (details.duplicatesRemoved !== undefined && details.duplicatesRemoved > 0) {\n    lines.push(`Total: ${details.totalRetrieved} raw / ${details.uniqueArticles} unique (${details.duplicatesRemoved} duplicates)`);\n  } else {\n    lines.push(`Total: ${details.totalRetrieved}/${details.totalHits} results`);\n  }\n  lines.push('');\n  lines.push('Databases:');\n\n  for (const db of details.databases) {\n    const statusIcon = getStatusIcon(db.status);\n    let line = `  ${statusIcon} ${db.provider.padEnd(10)} ${db.status.padEnd(12)} ${db.retrievedCount}/${db.totalHits}`;\n    if (db.error) {\n      line += ` (${db.error})`;\n    }\n    lines.push(line);\n  }\n\n  // Display notes if present\n  if (details.notes && details.notes.length > 0) {\n    lines.push('');\n    lines.push('Notes:');\n    lines.push(formatNotesList(details.notes));\n  }\n\n  return lines.join('\\n');\n}\n\nfunction getStatusIcon(status: string): string {\n  switch (status) {\n    case 'completed':\n      return '\\u2713'; // ✓\n    case 'failed':\n      return '\\u2717'; // ✗\n    case 'in_progress':\n      return '\\u280B'; // ⠋\n    case 'pending':\n      return '\\u25FC'; // ◼\n    default:\n      return ' ';\n  }\n}\n"],"names":[],"mappings":";;;;;AAsDA,eAAsB,uBACpB,aACA,SAC4B;AAC5B,QAAM,YAAY,MAAM,aAAa,WAAW;AAEhD,QAAM,WAAW,QAAQ,MACrB,YACA,UAAU,OAAO,CAAC,MAAM,EAAE,WAAW,WAAW;AAEpD,QAAM,WAAW,SAAS,IAAI,CAAC,OAAO;AAAA,IACpC,IAAI,EAAE;AAAA,IACN,MAAM,EAAE;AAAA,IACR,QAAQ,EAAE;AAAA,IACV,WAAW,EAAE;AAAA,IACb,UAAU,GAAG,EAAE,cAAc,IAAI,EAAE,SAAS;AAAA,EAAA,EAC5C;AAEF,SAAO;AAAA,IACL;AAAA,IACA,YAAY,UAAU;AAAA,IACtB,eAAe,SAAS;AAAA,IACxB,YAAY,QAAQ;AAAA,EAAA;AAExB;AAEA,eAAsB,kBACpB,WACA,aACyE;AACzE,MAAI;AACF,UAAM,UAAU,MAAM,YAAY,WAAW,WAAW;AAExD,UAAM,YAA+B,CAAA;AACrC,eAAW,CAAC,UAAU,QAAQ,KAAK,OAAO,QAAQ,QAAQ,SAAS,GAAG;AACpE,UAAI,CAAC,SAAU;AACf,YAAM,WAA4B;AAAA,QAChC;AAAA,QACA,QAAQ,SAAS;AAAA,QACjB,WAAW,SAAS,aAAa;AAAA,QACjC,gBAAgB,SAAS,kBAAkB;AAAA,MAAA;AAE7C,UAAI,SAAS,OAAO,SAAS;AAC3B,iBAAS,QAAQ,SAAS,MAAM;AAAA,MAClC;AACA,gBAAU,KAAK,QAAQ;AAAA,IACzB;AAEA,UAAM,iBAAiC;AAAA,MACrC,IAAI,QAAQ;AAAA,MACZ,MAAM,QAAQ;AAAA,MACd,QAAQ,QAAQ,QAAQ;AAAA,MACxB,WAAW,QAAQ;AAAA,MACnB,WAAW,QAAQ;AAAA,MACnB,WAAW,QAAQ,OAAO,QAAQ;AAAA,MAClC,WAAW,QAAQ,QAAQ;AAAA,MAC3B,gBAAgB,QAAQ,QAAQ;AAAA,MAChC;AAAA,IAAA;AAEF,QAAI,QAAQ,aAAa;AACvB,qBAAe,cAAc,QAAQ;AAAA,IACvC;AAGA,QAAI;AACF,YAAM,aAAa,KAAK,aAAa,SAAS;AAC9C,YAAM,QAAQ,MAAM,UAAU,UAAU;AACxC,UAAI,MAAM,SAAS,GAAG;AACpB,uBAAe,QAAQ;AAAA,MACzB;AAAA,IACF,QAAQ;AAAA,IAER;AAEA,WAAO;AAAA,MACL,SAAS;AAAA,MACT,SAAS;AAAA,IAAA;AAAA,EAEb,SAAS,OAAO;AACd,UAAM,UAAU,iBAAiB,QAAQ,MAAM,UAAU;AACzD,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO;AAAA,IAAA;AAAA,EAEX;AACF;AAEA,eAAsB,0BACpB,WACA,aACA,SACgE;AAChE,QAAM,WAA8D,CAAA;AACpE,QAAM,aAAa,KAAK,aAAa,SAAS;AAE9C,aAAW,CAAC,YAAY,KAAK,OAAO,QAAQ,QAAQ,SAAS,GAAG;AAC9D,UAAM,mBAAmB,MAAM,YAAY,YAAY,YAA4B;AACnF,aAAS,KAAK,GAAG,gBAAgB;AAAA,EACnC;AAEA,MAAI,SAAS,WAAW,GAAG;AACzB,WAAO,EAAE,gBAAgB,GAAG,mBAAmB,EAAA;AAAA,EACjD;AAEA,QAAM,SAAS,oBAAoB,QAAQ;AAC3C,SAAO;AAAA,IACL,gBAAgB,OAAO,SAAS;AAAA,IAChC,mBAAmB,OAAO;AAAA,EAAA;AAE9B;AAEO,SAAS,kBACd,QACA,SACQ;AACR,MAAI,QAAQ,MAAM;AAChB,WAAO,KAAK,UAAU,OAAO,UAAU,MAAM,CAAC;AAAA,EAChD;AAEA,MAAI,OAAO,SAAS,WAAW,GAAG;AAChC,QAAI,OAAO,eAAe,GAAG;AAC3B,aAAO;AAAA,IACT;AAEA,UAAM,iBAAiB,OAAO,aAAa,OAAO;AAClD,WAAO,uBAAuB,cAAc,qBAAqB,mBAAmB,IAAI,KAAK,GAAG;AAAA,EAClG;AAEA,QAAM,SAAS,GAAG,KAAK,OAAO,EAAE,CAAC,IAAI,OAAO,OAAO,EAAE,CAAC,IAAI,SAAS,OAAO,EAAE,CAAC,IAAI,WAAW,OAAO,EAAE,CAAC;AACtG,QAAM,YAAY,IAAI,OAAO,GAAG;AAEhC,QAAM,OAAO,OAAO,SAAS,IAAI,CAAC,MAAM;AACtC,UAAM,OAAO,IAAI,KAAK,EAAE,SAAS,EAAE,mBAAA;AACnC,WAAO,GAAG,EAAE,GAAG,OAAO,EAAE,CAAC,IAAI,EAAE,KAAK,OAAO,EAAE,CAAC,IAAI,EAAE,OAAO,OAAO,EAAE,CAAC,IAAI,EAAE,SAAS,OAAO,EAAE,CAAC,IAAI,IAAI;AAAA,EACxG,CAAC;AAED,QAAM,QAAQ,CAAC,QAAQ,WAAW,GAAG,IAAI;AAGzC,MAAI,CAAC,OAAO,cAAc,OAAO,aAAa,OAAO,eAAe;AAClE,UAAM,cAAc,OAAO,aAAa,OAAO;AAC/C,UAAM,KAAK,EAAE;AACb,UAAM,KAAK,IAAI,WAAW,qBAAqB,gBAAgB,IAAI,KAAK,GAAG,6BAA6B;AAAA,EAC1G;AAEA,SAAO,MAAM,KAAK,IAAI;AACxB;AAEO,SAAS,qBACd,SACA,SACQ;AACR,MAAI,QAAQ,MAAM;AAChB,WAAO,KAAK,UAAU,SAAS,MAAM,CAAC;AAAA,EACxC;AAEA,QAAM,QAAkB,CAAA;AAExB,QAAM,KAAK,YAAY,QAAQ,IAAI,EAAE;AACrC,QAAM,KAAK,OAAO,QAAQ,EAAE,EAAE;AAC9B,MAAI,QAAQ,aAAa;AACvB,UAAM,KAAK,gBAAgB,QAAQ,WAAW,EAAE;AAAA,EAClD;AACA,QAAM,KAAK,WAAW,QAAQ,MAAM,EAAE;AACtC,QAAM,KAAK,eAAe,QAAQ,SAAS,EAAE;AAC7C,QAAM,KAAK,YAAY,IAAI,KAAK,QAAQ,SAAS,EAAE,eAAA,CAAgB,EAAE;AACrE,QAAM,KAAK,YAAY,IAAI,KAAK,QAAQ,SAAS,EAAE,eAAA,CAAgB,EAAE;AACrE,QAAM,KAAK,EAAE;AACb,MAAI,QAAQ,sBAAsB,UAAa,QAAQ,oBAAoB,GAAG;AAC5E,UAAM,KAAK,UAAU,QAAQ,cAAc,UAAU,QAAQ,cAAc,YAAY,QAAQ,iBAAiB,cAAc;AAAA,EAChI,OAAO;AACL,UAAM,KAAK,UAAU,QAAQ,cAAc,IAAI,QAAQ,SAAS,UAAU;AAAA,EAC5E;AACA,QAAM,KAAK,EAAE;AACb,QAAM,KAAK,YAAY;AAEvB,aAAW,MAAM,QAAQ,WAAW;AAClC,UAAM,aAAa,cAAc,GAAG,MAAM;AAC1C,QAAI,OAAO,KAAK,UAAU,IAAI,GAAG,SAAS,OAAO,EAAE,CAAC,IAAI,GAAG,OAAO,OAAO,EAAE,CAAC,IAAI,GAAG,cAAc,IAAI,GAAG,SAAS;AACjH,QAAI,GAAG,OAAO;AACZ,cAAQ,KAAK,GAAG,KAAK;AAAA,IACvB;AACA,UAAM,KAAK,IAAI;AAAA,EACjB;AAGA,MAAI,QAAQ,SAAS,QAAQ,MAAM,SAAS,GAAG;AAC7C,UAAM,KAAK,EAAE;AACb,UAAM,KAAK,QAAQ;AACnB,UAAM,KAAK,gBAAgB,QAAQ,KAAK,CAAC;AAAA,EAC3C;AAEA,SAAO,MAAM,KAAK,IAAI;AACxB;AAEA,SAAS,cAAc,QAAwB;AAC7C,UAAQ,QAAA;AAAA,IACN,KAAK;AACH,aAAO;AAAA;AAAA,IACT,KAAK;AACH,aAAO;AAAA;AAAA,IACT,KAAK;AACH,aAAO;AAAA;AAAA,IACT,KAAK;AACH,aAAO;AAAA;AAAA,IACT;AACE,aAAO;AAAA,EAAA;AAEb;"}

package/dist/cli/index.d.ts.map

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

package/dist/cli/index.js

@@ -23,11 +23,12 @@ import { computeSummary, formatSummaryJson, formatSummary } from "./commands/sum
 import { parseResultsOptions, validateResultsInput, formatResultsJson, formatResultsList } from "./commands/results.js";
 import { loadNotes, formatAllSessionNotes, formatNotesList, addNote, addAssessment } from "./commands/notes.js";
 import { computeDiff, computeQueryDiff, formatDiffJson, formatDiff } from "./commands/diff.js";
+import { validateMergeSources, mergeArticles, formatMergeJson, formatMergeOutput, createMergedSession } from "./commands/merge.js";
 import { executeReviewInit } from "./commands/review/init.js";
 import { executeReviewStatus, formatStatusOutput } from "./commands/review/status.js";
 import { executeReviewList, formatListOutput } from "./commands/review/list.js";
 import { executeReviewExtract } from "./commands/review/extract.js";
-import { executeReviewMerge, formatMergeOutput } from "./commands/review/merge.js";
+import { executeReviewMerge, formatMergeOutput as formatMergeOutput$1 } from "./commands/review/merge.js";
 import { executeReviewMark } from "./commands/review/mark.js";
 import { executeReviewExport, formatExportOutput } from "./commands/review/export.js";
 import { executeReviewFinalize, formatFinalizeOutput } from "./commands/review/finalize.js";
@@ -295,7 +296,13 @@ Examples:
   $ search-hub search --db pubmed --query "diabetes[tiab]"  # Direct query
   $ search-hub search ./query.yaml --dry-run            # Preview translations
   $ search-hub search ./query.yaml --count-only         # Get hit counts only
-  $ search-hub search ./query.yaml --max-results 100    # Limit results`).action(
+  $ search-hub search ./query.yaml --max-results 100    # Limit results
+
+Query features (use "query init" to see full template):
+  filters:    year_from, year_to, language, publication_types
+  exclude:    NOT terms per block (terms.exclude)
+  mesh/eric:  controlled vocabulary (terms.mesh, terms.eric)
+  overrides:  per-database settings (pubmed, scopus, eric, arxiv)`).action(
     async (queryFile, options) => {
       const globalOpts = program.opts();
       try {
@@ -967,6 +974,135 @@ Query Refinement Workflow:
         } else {
           if (!globalOpts.quiet) {
             console.log(formatDiff(diff, sessionId1, sessionId2, showFilter, formatOptions));
+            const suggestion = formatSuggestion(getSuggestion({
+              command: "diff",
+              sessionId: sessionId2,
+              diffSession1Id: sessionId1,
+              diffAddedCount: diff.added.length,
+              diffRemovedCount: diff.removed.length
+            }));
+            if (suggestion) {
+              console.log(suggestion);
+            }
+          }
+        }
+        process.exitCode = EXIT_CODES.SUCCESS;
+      } catch (error) {
+        if (!globalOpts.quiet) {
+          console.error(
+            "Error:",
+            error instanceof Error ? error.message : error
+          );
+        }
+        process.exitCode = EXIT_CODES.SESSION_ERROR;
+      }
+    }
+  );
+  program.command("merge").description("Merge results from multiple search sessions").argument("<session-ids...>", "two or more session IDs to merge").option("--name <string>", "name for merged session").option("--dry-run", "show what would be merged without creating session").option("--json", "output as JSON").addHelpText("after", `
+Examples:
+  $ search-hub merge session-v4 session-v9                  # Merge two sessions
+  $ search-hub merge session-v4 session-v9 --name combined  # Merge with custom name
+  $ search-hub merge session-a session-b session-c          # Merge three sessions
+  $ search-hub merge session-v4 session-v9 --dry-run        # Preview merge`).action(
+    async (sessionIds, options) => {
+      const globalOpts = program.opts();
+      try {
+        if (sessionIds.length < 2) {
+          if (!globalOpts.quiet) {
+            console.error("Error: At least two session IDs are required for merge");
+          }
+          process.exitCode = EXIT_CODES.GENERAL_ERROR;
+          return;
+        }
+        const sessionsDir = await getSessionsDir(globalOpts);
+        const sessions = /* @__PURE__ */ new Map();
+        for (const sessionId of sessionIds) {
+          try {
+            const session = await loadSession(sessionId, sessionsDir);
+            sessions.set(sessionId, session);
+          } catch (error) {
+            if (!globalOpts.quiet) {
+              console.error(
+                `Error loading session '${sessionId}': ${error instanceof Error ? error.message : "Failed to load session"}`
+              );
+            }
+            process.exitCode = EXIT_CODES.SESSION_ERROR;
+            return;
+          }
+        }
+        const validation = validateMergeSources(sessions);
+        if (!validation.valid) {
+          if (!globalOpts.quiet) {
+            console.error(`Error: ${validation.error}`);
+          }
+          process.exitCode = EXIT_CODES.SESSION_ERROR;
+          return;
+        }
+        const sessionArticles = /* @__PURE__ */ new Map();
+        for (const [sessionId, session] of sessions) {
+          const articles = await loadSessionArticles(session, sessionId, sessionsDir);
+          sessionArticles.set(sessionId, articles);
+        }
+        const mergeResult = mergeArticles(sessionArticles);
+        const sources = [...sessions.entries()].map(([id, session]) => ({
+          id,
+          name: session.name,
+          count: mergeResult.perSession.get(id) ?? 0
+        }));
+        const byProviderCounts = /* @__PURE__ */ new Map();
+        for (const [provider, articles] of mergeResult.byProvider) {
+          byProviderCounts.set(provider, articles.length);
+        }
+        const firstSession = sessions.values().next().value;
+        const mergeName = options?.name ?? (firstSession ? firstSession.name + "-merged" : "merged");
+        if (options?.dryRun) {
+          const outputData2 = {
+            sessionId: "(dry-run)",
+            totalBefore: mergeResult.totalBefore,
+            totalAfter: mergeResult.totalAfter,
+            duplicatesRemoved: mergeResult.duplicatesRemoved,
+            sources,
+            byProvider: byProviderCounts
+          };
+          if (options.json) {
+            console.log(formatMergeJson(outputData2));
+          } else if (!globalOpts.quiet) {
+            console.log(formatMergeOutput(outputData2));
+          }
+          process.exitCode = EXIT_CODES.SUCCESS;
+          return;
+        }
+        const sessionSources = [...sessions.entries()].map(([id, session]) => ({
+          id,
+          name: session.name
+        }));
+        const mergedSession = await createMergedSession({
+          name: mergeName,
+          sources: sessionSources,
+          byProvider: mergeResult.byProvider,
+          totalRetrieved: mergeResult.totalAfter,
+          sessionsDir,
+          sourceSessionIds: sessionIds
+        });
+        const outputData = {
+          sessionId: mergedSession.id,
+          totalBefore: mergeResult.totalBefore,
+          totalAfter: mergeResult.totalAfter,
+          duplicatesRemoved: mergeResult.duplicatesRemoved,
+          sources,
+          byProvider: byProviderCounts
+        };
+        if (options?.json) {
+          console.log(formatMergeJson(outputData));
+        } else if (!globalOpts.quiet) {
+          console.log(formatMergeOutput(outputData));
+          const suggestion = getSuggestion({
+            command: "merge",
+            sessionId: mergedSession.id
+          });
+          const suggestionText = formatSuggestion(suggestion);
+          if (suggestionText) {
+            console.log(suggestionText);
           }
         }
         process.exitCode = EXIT_CODES.SUCCESS;
@@ -1343,7 +1479,7 @@ Examples:
       };
       const result = await executeReviewMerge(mergeOptions, sessionsDir);
       if (!globalOpts.quiet) {
-        console.log(formatMergeOutput(result, options.dryRun));
+        console.log(formatMergeOutput$1(result, options.dryRun));
         if (!options.dryRun) {
           const statusResult = await executeReviewStatus({ sessionId: options.session }, sessionsDir);
           const suggestion = formatSuggestion(getSuggestion({
@@ -1511,6 +1647,13 @@ Examples:
         process.exitCode = EXIT_CODES.SESSION_ERROR;
         return;
       }
+      if (!await sessionExists(sessionId, sessionsDir)) {
+        if (!globalOpts.quiet) {
+          console.error(`Error: session '${sessionId}' not found`);
+        }
+        process.exitCode = EXIT_CODES.SESSION_ERROR;
+        return;
+      }
       const sessionDir = join(sessionsDir, sessionId);
       const notes = await loadNotes(sessionDir);
       if (!globalOpts.quiet) {