@ncukondo/search-hub 0.19.0 → 0.20.1

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

@@ -1 +1 @@
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+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/search.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAC3D,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,+BAA+B,CAAC;AAC1E,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,uBAAuB,CAAC;AAIpD,MAAM,WAAW,oBAAoB;IACnC,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,SAAS,CAAC,EAAE,YAAY,EAAE,CAAC;IAC3B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,IAAI,CAAC,EAAE,WAAW,GAAG,MAAM,CAAC;IAC5B,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,kBAAkB;IACjC,EAAE,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACxB,KAAK,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC3B,IAAI,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC1B,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAChC,IAAI,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC1B,MAAM,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC7B,SAAS,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAChC,OAAO,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC9B,QAAQ,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC/B,MAAM,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CAC9B;AAED,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,OAAO,CAAC;IACf,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,CAAC,EAAE,YAAY,EAAE,CAAC;IAC3B,kBAAkB,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CAC1C;AAED,wBAAgB,kBAAkB,CAChC,SAAS,EAAE,MAAM,GAAG,SAAS,EAC7B,OAAO,EAAE,kBAAkB,GAC1B,oBAAoB,CAgDtB;AAED,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,oBAAoB,GAAG,gBAAgB,CA8BnF;AAED;;GAEG;AACH,wBAAsB,uBAAuB,CAC3C,SAAS,EAAE,YAAY,EAAE,EACzB,MAAM,EAAE,MAAM,GACb,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAC,CAa/C;AAED;;GAEG;AACH,wBAAgB,uBAAuB,CACrC,SAAS,EAAE,YAAY,EAAE,EACzB,MAAM,EAAE,MAAM,EACd,iBAAiB,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,oBAAoB,CAAC,GACvD,MAAM,CAWR;AAsCD;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,YAAY,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAmBhF;AAED;;GAEG;AACH,MAAM,WAAW,WAAW;IAC1B,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAGD;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CACnC,MAAM,EAAE,WAAW,EAAE,EACrB,UAAU,CAAC,EAAE,MAAM,GAClB,MAAM,CA8BR;AAGD;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,OAAO,EAAE,aAAa,EAAE,EACxB,UAAU,CAAC,EAAE,MAAM,GAClB,MAAM,CAsCR;AAED,wBAAsB,kBAAkB,CACtC,YAAY,EAAE,iBAAiB,EAAE,EACjC,OAAO,CAAC,EAAE,mBAAmB,GAC5B,OAAO,CAAC,MAAM,CAAC,CA4BjB;AAGD;;GAEG;AACH,wBAAgB,yBAAyB,CAAC,aAAa,EAAE,MAAM,EAAE,GAAG,MAAM,CAUzE"}

package/dist/cli/commands/search.js

@@ -32,6 +32,9 @@ function parseSearchOptions(queryFile, options) {
   if (options.strict) {
     result.strict = true;
   }
+  if (options.sort === "relevance" || options.sort === "date") {
+    result.sort = options.sort;
+  }
   return result;
 }
 function validateSearchInput(options) {

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

@@ -1 +1 @@
-{"version":3,"file":"search.js","sources":["../../../src/cli/commands/search.ts"],"sourcesContent":["import type { ProviderName } from '../../session/types.js';\nimport type { ConnectionTestResult } from '../../providers/base/types.js';\nimport type { Config } from '../../config/index.js';\nimport { parseProviderNames } from '../utils/validation.js';\nimport { createProviderInstance } from './search-executor.js';\n\nexport interface SearchCommandOptions {\n  queryFile?: string;\n  directQuery?: string;\n  providers?: ProviderName[];\n  sessionName?: string;\n  maxResults?: number;\n  dryRun?: boolean;\n  countOnly?: boolean;\n  preview?: boolean;\n  noResume?: boolean;\n  strict?: boolean;\n}\n\nexport interface CommandLineOptions {\n  db?: string | undefined;\n  query?: string | undefined;\n  name?: string | undefined;\n  maxResults?: string | undefined;\n  dryRun?: boolean | undefined;\n  countOnly?: boolean | undefined;\n  preview?: boolean | undefined;\n  noResume?: boolean | undefined;\n  strict?: boolean | undefined;\n}\n\nexport interface TranslationResult {\n  provider: string;\n  query: string;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\n/**\n * Options for enhanced dry-run output.\n */\nexport interface DryRunOutputOptions {\n  config?: Config;\n  providers?: ProviderName[];\n  skipConnectionTest?: boolean | undefined;\n}\n\nexport function parseSearchOptions(\n  queryFile: string | undefined,\n  options: CommandLineOptions\n): SearchCommandOptions {\n  const result: SearchCommandOptions = {};\n\n  if (queryFile) {\n    result.queryFile = queryFile;\n  }\n\n  if (options.query) {\n    result.directQuery = options.query;\n  }\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  if (options.name) {\n    result.sessionName = options.name;\n  }\n\n  if (options.maxResults) {\n    result.maxResults = parseInt(options.maxResults, 10);\n  }\n\n  if (options.dryRun) {\n    result.dryRun = true;\n  }\n\n  if (options.countOnly) {\n    result.countOnly = true;\n  }\n\n  if (options.preview) {\n    result.preview = true;\n  }\n\n  if (options.noResume) {\n    result.noResume = true;\n  }\n\n  if (options.strict) {\n    result.strict = true;\n  }\n\n  return result;\n}\n\nexport function validateSearchInput(options: SearchCommandOptions): ValidationResult {\n  if (!options.queryFile && !options.directQuery) {\n    return {\n      valid: false,\n      error: 'Either a query file or --query option is required',\n    };\n  }\n\n  if (options.directQuery && (!options.providers || options.providers.length === 0)) {\n    return {\n      valid: false,\n      error: 'Direct query (--query) requires --db option to specify the provider',\n    };\n  }\n\n  if (options.directQuery && options.providers && options.providers.length > 1) {\n    return {\n      valid: false,\n      error: 'Direct query (--query) can only be used with a single provider (--db)',\n    };\n  }\n\n  if (options.preview && options.countOnly) {\n    return {\n      valid: false,\n      error: '--preview and --count-only cannot be used together',\n    };\n  }\n\n  return { valid: true };\n}\n\n/**\n * Test provider connections and return results.\n */\nexport async function testProviderConnections(\n  providers: ProviderName[],\n  config: Config\n): Promise<Record<string, ConnectionTestResult>> {\n  const results: Record<string, ConnectionTestResult> = {};\n  await Promise.all(\n    providers.map(async (name) => {\n      const provider = createProviderInstance(name, config);\n      if (!provider) {\n        results[name] = { ok: false, error: 'Provider configuration incomplete' };\n        return;\n      }\n      results[name] = await provider.testConnection();\n    })\n  );\n  return results;\n}\n\n/**\n * Format provider readiness summary for dry-run output.\n */\nexport function formatProviderReadiness(\n  providers: ProviderName[],\n  config: Config,\n  connectionResults?: Record<string, ConnectionTestResult>\n): string {\n  const lines: string[] = [];\n  lines.push('Provider readiness:');\n  for (const provider of providers) {\n    const providerConfig = config.providers[provider];\n    const connResult = connectionResults?.[provider];\n    const status = getProviderStatus(provider, providerConfig, connResult);\n    const mark = status.ready ? '✓' : '✗';\n    lines.push(`  ${mark} ${provider.padEnd(10)}${status.message}`);\n  }\n  return lines.join('\\n');\n}\n\nfunction getProviderStatus(\n  provider: ProviderName,\n  providerConfig: { email?: string; api_key?: string },\n  connectionResult?: ConnectionTestResult\n): { ready: boolean; message: string } {\n  switch (provider) {\n    case 'pubmed': {\n      if (connectionResult && !connectionResult.ok) {\n        return { ready: false, message: `not ready (${connectionResult.error})` };\n      }\n      if (!providerConfig.email) {\n        return { ready: true, message: connectionResult ? 'ready (verified, email: not configured (recommended))' : 'ready (email: not configured (recommended))' };\n      }\n      return { ready: true, message: connectionResult ? 'ready (verified, email: configured)' : 'ready (email: configured)' };\n    }\n    case 'scopus': {\n      if (!providerConfig.api_key) {\n        return { ready: false, message: 'missing api_key (required)' };\n      }\n      if (connectionResult && !connectionResult.ok) {\n        return { ready: false, message: `not ready (${connectionResult.error})` };\n      }\n      return { ready: true, message: connectionResult ? 'ready (verified)' : 'ready' };\n    }\n    case 'eric':\n    case 'arxiv': {\n      if (connectionResult && !connectionResult.ok) {\n        return { ready: false, message: `not ready (${connectionResult.error})` };\n      }\n      return { ready: true, message: connectionResult ? 'ready (verified)' : 'ready' };\n    }\n    default:\n      return { ready: true, message: 'ready' };\n  }\n}\n\n/**\n * Format query diagnostics warnings for dry-run output.\n */\nexport function formatQueryDiagnostics(translations: TranslationResult[]): string {\n  const warnings: string[] = [];\n  for (const t of translations) {\n    if (t.provider === 'pubmed') {\n      if (/\\bNOT\\b/.test(t.query)) {\n        warnings.push('  ⚠ pubmed: query uses NOT operator (ensure correct syntax for exclusions)');\n      }\n      if (/\\*\\[(?:mh|mesh)\\]/i.test(t.query)) {\n        warnings.push('  ⚠ pubmed: wildcard in MeSH term — PubMed does not support wildcards in MeSH fields');\n      }\n    }\n  }\n  if (warnings.length === 0) {\n    return '';\n  }\n  const lines: string[] = [];\n  lines.push('Diagnostics:');\n  lines.push(...warnings);\n  return lines.join('\\n');\n}\n\n/**\n * Result of a count-only query for a single provider.\n */\nexport interface CountResult {\n  provider: string;\n  count: number;\n  error?: string;\n}\n\n\n/**\n * Preview result for a single provider\n */\nexport interface PreviewResult {\n  provider: string;\n  count: number;\n  titles: string[];\n  error?: string;\n}\n\n/**\n * Format count-only output for display.\n */\nexport function formatCountOnlyOutput(\n  counts: CountResult[],\n  queryLabel?: string\n): string {\n  const label = queryLabel ?? 'direct-query';\n  const lines: string[] = [];\n\n  lines.push(`Query: ${label} (count only)`);\n  lines.push('');\n\n  // Find the max provider name length for alignment (including colon)\n  const maxNameLen = Math.max(...counts.map((c) => c.provider.length + 1), 6);\n\n  // Calculate total (excluding errors)\n  let total = 0;\n\n  for (const c of counts) {\n    if (c.error) {\n      lines.push(`  ${(c.provider + ':').padEnd(maxNameLen)}  error: ${c.error}`);\n    } else {\n      const countStr = String(c.count).padStart(6);\n      lines.push(`  ${(c.provider + ':').padEnd(maxNameLen)} ${countStr} hits`);\n      total += c.count;\n    }\n  }\n\n  // Separator and total\n  const separatorLen = maxNameLen + 14;\n  lines.push(`  ${'─'.repeat(separatorLen)}`);\n  const totalStr = String(total).padStart(6);\n  lines.push(`  ${('total:').padEnd(maxNameLen)} ${totalStr} hits (before deduplication)`);\n\n  return lines.join('\\n');\n}\n\n\n/**\n * Format preview output showing counts and sample titles.\n */\nexport function formatPreviewOutput(\n  results: PreviewResult[],\n  queryLabel?: string\n): string {\n  const label = queryLabel ?? 'direct-query';\n  const lines: string[] = [];\n\n  lines.push(`Query: ${label} (preview)`);\n  lines.push('');\n\n  // Find the max provider name length for alignment (including colon)\n  const maxNameLen = Math.max(...results.map((r) => r.provider.length + 1), 6);\n\n  // Calculate total (excluding errors)\n  let total = 0;\n\n  for (const r of results) {\n    if (r.error) {\n      lines.push(`  ${(r.provider + ':').padEnd(maxNameLen)}  error: ${r.error}`);\n    } else {\n      const countStr = String(r.count).padStart(6);\n      lines.push(`  ${(r.provider + ':').padEnd(maxNameLen)} ${countStr} hits`);\n      total += r.count;\n\n      // Show sample titles\n      if (r.titles.length > 0) {\n        for (const title of r.titles) {\n          lines.push(`    • ${title}`);\n        }\n      }\n    }\n    lines.push('');\n  }\n\n  // Separator and total\n  const separatorLen = maxNameLen + 14;\n  lines.push(`  ${'─'.repeat(separatorLen)}`);\n  const totalStr = String(total).padStart(6);\n  lines.push(`  ${('total:').padEnd(maxNameLen)} ${totalStr} hits (before deduplication)`);\n\n  return lines.join('\\n');\n}\n\nexport async function formatDryRunOutput(\n  translations: TranslationResult[],\n  options?: DryRunOutputOptions\n): Promise<string> {\n  if (translations.length === 0) {\n    return 'No translations available.';\n  }\n  const sections: string[] = [];\n  if (options?.config && options?.providers) {\n    let connectionResults: Record<string, ConnectionTestResult> | undefined;\n    if (!options.skipConnectionTest) {\n      connectionResults = await testProviderConnections(options.providers, options.config);\n    }\n    sections.push(formatProviderReadiness(options.providers, options.config, connectionResults));\n    sections.push('');\n  }\n  const queryLines: string[] = [];\n  queryLines.push('Translated queries:');\n  queryLines.push('');\n  for (const t of translations) {\n    queryLines.push(`[${t.provider}]`);\n    queryLines.push(t.query);\n    queryLines.push('');\n  }\n  sections.push(queryLines.join('\\n'));\n  const diagnostics = formatQueryDiagnostics(translations);\n  if (diagnostics) {\n    sections.push(diagnostics);\n    sections.push('');\n  }\n  return sections.join('\\n');\n}\n\n\n/**\n * Format warning for short keywords that may cause noisy results.\n */\nexport function formatShortKeywordWarning(shortKeywords: string[]): string {\n  if (shortKeywords.length === 0) {\n    return '';\n  }\n\n  const keywordList = shortKeywords.join(', ');\n  return `⚠ Query contains short keywords: ${keywordList}\n  Short terms may match unrelated acronyms. 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'direct-query';\n  const lines: string[] = [];\n\n  lines.push(`Query: ${label} (preview)`);\n  lines.push('');\n\n  // Find the max provider name length for alignment (including colon)\n  const maxNameLen = Math.max(...results.map((r) => r.provider.length + 1), 6);\n\n  // Calculate total (excluding errors)\n  let total = 0;\n\n  for (const r of results) {\n    if (r.error) {\n      lines.push(`  ${(r.provider + ':').padEnd(maxNameLen)}  error: ${r.error}`);\n    } else {\n      const countStr = String(r.count).padStart(6);\n      lines.push(`  ${(r.provider + ':').padEnd(maxNameLen)} ${countStr} hits`);\n      total += r.count;\n\n      // Show sample titles\n      if (r.titles.length > 0) {\n        for (const title of r.titles) {\n          lines.push(`    • ${title}`);\n        }\n      }\n    }\n    lines.push('');\n  }\n\n  // Separator and total\n  const separatorLen = maxNameLen + 14;\n  lines.push(`  ${'─'.repeat(separatorLen)}`);\n  const totalStr = String(total).padStart(6);\n  lines.push(`  ${('total:').padEnd(maxNameLen)} ${totalStr} hits (before deduplication)`);\n\n  return lines.join('\\n');\n}\n\nexport async function formatDryRunOutput(\n  translations: TranslationResult[],\n  options?: DryRunOutputOptions\n): Promise<string> {\n  if (translations.length === 0) {\n    return 'No translations available.';\n  }\n  const sections: string[] = [];\n  if (options?.config && options?.providers) {\n    let connectionResults: Record<string, ConnectionTestResult> | undefined;\n    if (!options.skipConnectionTest) {\n      connectionResults = await testProviderConnections(options.providers, options.config);\n    }\n    sections.push(formatProviderReadiness(options.providers, options.config, connectionResults));\n    sections.push('');\n  }\n  const queryLines: string[] = [];\n  queryLines.push('Translated queries:');\n  queryLines.push('');\n  for (const t of translations) {\n    queryLines.push(`[${t.provider}]`);\n    queryLines.push(t.query);\n    queryLines.push('');\n  }\n  sections.push(queryLines.join('\\n'));\n  const diagnostics = formatQueryDiagnostics(translations);\n  if (diagnostics) {\n    sections.push(diagnostics);\n    sections.push('');\n  }\n  return sections.join('\\n');\n}\n\n\n/**\n * Format warning for short keywords that may cause noisy results.\n */\nexport function formatShortKeywordWarning(shortKeywords: string[]): string {\n  if (shortKeywords.length === 0) {\n    return '';\n  }\n\n  const keywordList = shortKeywords.join(', ');\n  return `⚠ Query contains short keywords: ${keywordList}\n  Short terms may match unrelated acronyms. 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package/dist/cli/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAQA,OAAO,EAAE,OAAO,EAAU,MAAM,WAAW,CAAC;AAyM5C;;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,CAiuFvC;AAED;;GAEG;AACH,wBAAsB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAG1C"}

package/dist/cli/index.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 import { config } from "dotenv";
-import { Command } from "commander";
+import { Command, Option } from "commander";
 import { VERSION } from "../version.js";
 import { init } from "./commands/init.js";
 import { EXIT_CODES } from "./exit-codes.js";
@@ -30,6 +30,7 @@ import { filterByQuery } from "./commands/query-filter.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 { parseRelatedOptions, validateRelatedInput, resolveSeeds, createRelatedSession, formatRelatedOutput } from "./commands/related.js";
 import { executeReviewInit } from "./commands/review/init.js";
 import { executeReviewStatus, formatStatusOutput } from "./commands/review/status.js";
 import { executeReviewList, formatListOutput } from "./commands/review/list.js";
@@ -41,7 +42,7 @@ import { executeReviewFinalize, formatFinalizeOutput } from "./commands/review/f
 import "zod";
 import "./commands/review/schema.js";
 import { registerFulltextCommands } from "./commands/fulltext/index.js";
-import { parseRegisterOptions, validateRegisterInput, hasReviewFile, getReviewSummary, formatNoIncludedArticlesError, formatPendingWarning, confirmPrompt, getIncludedArticles, formatReviewRequiredMessage, formatIgnoringReviewsNote, formatDryRunOutput as formatDryRunOutput$1, formatRegistrationSummary } from "./commands/register.js";
+import { parseRegisterOptions, validateRegisterInput, hasReviewFile, getReviewSummary, formatNoIncludedArticlesError, formatPendingWarning, confirmPrompt, getIncludedArticles, formatReviewRequiredMessage, formatIgnoringReviewsNote, formatDryRunOutput as formatDryRunOutput$1, formatRegistrationSummary, formatLibraryPath, formatDefaultLibraryHint } from "./commands/register.js";
 import { formatSuggestion } from "./suggestions/index.js";
 import { getSuggestion } from "./suggestions/rules.js";
 import { readLogEntries, computeQueryHash, appendLogEntry, buildPreviewLogEntry, buildCountLogEntry } from "./commands/query/iteration-log.js";
@@ -59,6 +60,7 @@ import { getSessionsDir } from "./utils/sessions-dir.js";
 import { expandPath } from "../utils/path.js";
 import { loadSessionArticles, loadSessionQuery } from "./commands/session-utils.js";
 import { parseIdentifierFile, checkCoverage, formatCheckResultJson, formatCheckResult } from "./commands/check.js";
+import { PubMedClient } from "../providers/pubmed/client.js";
 config({ quiet: true });
 function createProgram() {
   const program = new Command();
@@ -446,7 +448,7 @@ Examples:
       process.exitCode = EXIT_CODES.SESSION_ERROR;
     }
   });
-  program.command("search").description("Execute search across databases").argument("[query-file]", "path to query YAML file").option("--db <providers>", "target specific database(s), comma-separated").option("--query <string>", "direct query in database-native syntax (advanced; requires --db; prefer YAML files)").option("--name <string>", "session name").option("--max-results <n>", "limit results per database").option("--dry-run", "show translated queries without executing").option("--count-only", "get hit counts without downloading results").option("--preview", "get hit counts and first 5 titles without creating session").option("--skip-connection-test", "skip API connection test during dry-run").option("--no-resume", "start fresh even if session exists").option("--strict", "require all targeted databases to succeed (exit non-zero on partial failure)").addHelpText("after", `
+  program.command("search").description("Execute search across databases").argument("[query-file]", "path to query YAML file").option("--db <providers>", "target specific database(s), comma-separated").option("--query <string>", "direct query in database-native syntax (advanced; requires --db; prefer YAML files)").option("--name <string>", "session name").option("--max-results <n>", "limit results per database").addOption(new Option("--sort <method>", "sort results by relevance or date").choices(["relevance", "date"])).option("--dry-run", "show translated queries without executing").option("--count-only", "get hit counts without downloading results").option("--preview", "get hit counts and first 5 titles without creating session").option("--skip-connection-test", "skip API connection test during dry-run").option("--no-resume", "start fresh even if session exists").option("--strict", "require all targeted databases to succeed (exit non-zero on partial failure)").addHelpText("after", `
 Workflow position:
   query validate → [this command: search] → results / summary / diff
 
@@ -471,6 +473,7 @@ Query features (use "query init" to see full template):
           query: options?.query,
           name: options?.name,
           maxResults: options?.maxResults,
+          sort: options?.sort,
           dryRun: options?.dryRun,
           countOnly: options?.countOnly,
           preview: options?.preview,
@@ -662,6 +665,11 @@ Search completed. Session: ${result.sessionId}`);
                 } else {
                   console.log(`  ${provider}: ${stats.retrieved} results`);
                 }
+                if (stats.warnings && stats.warnings.length > 0) {
+                  for (const w of stats.warnings) {
+                    console.warn(`  ⚠ ${provider}: ${w}`);
+                  }
+                }
               }
             }
             if (result.sessionStatus === "partial" && result.results) {
@@ -1285,6 +1293,119 @@ Input file format (one identifier per line):
       }
     }
   );
+  program.command("related").description("Find related articles from seed PMIDs using PubMed ELink").argument("[pmids...]", "seed PMIDs").option("-n, --name <string>", "session name").option("-m, --max-results <number>", "max related articles to retrieve", "20").option("-s, --from-session <id>", "load seed PMIDs from existing session").option("--pmid <pmids...>", "seed PMIDs (alternative to positional args)").option("-t, --term <filter>", 'additional PubMed filter (e.g., "review[filter]")').addHelpText("after", `
+Examples:
+  $ search-hub related 12345678 23456789              # Find related articles
+  $ search-hub related 12345678 --name my-related     # Custom session name
+  $ search-hub related 12345678 -m 50                 # Get more results
+  $ search-hub related --from-session SESSION --pmid 12345678
+  $ search-hub related 12345678 -t "review[filter]"   # Filter by review type`).action(
+    async (pmidArgs, options) => {
+      const globalOpts = program.opts();
+      try {
+        const parsedOptions = parseRelatedOptions(pmidArgs, options ?? {});
+        const validation = validateRelatedInput(parsedOptions);
+        if (!validation.valid) {
+          if (!globalOpts.quiet) {
+            console.error(`Error: ${validation.error}`);
+          }
+          process.exitCode = EXIT_CODES.GENERAL_ERROR;
+          return;
+        }
+        const sessionsDir = await getSessionsDir(globalOpts);
+        let seedPmids;
+        try {
+          seedPmids = await resolveSeeds(parsedOptions, sessionsDir);
+        } catch (error) {
+          if (!globalOpts.quiet) {
+            console.error(
+              `Error: ${error instanceof Error ? error.message : "Failed to resolve seeds"}`
+            );
+          }
+          process.exitCode = EXIT_CODES.SESSION_ERROR;
+          return;
+        }
+        if (seedPmids.length === 0) {
+          if (!globalOpts.quiet) {
+            console.error("Error: No PMIDs found to use as seeds.");
+          }
+          process.exitCode = EXIT_CODES.GENERAL_ERROR;
+          return;
+        }
+        const config2 = await loadConfig(
+          globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}
+        );
+        const providerConfig = config2.providers.pubmed;
+        const pubmedConfig = {
+          email: providerConfig.email ?? "search-hub@example.com",
+          rateLimit: providerConfig.rate_limit,
+          timeout: providerConfig.timeout,
+          retries: providerConfig.retries
+        };
+        if (providerConfig.api_key) {
+          pubmedConfig.apiKey = providerConfig.api_key;
+        }
+        const rateLimiter = new RateLimiter({
+          tokensPerSecond: pubmedConfig.rateLimit ?? (pubmedConfig.apiKey ? 10 : 3)
+        });
+        const client = new PubMedClient(pubmedConfig, rateLimiter);
+        if (!globalOpts.quiet) {
+          console.log(`Finding related articles for ${seedPmids.length} seed PMIDs...`);
+        }
+        const relatedArticles = await client.findRelatedMerged({
+          ids: seedPmids,
+          maxResults: parsedOptions.maxResults,
+          ...parsedOptions.term && { term: parsedOptions.term }
+        });
+        const totalRelated = relatedArticles.length;
+        if (totalRelated === 0) {
+          if (!globalOpts.quiet) {
+            console.log("No related articles found.");
+          }
+          process.exitCode = EXIT_CODES.SUCCESS;
+          return;
+        }
+        const relatedPmids = relatedArticles.map((a) => a.id);
+        const articles = await client.fetch(relatedPmids);
+        const sessionName = parsedOptions.name ?? `related-${(/* @__PURE__ */ new Date()).toISOString().slice(0, 10)}`;
+        const sessionFile = await createRelatedSession({
+          name: sessionName,
+          seeds: {
+            ids: seedPmids,
+            ...parsedOptions.fromSession && { sourceSession: parsedOptions.fromSession }
+          },
+          articles,
+          sessionsDir
+        });
+        if (!globalOpts.quiet) {
+          console.log(formatRelatedOutput({
+            sessionId: sessionFile.id,
+            seedCount: seedPmids.length,
+            totalRelated,
+            retrievedCount: articles.length,
+            articles
+          }));
+          const suggestion = getSuggestion({
+            command: "related",
+            sessionId: sessionFile.id
+          });
+          const suggestionText = formatSuggestion(suggestion);
+          if (suggestionText) {
+            console.log(suggestionText);
+          }
+        }
+        process.exitCode = EXIT_CODES.SUCCESS;
+      } catch (error) {
+        if (!globalOpts.quiet) {
+          console.error(
+            "Error:",
+            error instanceof Error ? error.message : error
+          );
+        }
+        process.exitCode = EXIT_CODES.GENERAL_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
@@ -1567,7 +1688,10 @@ Failed to install reference-manager: ${installError instanceof Error ? installEr
             }
           }
           console.log(`
-Results saved to: ${join(sessionDir, "registration.json")}`);
+${formatLibraryPath(sessionDir)}`);
+          console.log(`Results saved to: ${join(sessionDir, "registration.json")}`);
+          console.log(`
+${formatDefaultLibraryHint(sessionDir)}`);
           const suggestion = formatSuggestion(getSuggestion({
             command: "register",
             sessionId,
@@ -1595,12 +1719,16 @@ Examples:
   $ search-hub review extract --session SESSION_ID --name title-screening  # Extract for review
   $ search-hub review merge --session SESSION_ID --name title-screening   # Merge reviews
   $ search-hub review export --session SESSION_ID --only included -o included.yaml`);
-  reviewCommand.command("init").description("Generate reviews.yaml from deduplicated search results").requiredOption("--session <id>", "session ID").option("-f, --force", "overwrite existing reviews.yaml", false).action(async (options) => {
+  reviewCommand.command("init").description("Generate reviews.yaml from deduplicated search results").requiredOption("--session <id>", "session ID").option("--mode <mode>", "review mode: screening (exclusion-based) or picking (inclusion-based)").option("-f, --force", "overwrite existing reviews.yaml", false).action(async (options) => {
     const globalOpts = program.opts();
     try {
+      if (options.mode && options.mode !== "screening" && options.mode !== "picking") {
+        throw new Error(`Invalid mode: "${options.mode}". Must be "screening" or "picking".`);
+      }
       const sessionsDir = await getSessionsDir(globalOpts);
       const initOptions = {
         sessionId: options.session,
+        ...options.mode && { mode: options.mode },
         ...options.force && { force: options.force }
       };
       const result = await executeReviewInit(initOptions, sessionsDir);