kirograph 1.2.2 → 1.3.0

package/dist/mcp/handlers/security.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../src/mcp/handlers/security.ts"],
-  "sourcesContent": ["import KiroGraph from '../../index';\nimport { clampLimit, truncate } from './utils';\n\nexport async function handleSecurity(toolName: string, args: Record<string, unknown>, cg: KiroGraph): Promise<string> {\n  switch (toolName) {\n    case 'kirograph_security': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n      if (!config.enableArchitecture) return 'Security requires architecture analysis. Set enableArchitecture: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      const depCount: { count: number } = rawDb.get(\n        `SELECT COUNT(*) as count FROM sec_dependencies`,\n      ) ?? { count: 0 };\n\n      const vulnCount: { count: number } = rawDb.get(\n        `SELECT COUNT(*) as count FROM sec_vulnerabilities`,\n      ) ?? { count: 0 };\n\n      const verdictRows: Array<{ verdict: string; count: number }> = rawDb.all(\n        `SELECT verdict, COUNT(*) as count FROM sec_reachability GROUP BY verdict`,\n      );\n      const verdicts: Record<string, number> = {};\n      for (const row of verdictRows) {\n        verdicts[row.verdict] = row.count;\n      }\n\n      const staleCount: { count: number } = rawDb.get(\n        `SELECT COUNT(*) as count FROM sec_dependencies WHERE vuln_data_stale = 1`,\n      ) ?? { count: 0 };\n\n      // Count suppressed CVEs\n      const { SuppressionManager: SecSuppressionManager } = await Promise.resolve().then(() => require('../../security/suppressions.js'));\n      const secSuppressions = new SecSuppressionManager(projectRoot);\n      const allCveIds: Array<{ cve_id: string }> = rawDb.all(`SELECT cve_id FROM sec_vulnerabilities`);\n      const suppressedCveCount = allCveIds.filter(r => secSuppressions.isSuppressed(r.cve_id)).length;\n      const visibleVulnCount = vulnCount.count - suppressedCveCount;\n\n      const lines: string[] = [\n        '# Security Overview',\n        '',\n        `Dependencies: ${depCount.count}`,\n        `Vulnerabilities: ${visibleVulnCount}${suppressedCveCount > 0 ? ` (${suppressedCveCount} suppressed)` : ''}`,\n      ];\n\n      if (visibleVulnCount > 0) {\n        const affected = verdicts['affected'] ?? 0;\n        const notAffected = verdicts['not_affected'] ?? 0;\n        const underInvestigation = verdicts['under_investigation'] ?? 0;\n        const pending = visibleVulnCount - affected - notAffected - underInvestigation;\n\n        lines.push('', '## Reachability Verdicts', '');\n        if (affected > 0) lines.push(`\u25CF Affected: ${affected}`);\n        if (notAffected > 0) lines.push(`\u25CF Not affected: ${notAffected}`);\n        if (underInvestigation > 0) lines.push(`\u25CF Under investigation: ${underInvestigation}`);\n        if (pending > 0) lines.push(`\u25CF Pending analysis: ${pending}`);\n      }\n\n      if (staleCount.count > 0) {\n        lines.push('', `\u26A0 ${staleCount.count} dependenc${staleCount.count === 1 ? 'y has' : 'ies have'} stale vulnerability data. Use kirograph_vulns with refresh=true to update.`);\n      }\n\n      // Check if vulnerability data is stale by age\n      const lastVulnCheck = (rawDb.get(\n        `SELECT MIN(last_vuln_check) as oldest FROM sec_dependencies WHERE last_vuln_check IS NOT NULL`,\n      ) as { oldest: number | null } | undefined)?.oldest;\n      if (lastVulnCheck != null) {\n        const ageMs = Date.now() - lastVulnCheck;\n        const ageDays = ageMs / (1000 * 60 * 60 * 24);\n        const maxAge = config.securityEnrichMaxAgeDays ?? 7;\n        if (ageDays > maxAge) {\n          lines.push('', `\u26A0 Vulnerability data is ${Math.floor(ageDays)} days old (max: ${maxAge}). Run kirograph vulns --refresh to update.`);\n        }\n      }\n\n      // Pattern SAST findings count\n      try {\n        const rawDbSec = db.getRawDb();\n        const tableExistsSec = rawDbSec.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='pattern_matches'\");\n        if (tableExistsSec) {\n          const patternCount = rawDbSec.get('SELECT COUNT(*) as cnt FROM pattern_matches')?.cnt ?? 0;\n          if (patternCount > 0) {\n            const critCount = rawDbSec.get(\"SELECT COUNT(*) as cnt FROM pattern_matches WHERE severity = 'critical'\")?.cnt ?? 0;\n            lines.push(`SAST findings: ${patternCount} pattern matches (${critCount} critical)`);\n          }\n        }\n      } catch { /* non-critical */ }\n\n      return lines.join('\\n');\n    }\n\n    case 'kirograph_vulns': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      // Handle refresh\n      if (args.refresh === true) {\n        const { OsvAdapter } = await Promise.resolve().then(() => require('../../security/vuln/osv-adapter.js'));\n        const { VulnerabilityDatabaseClient } = await Promise.resolve().then(() => require('../../security/vuln/client.js'));\n\n        const adapters = config.securityDatabases.map((dbName: string) => {\n          if (dbName.toUpperCase() === 'OSV') return new OsvAdapter();\n          return null;\n        }).filter(Boolean) as any[];\n\n        const client = new VulnerabilityDatabaseClient(adapters, db, undefined, projectRoot);\n        await client.enrichAll();\n      }\n\n      // Build query\n      let query = `\n        SELECT\n          v.node_id, v.cve_id, v.severity_score, v.fixed_version, v.summary,\n          v.epss_score, v.epss_percentile, v.risk_score,\n          d.package_name, d.ecosystem, d.resolved_version, d.declared_constraint,\n          r.verdict\n        FROM sec_vulnerabilities v\n        LEFT JOIN edges e ON e.target = v.node_id AND e.kind = 'has_vulnerability'\n        LEFT JOIN sec_dependencies d ON d.node_id = e.source\n        LEFT JOIN sec_reachability r ON r.vulnerability_node_id = v.node_id\n        WHERE 1=1\n      `;\n      const params: any[] = [];\n\n      // Severity filter\n      if (args.severity) {\n        const severityRanges: Record<string, [number, number]> = {\n          critical: [9.0, 10.0],\n          high: [7.0, 8.9],\n          medium: [4.0, 6.9],\n          low: [0.1, 3.9],\n        };\n        const range = severityRanges[(args.severity as string).toLowerCase()];\n        if (!range) return `Invalid severity: ${args.severity}. Use: critical, high, medium, low`;\n        query += ` AND v.severity_score >= ? AND v.severity_score <= ?`;\n        params.push(range[0], range[1]);\n      }\n\n      // Verdict filter\n      if (args.verdict) {\n        const validVerdicts = ['affected', 'not_affected', 'under_investigation'];\n        if (!validVerdicts.includes(args.verdict as string)) {\n          return `Invalid verdict: ${args.verdict}. Use: affected, not_affected, under_investigation`;\n        }\n        query += ` AND r.verdict = ?`;\n        params.push(args.verdict);\n      }\n\n      const limit = clampLimit(args.limit as number | undefined, 20);\n      query += ` ORDER BY v.risk_score DESC NULLS LAST LIMIT ?`;\n      params.push(limit);\n\n      const rows: Array<{\n        node_id: string;\n        cve_id: string;\n        severity_score: number | null;\n        fixed_version: string | null;\n        summary: string | null;\n        epss_score: number | null;\n        epss_percentile: number | null;\n        risk_score: number | null;\n        package_name: string | null;\n        ecosystem: string | null;\n        resolved_version: string | null;\n        declared_constraint: string | null;\n        verdict: string | null;\n      }> = rawDb.all(query, params);\n\n      // Deduplicate by (cve_id, package_name, ecosystem) \u2014 same CVE can appear multiple\n      // times when a package is declared in multiple manifests (monorepo).\n      const verdictRankMcp = (v: string | null) =>\n        v === 'affected' ? 3 : v === 'under_investigation' ? 2 : v === 'not_affected' ? 1 : 0;\n      const dedupMapMcp = new Map<string, typeof rows[0]>();\n      for (const row of rows) {\n        const key = `${row.cve_id}::${row.package_name ?? ''}::${row.ecosystem ?? ''}`;\n        const ex = dedupMapMcp.get(key);\n        if (!ex || verdictRankMcp(row.verdict) > verdictRankMcp(ex.verdict)) dedupMapMcp.set(key, row);\n      }\n      const dedupedRowsMcp = [...dedupMapMcp.values()];\n\n      // Filter out suppressed CVEs\n      const { SuppressionManager } = await Promise.resolve().then(() => require('../../security/suppressions.js'));\n      const suppressionMgr = new SuppressionManager(projectRoot);\n      const suppressedCount = dedupedRowsMcp.filter(row => suppressionMgr.isSuppressed(row.cve_id)).length;\n      const filteredRows = dedupedRowsMcp.filter(row => !suppressionMgr.isSuppressed(row.cve_id));\n\n      if (filteredRows.length === 0) {\n        const noMatch = 'No vulnerabilities found' + ((args.severity || args.verdict) ? ' matching filters.' : '.');\n        return suppressedCount > 0 ? `${noMatch} (${suppressedCount} suppressed)` : noMatch;\n      }\n\n      const { formatFixSuggestion } = await Promise.resolve().then(() => require('../../security/export/fix-suggestions.js'));\n\n      const lines: string[] = [`Vulnerabilities (${filteredRows.length}${suppressedCount > 0 ? `, ${suppressedCount} suppressed` : ''}):\\n`];\n\n      for (const row of filteredRows) {\n        const score = row.severity_score;\n        let severityLabel: string;\n        if (score == null) severityLabel = 'UNKNOWN';\n        else if (score >= 9.0) severityLabel = 'CRITICAL';\n        else if (score >= 7.0) severityLabel = 'HIGH';\n        else if (score >= 4.0) severityLabel = 'MEDIUM';\n        else severityLabel = 'LOW';\n\n        let verdictLabel: string;\n        if (!row.verdict) verdictLabel = 'pending';\n        else if (row.verdict === 'affected') verdictLabel = 'affected';\n        else if (row.verdict === 'not_affected') verdictLabel = 'not affected';\n        else verdictLabel = 'investigating';\n\n        const pkg = row.package_name\n          ? `${row.package_name}@${row.resolved_version || row.declared_constraint || '?'}`\n          : 'unknown package';\n\n        const epssNote = row.epss_score != null\n          ? ` [EPSS: ${row.epss_score.toFixed(2)}]`\n          : '';\n        const riskNote = row.risk_score != null\n          ? ` [Risk: ${row.risk_score.toFixed(1)}]`\n          : '';\n        lines.push(`${severityLabel}  ${row.cve_id}  ${pkg}  [${verdictLabel}]${epssNote}${riskNote}`);\n\n        if (row.summary && row.summary !== 'Manually registered') {\n          const truncSummary = row.summary.length > 120 ? row.summary.slice(0, 120) + '\u2026' : row.summary;\n          lines.push(`  ${truncSummary}`);\n        }\n\n        if (row.fixed_version && row.ecosystem && row.package_name) {\n          const fix = formatFixSuggestion(row.ecosystem, row.package_name, row.fixed_version);\n          if (fix) lines.push(`  ${fix}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_vuln_add': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const cveId = args.cveId as string;\n      const pkgName = args.package as string;\n      if (!cveId) return 'Error: cveId is required.';\n      if (!pkgName) return 'Error: package is required.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      // Find matching Dependency_Node\n      const depRow: { node_id: string; ecosystem: string } | undefined = rawDb.get(\n        `SELECT node_id, ecosystem FROM sec_dependencies WHERE package_name = ?`,\n        [pkgName],\n      );\n\n      if (!depRow) {\n        return `No dependency found matching \"${pkgName}\". Run kirograph index first to discover dependencies.`;\n      }\n\n      // Create Vulnerability_Node\n      const vulnNodeId = `vuln:${cveId}`;\n      const now = Date.now();\n      const severity = args.severity as number | undefined;\n      const summary = (args.summary as string) ?? 'Manually registered';\n      const fixedVersion = (args.fixedVersion as string) ?? null;\n\n      rawDb.run(\n        `INSERT OR REPLACE INTO nodes\n          (id, kind, name, qualified_name, file_path, language,\n           start_line, end_line, start_column, end_column,\n           is_exported, is_async, is_static, is_abstract, updated_at)\n         VALUES (?, 'vulnerability', ?, ?, '', 'unknown', 0, 0, 0, 0, 0, 0, 0, 0, ?)`,\n        [vulnNodeId, cveId, cveId, now],\n      );\n\n      rawDb.run(\n        `INSERT OR REPLACE INTO sec_vulnerabilities\n          (node_id, cve_id, severity_score, affected_ranges, fixed_version, summary, source_database)\n         VALUES (?, ?, ?, '[]', ?, ?, 'manual')`,\n        [vulnNodeId, cveId, severity ?? null, fixedVersion, summary],\n      );\n\n      // Create has_vulnerability edge\n      rawDb.run(\n        `INSERT OR IGNORE INTO edges (source, target, kind, confidence, confidence_score)\n         VALUES (?, ?, 'has_vulnerability', 'extracted', 1.0)`,\n        [depRow.node_id, vulnNodeId],\n      );\n\n      return `Registered ${cveId} against ${pkgName}.`;\n    }\n\n    case 'kirograph_vuln_suppress': {\n      const projectRoot = cg.getProjectRoot();\n      const cveId = args.cveId as string;\n      if (!cveId) return 'Error: cveId is required.';\n\n      const { SuppressionManager } = await Promise.resolve().then(() => require('../../security/suppressions.js'));\n      const manager = new SuppressionManager(projectRoot);\n      manager.add(cveId, args.reason as string | undefined, args.expires as string | undefined);\n\n      const reasonNote = args.reason ? ` Reason: ${args.reason}.` : '';\n      const expiresNote = args.expires ? ` Expires: ${args.expires}.` : '';\n      return `${cveId} suppressed.${reasonNote}${expiresNote}`;\n    }\n\n    case 'kirograph_sbom': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { SBOMExporter } = await Promise.resolve().then(() => require('../../security/export/sbom.js'));\n      const exporter = new SBOMExporter(db, projectRoot);\n      const json = exporter.exportJSON();\n\n      return truncate(json);\n    }\n\n    case 'kirograph_vex': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { VEXExporter } = await Promise.resolve().then(() => require('../../security/export/vex.js'));\n      const exporter = new VEXExporter(db, projectRoot);\n      const json = exporter.exportJSON();\n\n      return truncate(json);\n    }\n\n    case 'kirograph_reachability': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const target = args.target as string;\n      if (!target) return 'Error: target is required (dependency name or CVE ID).';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      // Try to find target as a CVE ID in sec_vulnerabilities\n      let vulnerabilityNodeId: string | null = null;\n      let targetLabel = target;\n\n      const vulnRow: { node_id: string } | undefined = rawDb.get(\n        `SELECT node_id FROM sec_vulnerabilities WHERE cve_id = ?`,\n        [target],\n      );\n\n      if (vulnRow) {\n        vulnerabilityNodeId = vulnRow.node_id;\n      } else {\n        // Try to find target as a dependency name\n        const depRow: { node_id: string; package_name: string } | undefined = rawDb.get(\n          `SELECT node_id, package_name FROM sec_dependencies WHERE package_name = ?`,\n          [target],\n        );\n\n        if (depRow) {\n          targetLabel = depRow.package_name;\n          // Find vulnerabilities linked to this dependency\n          const vulnEdge: { target: string } | undefined = rawDb.get(\n            `SELECT target FROM edges WHERE source = ? AND kind = 'has_vulnerability' LIMIT 1`,\n            [depRow.node_id],\n          );\n\n          if (vulnEdge) {\n            vulnerabilityNodeId = vulnEdge.target;\n          } else {\n            return `No vulnerabilities found for dependency \"${target}\". The dependency exists but has no known vulnerabilities.`;\n          }\n        } else {\n          return `Target \"${target}\" not found. Provide a valid CVE ID or dependency package name.`;\n        }\n      }\n\n      // Run reachability analysis\n      const { ReachabilityAnalyzer, explainReachability } = await Promise.resolve().then(() => require('../../security/reachability.js'));\n      const analyzer = new ReachabilityAnalyzer(db, config);\n      const result = await analyzer.analyze(vulnerabilityNodeId);\n\n      const lines: string[] = [\n        `# Reachability: ${targetLabel}`,\n        '',\n        `Verdict: ${result.verdict}`,\n        `Reaching entry points: ${result.reachingEntryPointCount}`,\n        '',\n        `Why: ${explainReachability(result)}`,\n      ];\n\n      if (result.paths.length > 0) {\n        lines.push('', '## Paths');\n        for (const p of result.paths.slice(0, 5)) {\n          lines.push(`- From ${p.entryPoint}: ${p.path.join(' \u2192 ')}`);\n        }\n        if (result.paths.length > 5) {\n          lines.push(`  \u2026and ${result.paths.length - 5} more paths`);\n        }\n      }\n\n      if (result.unresolvedSymbols.length > 0) {\n        lines.push('', '## Unresolved Symbols');\n        for (const sym of result.unresolvedSymbols.slice(0, 10)) {\n          lines.push(`- ${sym}`);\n        }\n        if (result.unresolvedSymbols.length > 10) {\n          lines.push(`  \u2026and ${result.unresolvedSymbols.length - 10} more`);\n        }\n      }\n\n      // Get impact summary if affected\n      if (result.verdict === 'affected') {\n        const impact = await analyzer.getImpactSummary(vulnerabilityNodeId);\n        if (impact) {\n          lines.push('', '## Impact Summary');\n          if (impact.affectedLayers.length > 0) {\n            lines.push(`Affected layers: ${impact.affectedLayers.join(', ')}`);\n          }\n          lines.push(`Affected entry points: ${impact.affectedEntryPoints.length}`);\n          lines.push(`Distinct paths: ${impact.distinctPathCount}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_staleness': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      const threshold = typeof args.threshold === 'number' ? args.threshold : 0.3;\n\n      // Optionally refresh staleness data from registries\n      if (args.refresh === true) {\n        const { StalenessChecker } = await Promise.resolve().then(() => require('../../security/staleness.js'));\n        const checker = new StalenessChecker(db);\n        await checker.checkAll();\n      }\n\n      const rows: Array<{\n        package_name: string;\n        ecosystem: string;\n        resolved_version: string | null;\n        declared_constraint: string;\n        latest_version: string | null;\n        latest_published: number | null;\n        staleness_score: number | null;\n      }> = rawDb.all(\n        `SELECT package_name, ecosystem, resolved_version, declared_constraint,\n                latest_version, latest_published, staleness_score\n         FROM sec_dependencies\n         WHERE staleness_score >= ?\n         ORDER BY staleness_score DESC`,\n        [threshold],\n      );\n\n      if (rows.length === 0) {\n        return `No dependencies found with staleness_score >= ${threshold}.` +\n          (args.refresh ? '' : ' Use refresh=true to fetch latest version data from registries.');\n      }\n\n      const lines: string[] = [`Stale Dependencies (threshold: ${threshold}):\\n`];\n      for (const row of rows) {\n        const resolved = row.resolved_version ?? row.declared_constraint ?? '?';\n        const latest = row.latest_version ?? '?';\n        const score = row.staleness_score ?? 0;\n        const months = row.latest_published\n          ? Math.round((Date.now() - row.latest_published) / (1000 * 60 * 60 * 24 * 30))\n          : null;\n        const bar = '\u2588'.repeat(Math.round(score * 10)) + '\u2591'.repeat(10 - Math.round(score * 10));\n        const monthsStr = months !== null ? `, ${months}mo since latest` : '';\n        lines.push(`${row.package_name} (${row.ecosystem}): ${resolved} \u2192 ${latest}${monthsStr}`);\n        lines.push(`  ${bar} ${score.toFixed(2)}`);\n      }\n\n      const totalCount: { count: number } = rawDb.get(`SELECT COUNT(*) as count FROM sec_dependencies`) ?? { count: 0 };\n      lines.push('', `${rows.length} of ${totalCount.count} dependencies are stale (score >= ${threshold})`);\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_licenses': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      const deps: Array<{\n        package_name: string;\n        ecosystem: string;\n        license: string | null;\n      }> = rawDb.all(\n        `SELECT package_name, ecosystem, license FROM sec_dependencies ORDER BY ecosystem, package_name`,\n      );\n\n      const { checkLicensePolicy } = await Promise.resolve().then(() => require('../../security/license.js'));\n      const policy = config.securityLicensePolicy;\n      const violations = checkLicensePolicy(deps, policy);\n\n      if (args.policy === true) {\n        // Return only violations\n        if (violations.length === 0) {\n          return 'No license policy violations found.';\n        }\n        const lines: string[] = ['# License Policy Violations\\n'];\n        for (const v of violations) {\n          lines.push(`${v.severity.toUpperCase()}  ${v.packageName} [${v.ecosystem}]  ${v.license}`);\n        }\n        const denyCount = violations.filter(v => v.severity === 'deny').length;\n        const warnCount = violations.filter(v => v.severity === 'warn').length;\n        lines.push('');\n        if (denyCount > 0) lines.push(`${denyCount} denied license${denyCount !== 1 ? 's' : ''}`);\n        if (warnCount > 0) lines.push(`${warnCount} license warning${warnCount !== 1 ? 's' : ''}`);\n        return truncate(lines.join('\\n'));\n      }\n\n      // Full listing\n      if (deps.length === 0) {\n        return 'No dependencies found. Run kirograph index first.';\n      }\n\n      const violationMap = new Map<string, 'deny' | 'warn'>();\n      for (const v of violations) {\n        violationMap.set(`${v.ecosystem}:${v.packageName}`, v.severity);\n      }\n\n      const lines: string[] = [`# License Report (${deps.length} dependencies)\\n`];\n\n      // Violations first\n      if (violations.length > 0) {\n        lines.push('## Policy Violations\\n');\n        for (const v of violations) {\n          lines.push(`${v.severity.toUpperCase()}  ${v.packageName} [${v.ecosystem}]  ${v.license}`);\n        }\n        lines.push('');\n      }\n\n      lines.push('## All Dependencies\\n');\n      lines.push('package | ecosystem | license | status');\n      lines.push('------- | --------- | ------- | ------');\n\n      for (const dep of deps) {\n        const key = `${dep.ecosystem}:${dep.package_name}`;\n        const violation = violationMap.get(key);\n        const license = dep.license ?? '(unknown)';\n        const status = violation ?? (dep.license ? 'ok' : 'unknown');\n        lines.push(`${dep.package_name} | ${dep.ecosystem} | ${license} | ${status}`);\n      }\n\n      const denyCount = violations.filter(v => v.severity === 'deny').length;\n      const warnCount = violations.filter(v => v.severity === 'warn').length;\n      const unknownCount = deps.filter(d => !d.license).length;\n\n      lines.push('');\n      if (denyCount > 0) lines.push(`${denyCount} denied license${denyCount !== 1 ? 's' : ''}`);\n      if (warnCount > 0) lines.push(`${warnCount} license warning${warnCount !== 1 ? 's' : ''}`);\n      if (unknownCount > 0) lines.push(`${unknownCount} unknown license${unknownCount !== 1 ? 's' : ''}`);\n      if (denyCount === 0 && warnCount === 0) lines.push('No policy violations');\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_attack_surface': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { AttackSurfaceAnalyzer } = await Promise.resolve().then(() => require('../../security/attack-surface.js'));\n      const analyzer = new AttackSurfaceAnalyzer(db);\n      const result = await analyzer.analyze();\n\n      if (result.totalRoutes === 0) {\n        return 'No route nodes found in the graph. Ensure the project has been indexed with architecture analysis enabled.';\n      }\n\n      const limit = clampLimit(args.limit as number | undefined, 20);\n      const routes = (args.publicOnly === true)\n        ? result.criticalPaths.filter(r => r.exposureLevel === 'public')\n        : result.criticalPaths;\n\n      const lines: string[] = [\n        '# Attack Surface',\n        '',\n        `Total routes: ${result.totalRoutes}  Public: ${result.publicRoutes}  Authenticated: ${result.authenticatedRoutes}  Routes with vulns: ${result.routesWithVulns}`,\n        '',\n      ];\n\n      const displayed = routes.slice(0, limit);\n      if (displayed.length === 0) {\n        lines.push(args.publicOnly === true\n          ? 'No public routes with vulnerable dependencies found.'\n          : 'No routes with vulnerable dependencies found.');\n      } else {\n        for (const entry of displayed) {\n          const authTag = entry.isAuthenticated ? '[auth]' : '[public]';\n          const riskTag = entry.riskScore > 0 ? ` risk=${entry.riskScore.toFixed(1)}` : '';\n          lines.push(`${authTag} ${entry.route} (${entry.exposureLevel})${riskTag}  ${entry.filePath}`);\n          for (const dep of entry.vulnerableDeps.slice(0, 3)) {\n            lines.push(`  \u2514 ${dep.cveId} via ${dep.packageName} (${dep.hopCount} hop${dep.hopCount !== 1 ? 's' : ''}${dep.verdict ? `, ${dep.verdict}` : ''})`);\n          }\n          if (entry.vulnerableDeps.length > 3) {\n            lines.push(`  \u2514 \u2026and ${entry.vulnerableDeps.length - 3} more vulns`);\n          }\n        }\n        if (routes.length > limit) {\n          lines.push('', `\u2026and ${routes.length - limit} more routes (increase limit to see all)`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_secrets': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { SecretsScanner } = await Promise.resolve().then(() => require('../../security/secrets.js'));\n      const scanner = new SecretsScanner(db, projectRoot);\n      const result = await scanner.scan({ includeTests: args.includeTests === true });\n\n      if (result.totalFindings === 0) {\n        return `No secrets found. Scanned ${result.filesScanned} file${result.filesScanned !== 1 ? 's' : ''}.`;\n      }\n\n      let findings = result.findings;\n      if (args.severity) {\n        findings = findings.filter(f => f.severity === (args.severity as string));\n      }\n\n      if (findings.length === 0) {\n        return `No secrets found matching severity \"${args.severity}\". Total findings (all severities): ${result.totalFindings}.`;\n      }\n\n      const lines: string[] = [\n        `# Secrets Scan (${result.filesScanned} files scanned)`,\n        '',\n        `Found: ${result.totalFindings}  Critical: ${result.criticalCount}  High: ${result.highCount}`,\n        '',\n      ];\n\n      for (const f of findings) {\n        lines.push(`${f.severity.toUpperCase()}  ${f.type}`);\n        lines.push(`  ${f.filePath}:${f.line}:${f.column}  snippet: ${f.snippet}`);\n        if (f.nodeName) {\n          lines.push(`  in function: ${f.nodeName}`);\n        }\n        if (f.entryPointCount > 0) {\n          lines.push(`  reachable from ${f.entryPointCount} entry point${f.entryPointCount !== 1 ? 's' : ''}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_security_flows': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { DataFlowAnalyzer } = await Promise.resolve().then(() => require('../../security/data-flows.js'));\n      const analyzer = new DataFlowAnalyzer(db);\n      let findings = await analyzer.analyze();\n\n      const typeFilter = (args.type as string | undefined) ?? 'all';\n      const TYPE_MAP: Record<string, string> = {\n        sql: 'sql-injection',\n        eval: 'dangerous-eval',\n        deserialize: 'unsafe-deserialize',\n        path: 'path-traversal',\n        crypto: 'hardcoded-crypto',\n      };\n\n      if (typeFilter !== 'all') {\n        const mapped = TYPE_MAP[typeFilter];\n        if (!mapped) return `Invalid type filter \"${typeFilter}\". Use: sql, eval, deserialize, path, crypto, all`;\n        findings = findings.filter(f => f.type === mapped);\n      }\n\n      if (findings.length === 0) {\n        return typeFilter === 'all'\n          ? 'No dangerous data flows detected.'\n          : `No \"${typeFilter}\" findings detected.`;\n      }\n\n      const lines: string[] = [\n        `# Security Flows (${findings.length} finding${findings.length !== 1 ? 's' : ''})`,\n        '',\n      ];\n\n      for (const f of findings) {\n        lines.push(`${f.severity.toUpperCase()}  [${f.owaspCategory}]  ${f.type}`);\n        lines.push(`  ${f.filePath}:${f.line}  symbol: ${f.symbol}`);\n        lines.push(`  ${f.description}`);\n        lines.push(`  Fix: ${f.recommendation}`);\n        lines.push('');\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_supply_chain': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { SupplyChainChecker } = await Promise.resolve().then(() => require('../../security/supply-chain.js'));\n      const checker = new SupplyChainChecker(db);\n      const { results, errors } = await checker.checkAll();\n\n      const RISK_ORDER: Record<string, number> = { critical: 0, high: 1, medium: 2, low: 3, unknown: 4 };\n      const thresholdArg = args.threshold as string | undefined;\n      const thresholdOrder = thresholdArg ? (RISK_ORDER[thresholdArg] ?? 4) : 2; // default: medium and above\n\n      const filtered = results\n        .filter(r => (RISK_ORDER[r.riskLevel] ?? 4) <= thresholdOrder)\n        .sort((a, b) => (RISK_ORDER[a.riskLevel] ?? 4) - (RISK_ORDER[b.riskLevel] ?? 4));\n\n      if (filtered.length === 0) {\n        return `No supply chain risks found at threshold \"${thresholdArg ?? 'medium'}\" or above. Checked ${results.length} dependencies.`;\n      }\n\n      const lines: string[] = [\n        `# Supply Chain Health (${filtered.length} risks, threshold: ${thresholdArg ?? 'medium'})`,\n        '',\n      ];\n\n      for (const r of filtered) {\n        const scoreStr = r.scorecardScore !== null ? ` scorecard=${r.scorecardScore.toFixed(1)}/10` : '';\n        const maintainerStr = r.maintainerCount !== null ? ` maintainers=${r.maintainerCount}` : '';\n        lines.push(`${r.riskLevel.toUpperCase()}  ${r.packageName} (${r.ecosystem})${scoreStr}${maintainerStr}`);\n        for (const reason of r.riskReasons) {\n          lines.push(`  \u2022 ${reason}`);\n        }\n      }\n\n      if (errors.length > 0) {\n        lines.push('', `\u26A0 ${errors.length} package${errors.length !== 1 ? 's' : ''} could not be checked (network errors)`);\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_dep_confusion': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { DepConfusionChecker } = await Promise.resolve().then(() => require('../../security/dep-confusion.js'));\n      const checker = new DepConfusionChecker(db);\n      const findings = await checker.check();\n\n      if (findings.length === 0) {\n        return 'No dependency confusion vulnerabilities detected.';\n      }\n\n      const RISK_ORDER: Record<string, number> = { critical: 0, high: 1, medium: 2 };\n      const sorted = [...findings].sort((a, b) => (RISK_ORDER[a.riskLevel] ?? 3) - (RISK_ORDER[b.riskLevel] ?? 3));\n\n      const lines: string[] = [\n        `# Dependency Confusion (${findings.length} finding${findings.length !== 1 ? 's' : ''})`,\n        '',\n      ];\n\n      for (const f of sorted) {\n        lines.push(`${f.riskLevel.toUpperCase()}  ${f.packageName} (${f.ecosystem})`);\n        lines.push(`  ${f.explanation}`);\n        if (f.publicExists && f.publicVersion) {\n          lines.push(`  Public version: ${f.publicVersion}${f.publicPublishedAt ? `  published: ${f.publicPublishedAt}` : ''}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_remediation': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { RemediationTracker } = await Promise.resolve().then(() => require('../../security/remediation.js'));\n      const tracker = new RemediationTracker(db);\n      let statuses = tracker.getStatus();\n\n      if (args.overdueOnly === true) {\n        statuses = statuses.filter(s => s.isOverdue);\n      }\n\n      if (statuses.length === 0) {\n        return args.overdueOnly === true\n          ? 'No overdue vulnerabilities found.'\n          : 'No open vulnerabilities with SLA tracking data found.';\n      }\n\n      // Sort: overdue first, then by slaStatus, then by severity desc\n      const SLA_ORDER: Record<string, number> = { overdue: 0, warning: 1, no_fix: 2, ok: 3 };\n      statuses.sort((a, b) => {\n        const slaA = SLA_ORDER[a.slaStatus] ?? 3;\n        const slaB = SLA_ORDER[b.slaStatus] ?? 3;\n        if (slaA !== slaB) return slaA - slaB;\n        return (b.severity ?? 0) - (a.severity ?? 0);\n      });\n\n      const overdueCount = statuses.filter(s => s.isOverdue).length;\n      const warningCount = statuses.filter(s => s.slaStatus === 'warning').length;\n\n      const lines: string[] = [\n        `# Remediation SLA (${statuses.length} open${overdueCount > 0 ? `, ${overdueCount} overdue` : ''}${warningCount > 0 ? `, ${warningCount} warning` : ''})`,\n        '',\n      ];\n\n      for (const s of statuses) {\n        const severityLabel = s.severity == null ? 'UNKNOWN'\n          : s.severity >= 9 ? 'CRITICAL'\n          : s.severity >= 7 ? 'HIGH'\n          : s.severity >= 4 ? 'MEDIUM'\n          : 'LOW';\n\n        const slaTag = s.slaStatus === 'overdue' ? '[OVERDUE]'\n          : s.slaStatus === 'warning' ? '[WARNING]'\n          : s.slaStatus === 'no_fix' ? '[NO_FIX]'\n          : '[OK]';\n\n        lines.push(`${slaTag}  ${severityLabel}  ${s.cveId}  ${s.packageName}`);\n        if (s.daysOpen !== null) lines.push(`  Open for ${s.daysOpen} day${s.daysOpen !== 1 ? 's' : ''}`);\n        if (s.daysWithFixAvailable !== null) lines.push(`  Fix available for ${s.daysWithFixAvailable} day${s.daysWithFixAvailable !== 1 ? 's' : ''}`);\n        if (s.slaDeadline !== null) {\n          const deadlineDate = new Date(s.slaDeadline).toISOString().slice(0, 10);\n          lines.push(`  SLA deadline: ${deadlineDate}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    default:\n      return `Unknown tool: ${toolName}`;\n  }\n}\n"],
-  "mappings": 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+  "sourcesContent": ["import KiroGraph from '../../index';\nimport { clampLimit, truncate } from './utils';\n\nexport async function handleSecurity(toolName: string, args: Record<string, unknown>, cg: KiroGraph): Promise<string> {\n  switch (toolName) {\n    case 'kirograph_security': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n      if (!config.enableArchitecture) return 'Security requires architecture analysis. Set enableArchitecture: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      const depCount: { count: number } = rawDb.get(\n        `SELECT COUNT(*) as count FROM sec_dependencies`,\n      ) ?? { count: 0 };\n\n      const vulnCount: { count: number } = rawDb.get(\n        `SELECT COUNT(*) as count FROM sec_vulnerabilities`,\n      ) ?? { count: 0 };\n\n      const verdictRows: Array<{ verdict: string; count: number }> = rawDb.all(\n        `SELECT verdict, COUNT(*) as count FROM sec_reachability GROUP BY verdict`,\n      );\n      const verdicts: Record<string, number> = {};\n      for (const row of verdictRows) {\n        verdicts[row.verdict] = row.count;\n      }\n\n      const staleCount: { count: number } = rawDb.get(\n        `SELECT COUNT(*) as count FROM sec_dependencies WHERE vuln_data_stale = 1`,\n      ) ?? { count: 0 };\n\n      // Count suppressed CVEs\n      const { SuppressionManager: SecSuppressionManager } = await Promise.resolve().then(() => require('../../security/suppressions.js'));\n      const secSuppressions = new SecSuppressionManager(projectRoot);\n      const allCveIds: Array<{ cve_id: string }> = rawDb.all(`SELECT cve_id FROM sec_vulnerabilities`);\n      const suppressedCveCount = allCveIds.filter(r => secSuppressions.isSuppressed(r.cve_id)).length;\n      const visibleVulnCount = vulnCount.count - suppressedCveCount;\n\n      const lines: string[] = [\n        '# Security Overview',\n        '',\n        `Dependencies: ${depCount.count}`,\n        `Vulnerabilities: ${visibleVulnCount}${suppressedCveCount > 0 ? ` (${suppressedCveCount} suppressed)` : ''}`,\n      ];\n\n      if (visibleVulnCount > 0) {\n        const affected = verdicts['affected'] ?? 0;\n        const notAffected = verdicts['not_affected'] ?? 0;\n        const underInvestigation = verdicts['under_investigation'] ?? 0;\n        const pending = visibleVulnCount - affected - notAffected - underInvestigation;\n\n        lines.push('', '## Reachability Verdicts', '');\n        if (affected > 0) lines.push(`\u25CF Affected: ${affected}`);\n        if (notAffected > 0) lines.push(`\u25CF Not affected: ${notAffected}`);\n        if (underInvestigation > 0) lines.push(`\u25CF Under investigation: ${underInvestigation}`);\n        if (pending > 0) lines.push(`\u25CF Pending analysis: ${pending}`);\n      }\n\n      if (staleCount.count > 0) {\n        lines.push('', `\u26A0 ${staleCount.count} dependenc${staleCount.count === 1 ? 'y has' : 'ies have'} stale vulnerability data. Use kirograph_vulns with refresh=true to update.`);\n      }\n\n      // Check if vulnerability data is stale by age\n      const lastVulnCheck = (rawDb.get(\n        `SELECT MIN(last_vuln_check) as oldest FROM sec_dependencies WHERE last_vuln_check IS NOT NULL`,\n      ) as { oldest: number | null } | undefined)?.oldest;\n      if (lastVulnCheck != null) {\n        const ageMs = Date.now() - lastVulnCheck;\n        const ageDays = ageMs / (1000 * 60 * 60 * 24);\n        const maxAge = config.securityEnrichMaxAgeDays ?? 7;\n        if (ageDays > maxAge) {\n          lines.push('', `\u26A0 Vulnerability data is ${Math.floor(ageDays)} days old (max: ${maxAge}). Run kirograph vulns --refresh to update.`);\n        }\n      }\n\n      // Pattern SAST findings count\n      try {\n        const rawDbSec = db.getRawDb();\n        const tableExistsSec = rawDbSec.get(\"SELECT name FROM sqlite_master WHERE type='table' AND name='pattern_matches'\");\n        if (tableExistsSec) {\n          const patternCount = rawDbSec.get('SELECT COUNT(*) as cnt FROM pattern_matches')?.cnt ?? 0;\n          if (patternCount > 0) {\n            const critCount = rawDbSec.get(\"SELECT COUNT(*) as cnt FROM pattern_matches WHERE severity = 'critical'\")?.cnt ?? 0;\n            lines.push(`SAST findings: ${patternCount} pattern matches (${critCount} critical)`);\n          }\n        }\n      } catch { /* non-critical */ }\n\n      return lines.join('\\n');\n    }\n\n    case 'kirograph_vulns': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      // Handle refresh\n      if (args.refresh === true) {\n        const { OsvAdapter } = await Promise.resolve().then(() => require('../../security/vuln/osv-adapter.js'));\n        const { VulnerabilityDatabaseClient } = await Promise.resolve().then(() => require('../../security/vuln/client.js'));\n\n        const adapters = config.securityDatabases.map((dbName: string) => {\n          if (dbName.toUpperCase() === 'OSV') return new OsvAdapter();\n          return null;\n        }).filter(Boolean) as any[];\n\n        const client = new VulnerabilityDatabaseClient(adapters, db, undefined, projectRoot);\n        await client.enrichAll();\n      }\n\n      // Build query\n      let query = `\n        SELECT\n          v.node_id, v.cve_id, v.severity_score, v.fixed_version, v.summary,\n          v.epss_score, v.epss_percentile, v.risk_score,\n          d.package_name, d.ecosystem, d.resolved_version, d.declared_constraint,\n          r.verdict\n        FROM sec_vulnerabilities v\n        LEFT JOIN edges e ON e.target = v.node_id AND e.kind = 'has_vulnerability'\n        LEFT JOIN sec_dependencies d ON d.node_id = e.source\n        LEFT JOIN sec_reachability r ON r.vulnerability_node_id = v.node_id\n        WHERE 1=1\n      `;\n      const params: any[] = [];\n\n      // Severity filter\n      if (args.severity) {\n        const severityRanges: Record<string, [number, number]> = {\n          critical: [9.0, 10.0],\n          high: [7.0, 8.9],\n          medium: [4.0, 6.9],\n          low: [0.1, 3.9],\n        };\n        const range = severityRanges[(args.severity as string).toLowerCase()];\n        if (!range) return `Invalid severity: ${args.severity}. Use: critical, high, medium, low`;\n        query += ` AND v.severity_score >= ? AND v.severity_score <= ?`;\n        params.push(range[0], range[1]);\n      }\n\n      // Verdict filter\n      if (args.verdict) {\n        const validVerdicts = ['affected', 'not_affected', 'under_investigation'];\n        if (!validVerdicts.includes(args.verdict as string)) {\n          return `Invalid verdict: ${args.verdict}. Use: affected, not_affected, under_investigation`;\n        }\n        query += ` AND r.verdict = ?`;\n        params.push(args.verdict);\n      }\n\n      const limit = clampLimit(args.limit as number | undefined, 20);\n      query += ` ORDER BY v.risk_score DESC NULLS LAST LIMIT ?`;\n      params.push(limit);\n\n      const rows: Array<{\n        node_id: string;\n        cve_id: string;\n        severity_score: number | null;\n        fixed_version: string | null;\n        summary: string | null;\n        epss_score: number | null;\n        epss_percentile: number | null;\n        risk_score: number | null;\n        package_name: string | null;\n        ecosystem: string | null;\n        resolved_version: string | null;\n        declared_constraint: string | null;\n        verdict: string | null;\n      }> = rawDb.all(query, params);\n\n      // Deduplicate by (cve_id, package_name, ecosystem) \u2014 same CVE can appear multiple\n      // times when a package is declared in multiple manifests (monorepo).\n      const verdictRankMcp = (v: string | null) =>\n        v === 'affected' ? 3 : v === 'under_investigation' ? 2 : v === 'not_affected' ? 1 : 0;\n      const dedupMapMcp = new Map<string, typeof rows[0]>();\n      for (const row of rows) {\n        const key = `${row.cve_id}::${row.package_name ?? ''}::${row.ecosystem ?? ''}`;\n        const ex = dedupMapMcp.get(key);\n        if (!ex || verdictRankMcp(row.verdict) > verdictRankMcp(ex.verdict)) dedupMapMcp.set(key, row);\n      }\n      const dedupedRowsMcp = [...dedupMapMcp.values()];\n\n      // Filter out suppressed CVEs\n      const { SuppressionManager } = await Promise.resolve().then(() => require('../../security/suppressions.js'));\n      const suppressionMgr = new SuppressionManager(projectRoot);\n      const suppressedCount = dedupedRowsMcp.filter(row => suppressionMgr.isSuppressed(row.cve_id)).length;\n      const filteredRows = dedupedRowsMcp.filter(row => !suppressionMgr.isSuppressed(row.cve_id));\n\n      if (filteredRows.length === 0) {\n        const noMatch = 'No vulnerabilities found' + ((args.severity || args.verdict) ? ' matching filters.' : '.');\n        return suppressedCount > 0 ? `${noMatch} (${suppressedCount} suppressed)` : noMatch;\n      }\n\n      const { formatFixSuggestion } = await Promise.resolve().then(() => require('../../security/export/fix-suggestions.js'));\n\n      const lines: string[] = [`Vulnerabilities (${filteredRows.length}${suppressedCount > 0 ? `, ${suppressedCount} suppressed` : ''}):\\n`];\n\n      for (const row of filteredRows) {\n        const score = row.severity_score;\n        let severityLabel: string;\n        if (score == null) severityLabel = 'UNKNOWN';\n        else if (score >= 9.0) severityLabel = 'CRITICAL';\n        else if (score >= 7.0) severityLabel = 'HIGH';\n        else if (score >= 4.0) severityLabel = 'MEDIUM';\n        else severityLabel = 'LOW';\n\n        let verdictLabel: string;\n        if (!row.verdict) verdictLabel = 'pending';\n        else if (row.verdict === 'affected') verdictLabel = 'affected';\n        else if (row.verdict === 'not_affected') verdictLabel = 'not affected';\n        else verdictLabel = 'investigating';\n\n        const pkg = row.package_name\n          ? `${row.package_name}@${row.resolved_version || row.declared_constraint || '?'}`\n          : 'unknown package';\n\n        const epssNote = row.epss_score != null\n          ? ` [EPSS: ${row.epss_score.toFixed(2)}]`\n          : '';\n        const riskNote = row.risk_score != null\n          ? ` [Risk: ${row.risk_score.toFixed(1)}]`\n          : '';\n        lines.push(`${severityLabel}  ${row.cve_id}  ${pkg}  [${verdictLabel}]${epssNote}${riskNote}`);\n\n        if (row.summary && row.summary !== 'Manually registered') {\n          const truncSummary = row.summary.length > 120 ? row.summary.slice(0, 120) + '\u2026' : row.summary;\n          lines.push(`  ${truncSummary}`);\n        }\n\n        if (row.fixed_version && row.ecosystem && row.package_name) {\n          const fix = formatFixSuggestion(row.ecosystem, row.package_name, row.fixed_version);\n          if (fix) lines.push(`  ${fix}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_vuln_add': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const cveId = args.cveId as string;\n      const pkgName = args.package as string;\n      if (!cveId) return 'Error: cveId is required.';\n      if (!pkgName) return 'Error: package is required.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      // Find matching Dependency_Node\n      const depRow: { node_id: string; ecosystem: string } | undefined = rawDb.get(\n        `SELECT node_id, ecosystem FROM sec_dependencies WHERE package_name = ?`,\n        [pkgName],\n      );\n\n      if (!depRow) {\n        return `No dependency found matching \"${pkgName}\". Run kirograph index first to discover dependencies.`;\n      }\n\n      // Create Vulnerability_Node\n      const vulnNodeId = `vuln:${cveId}`;\n      const now = Date.now();\n      const severity = args.severity as number | undefined;\n      const summary = (args.summary as string) ?? 'Manually registered';\n      const fixedVersion = (args.fixedVersion as string) ?? null;\n\n      rawDb.run(\n        `INSERT OR REPLACE INTO nodes\n          (id, kind, name, qualified_name, file_path, language,\n           start_line, end_line, start_column, end_column,\n           is_exported, is_async, is_static, is_abstract, updated_at)\n         VALUES (?, 'vulnerability', ?, ?, '', 'unknown', 0, 0, 0, 0, 0, 0, 0, 0, ?)`,\n        [vulnNodeId, cveId, cveId, now],\n      );\n\n      rawDb.run(\n        `INSERT OR REPLACE INTO sec_vulnerabilities\n          (node_id, cve_id, severity_score, affected_ranges, fixed_version, summary, source_database)\n         VALUES (?, ?, ?, '[]', ?, ?, 'manual')`,\n        [vulnNodeId, cveId, severity ?? null, fixedVersion, summary],\n      );\n\n      // Create has_vulnerability edge\n      rawDb.run(\n        `INSERT OR IGNORE INTO edges (source, target, kind, confidence, confidence_score)\n         VALUES (?, ?, 'has_vulnerability', 'extracted', 1.0)`,\n        [depRow.node_id, vulnNodeId],\n      );\n\n      return `Registered ${cveId} against ${pkgName}.`;\n    }\n\n    case 'kirograph_vuln_suppress': {\n      const projectRoot = cg.getProjectRoot();\n      const cveId = args.cveId as string;\n      if (!cveId) return 'Error: cveId is required.';\n\n      const { SuppressionManager } = await Promise.resolve().then(() => require('../../security/suppressions.js'));\n      const manager = new SuppressionManager(projectRoot);\n      manager.add(cveId, args.reason as string | undefined, args.expires as string | undefined);\n\n      const reasonNote = args.reason ? ` Reason: ${args.reason}.` : '';\n      const expiresNote = args.expires ? ` Expires: ${args.expires}.` : '';\n      return `${cveId} suppressed.${reasonNote}${expiresNote}`;\n    }\n\n    case 'kirograph_sbom': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { SBOMExporter } = await Promise.resolve().then(() => require('../../security/export/sbom.js'));\n      const exporter = new SBOMExporter(db, projectRoot);\n      const json = exporter.exportJSON();\n\n      return truncate(json);\n    }\n\n    case 'kirograph_vex': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { VEXExporter } = await Promise.resolve().then(() => require('../../security/export/vex.js'));\n      const exporter = new VEXExporter(db, projectRoot);\n      const json = exporter.exportJSON();\n\n      return truncate(json);\n    }\n\n    case 'kirograph_reachability': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const target = args.target as string;\n      if (!target) return 'Error: target is required (dependency name or CVE ID).';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      // Try to find target as a CVE ID in sec_vulnerabilities\n      let vulnerabilityNodeId: string | null = null;\n      let targetLabel = target;\n\n      const vulnRow: { node_id: string } | undefined = rawDb.get(\n        `SELECT node_id FROM sec_vulnerabilities WHERE cve_id = ?`,\n        [target],\n      );\n\n      if (vulnRow) {\n        vulnerabilityNodeId = vulnRow.node_id;\n      } else {\n        // Try to find target as a dependency name\n        const depRow: { node_id: string; package_name: string } | undefined = rawDb.get(\n          `SELECT node_id, package_name FROM sec_dependencies WHERE package_name = ?`,\n          [target],\n        );\n\n        if (depRow) {\n          targetLabel = depRow.package_name;\n          // Find vulnerabilities linked to this dependency\n          const vulnEdge: { target: string } | undefined = rawDb.get(\n            `SELECT target FROM edges WHERE source = ? AND kind = 'has_vulnerability' LIMIT 1`,\n            [depRow.node_id],\n          );\n\n          if (vulnEdge) {\n            vulnerabilityNodeId = vulnEdge.target;\n          } else {\n            return `No vulnerabilities found for dependency \"${target}\". The dependency exists but has no known vulnerabilities.`;\n          }\n        } else {\n          return `Target \"${target}\" not found. Provide a valid CVE ID or dependency package name.`;\n        }\n      }\n\n      // Run reachability analysis\n      const { ReachabilityAnalyzer, explainReachability } = await Promise.resolve().then(() => require('../../security/reachability.js'));\n      const analyzer = new ReachabilityAnalyzer(db, config);\n      const result = await analyzer.analyze(vulnerabilityNodeId);\n\n      const lines: string[] = [\n        `# Reachability: ${targetLabel}`,\n        '',\n        `Verdict: ${result.verdict}`,\n        `Reaching entry points: ${result.reachingEntryPointCount}`,\n        '',\n        `Why: ${explainReachability(result)}`,\n      ];\n\n      if (result.paths.length > 0) {\n        lines.push('', '## Paths');\n        for (const p of result.paths.slice(0, 5)) {\n          lines.push(`- From ${p.entryPoint}: ${p.path.join(' \u2192 ')}`);\n        }\n        if (result.paths.length > 5) {\n          lines.push(`  \u2026and ${result.paths.length - 5} more paths`);\n        }\n      }\n\n      if (result.unresolvedSymbols.length > 0) {\n        lines.push('', '## Unresolved Symbols');\n        for (const sym of result.unresolvedSymbols.slice(0, 10)) {\n          lines.push(`- ${sym}`);\n        }\n        if (result.unresolvedSymbols.length > 10) {\n          lines.push(`  \u2026and ${result.unresolvedSymbols.length - 10} more`);\n        }\n      }\n\n      // Get impact summary if affected\n      if (result.verdict === 'affected') {\n        const impact = await analyzer.getImpactSummary(vulnerabilityNodeId);\n        if (impact) {\n          lines.push('', '## Impact Summary');\n          if (impact.affectedLayers.length > 0) {\n            lines.push(`Affected layers: ${impact.affectedLayers.join(', ')}`);\n          }\n          lines.push(`Affected entry points: ${impact.affectedEntryPoints.length}`);\n          lines.push(`Distinct paths: ${impact.distinctPathCount}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_staleness': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      const threshold = typeof args.threshold === 'number' ? args.threshold : 0.3;\n\n      // Optionally refresh staleness data from registries\n      if (args.refresh === true) {\n        const { StalenessChecker } = await Promise.resolve().then(() => require('../../security/staleness.js'));\n        const checker = new StalenessChecker(db);\n        await checker.checkAll();\n      }\n\n      const rows: Array<{\n        package_name: string;\n        ecosystem: string;\n        resolved_version: string | null;\n        declared_constraint: string;\n        latest_version: string | null;\n        latest_published: number | null;\n        staleness_score: number | null;\n      }> = rawDb.all(\n        `SELECT package_name, ecosystem, resolved_version, declared_constraint,\n                latest_version, latest_published, staleness_score\n         FROM sec_dependencies\n         WHERE staleness_score >= ?\n         ORDER BY staleness_score DESC`,\n        [threshold],\n      );\n\n      if (rows.length === 0) {\n        return `No dependencies found with staleness_score >= ${threshold}.` +\n          (args.refresh ? '' : ' Use refresh=true to fetch latest version data from registries.');\n      }\n\n      const lines: string[] = [`Stale Dependencies (threshold: ${threshold}):\\n`];\n      for (const row of rows) {\n        const resolved = row.resolved_version ?? row.declared_constraint ?? '?';\n        const latest = row.latest_version ?? '?';\n        const score = row.staleness_score ?? 0;\n        const months = row.latest_published\n          ? Math.round((Date.now() - row.latest_published) / (1000 * 60 * 60 * 24 * 30))\n          : null;\n        const bar = '\u2588'.repeat(Math.round(score * 10)) + '\u2591'.repeat(10 - Math.round(score * 10));\n        const monthsStr = months !== null ? `, ${months}mo since latest` : '';\n        lines.push(`${row.package_name} (${row.ecosystem}): ${resolved} \u2192 ${latest}${monthsStr}`);\n        lines.push(`  ${bar} ${score.toFixed(2)}`);\n      }\n\n      const totalCount: { count: number } = rawDb.get(`SELECT COUNT(*) as count FROM sec_dependencies`) ?? { count: 0 };\n      lines.push('', `${rows.length} of ${totalCount.count} dependencies are stale (score >= ${threshold})`);\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_licenses': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n      const rawDb = db.getRawDb();\n\n      const deps: Array<{\n        package_name: string;\n        ecosystem: string;\n        license: string | null;\n      }> = rawDb.all(\n        `SELECT package_name, ecosystem, license FROM sec_dependencies ORDER BY ecosystem, package_name`,\n      );\n\n      const { checkLicensePolicy } = await Promise.resolve().then(() => require('../../security/license.js'));\n      const policy = config.securityLicensePolicy;\n      const violations = checkLicensePolicy(deps, policy);\n\n      if (args.policy === true) {\n        // Return only violations\n        if (violations.length === 0) {\n          return 'No license policy violations found.';\n        }\n        const lines: string[] = ['# License Policy Violations\\n'];\n        for (const v of violations) {\n          lines.push(`${v.severity.toUpperCase()}  ${v.packageName} [${v.ecosystem}]  ${v.license}`);\n        }\n        const denyCount = violations.filter(v => v.severity === 'deny').length;\n        const warnCount = violations.filter(v => v.severity === 'warn').length;\n        lines.push('');\n        if (denyCount > 0) lines.push(`${denyCount} denied license${denyCount !== 1 ? 's' : ''}`);\n        if (warnCount > 0) lines.push(`${warnCount} license warning${warnCount !== 1 ? 's' : ''}`);\n        return truncate(lines.join('\\n'));\n      }\n\n      // Full listing\n      if (deps.length === 0) {\n        return 'No dependencies found. Run kirograph index first.';\n      }\n\n      const violationMap = new Map<string, 'deny' | 'warn'>();\n      for (const v of violations) {\n        violationMap.set(`${v.ecosystem}:${v.packageName}`, v.severity);\n      }\n\n      const lines: string[] = [`# License Report (${deps.length} dependencies)\\n`];\n\n      // Violations first\n      if (violations.length > 0) {\n        lines.push('## Policy Violations\\n');\n        for (const v of violations) {\n          lines.push(`${v.severity.toUpperCase()}  ${v.packageName} [${v.ecosystem}]  ${v.license}`);\n        }\n        lines.push('');\n      }\n\n      lines.push('## All Dependencies\\n');\n      lines.push('package | ecosystem | license | status');\n      lines.push('------- | --------- | ------- | ------');\n\n      for (const dep of deps) {\n        const key = `${dep.ecosystem}:${dep.package_name}`;\n        const violation = violationMap.get(key);\n        const license = dep.license ?? '(unknown)';\n        const status = violation ?? (dep.license ? 'ok' : 'unknown');\n        lines.push(`${dep.package_name} | ${dep.ecosystem} | ${license} | ${status}`);\n      }\n\n      const denyCount = violations.filter(v => v.severity === 'deny').length;\n      const warnCount = violations.filter(v => v.severity === 'warn').length;\n      const unknownCount = deps.filter(d => !d.license).length;\n\n      lines.push('');\n      if (denyCount > 0) lines.push(`${denyCount} denied license${denyCount !== 1 ? 's' : ''}`);\n      if (warnCount > 0) lines.push(`${warnCount} license warning${warnCount !== 1 ? 's' : ''}`);\n      if (unknownCount > 0) lines.push(`${unknownCount} unknown license${unknownCount !== 1 ? 's' : ''}`);\n      if (denyCount === 0 && warnCount === 0) lines.push('No policy violations');\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_attack_surface': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { AttackSurfaceAnalyzer } = await Promise.resolve().then(() => require('../../security/attack-surface.js'));\n      const analyzer = new AttackSurfaceAnalyzer(db, {\n        authDetectionMode: config.securityAuthDetectionMode,\n        authConfidenceThreshold: config.securityAuthConfidenceThreshold,\n        jevApiKey: config.jevApiKey,\n        jevBaseUrl: config.jevBaseUrl,\n        jevModel: config.jevModel,\n      });\n      let result;\n      try {\n        result = await analyzer.analyze();\n      } catch (err) {\n        return `Error: ${err instanceof Error ? err.message : String(err)}`;\n      }\n\n      if (result.totalRoutes === 0) {\n        return 'No route nodes found in the graph. Ensure the project has been indexed with architecture analysis enabled.';\n      }\n\n      const limit = clampLimit(args.limit as number | undefined, 20);\n      const routes = (args.publicOnly === true)\n        ? result.criticalPaths.filter(r => r.exposureLevel === 'public')\n        : result.criticalPaths;\n\n      const lines: string[] = [\n        '# Attack Surface',\n        '',\n        `Total routes: ${result.totalRoutes}  Public: ${result.publicRoutes}  Authenticated: ${result.authenticatedRoutes}  Routes with vulns: ${result.routesWithVulns}`,\n        '',\n      ];\n\n      const displayed = routes.slice(0, limit);\n      if (displayed.length === 0) {\n        lines.push(args.publicOnly === true\n          ? 'No public routes with vulnerable dependencies found.'\n          : 'No routes with vulnerable dependencies found.');\n      } else {\n        for (const entry of displayed) {\n          const authTag = entry.isAuthenticated ? '[auth]' : '[public]';\n          const riskTag = entry.riskScore > 0 ? ` risk=${entry.riskScore.toFixed(1)}` : '';\n          lines.push(`${authTag} ${entry.route} (${entry.exposureLevel})${riskTag}  ${entry.filePath}`);\n          for (const dep of entry.vulnerableDeps.slice(0, 3)) {\n            lines.push(`  \u2514 ${dep.cveId} via ${dep.packageName} (${dep.hopCount} hop${dep.hopCount !== 1 ? 's' : ''}${dep.verdict ? `, ${dep.verdict}` : ''})`);\n          }\n          if (entry.vulnerableDeps.length > 3) {\n            lines.push(`  \u2514 \u2026and ${entry.vulnerableDeps.length - 3} more vulns`);\n          }\n        }\n        if (routes.length > limit) {\n          lines.push('', `\u2026and ${routes.length - limit} more routes (increase limit to see all)`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_secrets': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { SecretsScanner } = await Promise.resolve().then(() => require('../../security/secrets.js'));\n      const scanner = new SecretsScanner(db, projectRoot);\n      const result = await scanner.scan({ includeTests: args.includeTests === true });\n\n      if (result.totalFindings === 0) {\n        return `No secrets found. Scanned ${result.filesScanned} file${result.filesScanned !== 1 ? 's' : ''}.`;\n      }\n\n      let findings = result.findings;\n      if (args.severity) {\n        findings = findings.filter(f => f.severity === (args.severity as string));\n      }\n\n      if (findings.length === 0) {\n        return `No secrets found matching severity \"${args.severity}\". Total findings (all severities): ${result.totalFindings}.`;\n      }\n\n      const lines: string[] = [\n        `# Secrets Scan (${result.filesScanned} files scanned)`,\n        '',\n        `Found: ${result.totalFindings}  Critical: ${result.criticalCount}  High: ${result.highCount}`,\n        '',\n      ];\n\n      for (const f of findings) {\n        lines.push(`${f.severity.toUpperCase()}  ${f.type}`);\n        lines.push(`  ${f.filePath}:${f.line}:${f.column}  snippet: ${f.snippet}`);\n        if (f.nodeName) {\n          lines.push(`  in function: ${f.nodeName}`);\n        }\n        if (f.entryPointCount > 0) {\n          lines.push(`  reachable from ${f.entryPointCount} entry point${f.entryPointCount !== 1 ? 's' : ''}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_security_flows': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { DataFlowAnalyzer } = await Promise.resolve().then(() => require('../../security/data-flows.js'));\n      const analyzer = new DataFlowAnalyzer(db);\n      let findings = await analyzer.analyze();\n\n      const typeFilter = (args.type as string | undefined) ?? 'all';\n      const TYPE_MAP: Record<string, string> = {\n        sql: 'sql-injection',\n        eval: 'dangerous-eval',\n        deserialize: 'unsafe-deserialize',\n        path: 'path-traversal',\n        crypto: 'hardcoded-crypto',\n      };\n\n      if (typeFilter !== 'all') {\n        const mapped = TYPE_MAP[typeFilter];\n        if (!mapped) return `Invalid type filter \"${typeFilter}\". Use: sql, eval, deserialize, path, crypto, all`;\n        findings = findings.filter(f => f.type === mapped);\n      }\n\n      if (findings.length === 0) {\n        return typeFilter === 'all'\n          ? 'No dangerous data flows detected.'\n          : `No \"${typeFilter}\" findings detected.`;\n      }\n\n      const lines: string[] = [\n        `# Security Flows (${findings.length} finding${findings.length !== 1 ? 's' : ''})`,\n        '',\n      ];\n\n      for (const f of findings) {\n        lines.push(`${f.severity.toUpperCase()}  [${f.owaspCategory}]  ${f.type}`);\n        lines.push(`  ${f.filePath}:${f.line}  symbol: ${f.symbol}`);\n        lines.push(`  ${f.description}`);\n        lines.push(`  Fix: ${f.recommendation}`);\n        lines.push('');\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_supply_chain': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { SupplyChainChecker } = await Promise.resolve().then(() => require('../../security/supply-chain.js'));\n      const checker = new SupplyChainChecker(db);\n      const { results, errors } = await checker.checkAll();\n\n      const RISK_ORDER: Record<string, number> = { critical: 0, high: 1, medium: 2, low: 3, unknown: 4 };\n      const thresholdArg = args.threshold as string | undefined;\n      const thresholdOrder = thresholdArg ? (RISK_ORDER[thresholdArg] ?? 4) : 2; // default: medium and above\n\n      const filtered = results\n        .filter(r => (RISK_ORDER[r.riskLevel] ?? 4) <= thresholdOrder)\n        .sort((a, b) => (RISK_ORDER[a.riskLevel] ?? 4) - (RISK_ORDER[b.riskLevel] ?? 4));\n\n      if (filtered.length === 0) {\n        return `No supply chain risks found at threshold \"${thresholdArg ?? 'medium'}\" or above. Checked ${results.length} dependencies.`;\n      }\n\n      const lines: string[] = [\n        `# Supply Chain Health (${filtered.length} risks, threshold: ${thresholdArg ?? 'medium'})`,\n        '',\n      ];\n\n      for (const r of filtered) {\n        const scoreStr = r.scorecardScore !== null ? ` scorecard=${r.scorecardScore.toFixed(1)}/10` : '';\n        const maintainerStr = r.maintainerCount !== null ? ` maintainers=${r.maintainerCount}` : '';\n        lines.push(`${r.riskLevel.toUpperCase()}  ${r.packageName} (${r.ecosystem})${scoreStr}${maintainerStr}`);\n        for (const reason of r.riskReasons) {\n          lines.push(`  \u2022 ${reason}`);\n        }\n      }\n\n      if (errors.length > 0) {\n        lines.push('', `\u26A0 ${errors.length} package${errors.length !== 1 ? 's' : ''} could not be checked (network errors)`);\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_dep_confusion': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { DepConfusionChecker } = await Promise.resolve().then(() => require('../../security/dep-confusion.js'));\n      const checker = new DepConfusionChecker(db);\n      const findings = await checker.check();\n\n      if (findings.length === 0) {\n        return 'No dependency confusion vulnerabilities detected.';\n      }\n\n      const RISK_ORDER: Record<string, number> = { critical: 0, high: 1, medium: 2 };\n      const sorted = [...findings].sort((a, b) => (RISK_ORDER[a.riskLevel] ?? 3) - (RISK_ORDER[b.riskLevel] ?? 3));\n\n      const lines: string[] = [\n        `# Dependency Confusion (${findings.length} finding${findings.length !== 1 ? 's' : ''})`,\n        '',\n      ];\n\n      for (const f of sorted) {\n        lines.push(`${f.riskLevel.toUpperCase()}  ${f.packageName} (${f.ecosystem})`);\n        lines.push(`  ${f.explanation}`);\n        if (f.publicExists && f.publicVersion) {\n          lines.push(`  Public version: ${f.publicVersion}${f.publicPublishedAt ? `  published: ${f.publicPublishedAt}` : ''}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    case 'kirograph_remediation': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableSecurity) return 'Security analysis is not enabled. Set enableSecurity: true in .kirograph/config.json and run kirograph index.';\n\n      const db = cg.getDatabase();\n      db.applySecuritySchema();\n\n      const { RemediationTracker } = await Promise.resolve().then(() => require('../../security/remediation.js'));\n      const tracker = new RemediationTracker(db);\n      let statuses = tracker.getStatus();\n\n      if (args.overdueOnly === true) {\n        statuses = statuses.filter(s => s.isOverdue);\n      }\n\n      if (statuses.length === 0) {\n        return args.overdueOnly === true\n          ? 'No overdue vulnerabilities found.'\n          : 'No open vulnerabilities with SLA tracking data found.';\n      }\n\n      // Sort: overdue first, then by slaStatus, then by severity desc\n      const SLA_ORDER: Record<string, number> = { overdue: 0, warning: 1, no_fix: 2, ok: 3 };\n      statuses.sort((a, b) => {\n        const slaA = SLA_ORDER[a.slaStatus] ?? 3;\n        const slaB = SLA_ORDER[b.slaStatus] ?? 3;\n        if (slaA !== slaB) return slaA - slaB;\n        return (b.severity ?? 0) - (a.severity ?? 0);\n      });\n\n      const overdueCount = statuses.filter(s => s.isOverdue).length;\n      const warningCount = statuses.filter(s => s.slaStatus === 'warning').length;\n\n      const lines: string[] = [\n        `# Remediation SLA (${statuses.length} open${overdueCount > 0 ? `, ${overdueCount} overdue` : ''}${warningCount > 0 ? `, ${warningCount} warning` : ''})`,\n        '',\n      ];\n\n      for (const s of statuses) {\n        const severityLabel = s.severity == null ? 'UNKNOWN'\n          : s.severity >= 9 ? 'CRITICAL'\n          : s.severity >= 7 ? 'HIGH'\n          : s.severity >= 4 ? 'MEDIUM'\n          : 'LOW';\n\n        const slaTag = s.slaStatus === 'overdue' ? '[OVERDUE]'\n          : s.slaStatus === 'warning' ? '[WARNING]'\n          : s.slaStatus === 'no_fix' ? '[NO_FIX]'\n          : '[OK]';\n\n        lines.push(`${slaTag}  ${severityLabel}  ${s.cveId}  ${s.packageName}`);\n        if (s.daysOpen !== null) lines.push(`  Open for ${s.daysOpen} day${s.daysOpen !== 1 ? 's' : ''}`);\n        if (s.daysWithFixAvailable !== null) lines.push(`  Fix available for ${s.daysWithFixAvailable} day${s.daysWithFixAvailable !== 1 ? 's' : ''}`);\n        if (s.slaDeadline !== null) {\n          const deadlineDate = new Date(s.slaDeadline).toISOString().slice(0, 10);\n          lines.push(`  SLA deadline: ${deadlineDate}`);\n        }\n      }\n\n      return truncate(lines.join('\\n'));\n    }\n\n    default:\n      return `Unknown tool: ${toolName}`;\n  }\n}\n"],
+  "mappings": 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   "names": ["lines", "denyCount", "warnCount"]
 }

package/dist/mcp/handlers/wiki.js

@@ -125,10 +125,20 @@ Produce WIKI_DIFF blocks following SCHEMA.md, then call kirograph_wiki_apply_dif
       const db = cg.getDatabase();
       db.applyWikiSchema();
       const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + "/.kirograph", {
+        wikiContradictionMode: config.wikiContradictionMode,
+        wikiContradictionConfidenceThreshold: config.wikiContradictionConfidenceThreshold,
+        jevApiKey: config.jevApiKey,
+        jevBaseUrl: config.jevBaseUrl,
+        jevModel: config.jevModel,
         typedPages: config.wikiTypedPages
       });
       wiki.initialize();
-      const issues = wiki.lint();
+      let issues;
+      try {
+        issues = await wiki.lint();
+      } catch (err) {
+        return `Error: ${err instanceof Error ? err.message : String(err)}`;
+      }
       if (issues.length === 0) return "\u2713 Wiki lint passed \u2014 no issues found.";
       const lines = [`Wiki Lint \u2014 ${issues.length} issue(s)`, ""];
       for (const issue of issues) {

package/dist/mcp/handlers/wiki.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../src/mcp/handlers/wiki.ts"],
-  "sourcesContent": ["import KiroGraph from '../../index';\n\nexport async function handleWiki(toolName: string, args: Record<string, unknown>, cg: KiroGraph): Promise<string> {\n  switch (toolName) {\n    case 'kirograph_wiki_ingest': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        autoResolveConflicts: (config as any).wikiAutoResolveConflicts ?? false,\n      });\n      wiki.initialize();\n\n      const source = args.source as string ?? '';\n      const sourceName = args.sourceName as string ?? 'source';\n      if (!source) return 'source is required';\n\n      if (config.wikiSynthesisMode === 'local') {\n        wiki.queueSource(source, sourceName);\n        const count = wiki.getQueueCount();\n        return `Source \"${sourceName}\" queued for local wiki synthesis (${count} in queue). The agentStop hook will run \"kirograph wiki synthesize\" automatically.`;\n      }\n\n      const prompt = wiki.getIngestPrompt(source, sourceName);\n      return `WIKI_INGEST_PROMPT\\n${prompt}\\n\\nProduce WIKI_DIFF blocks following SCHEMA.md, then call kirograph_wiki_apply_diff with the diff string.`;\n    }\n\n    case 'kirograph_wiki_apply_diff': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        autoResolveConflicts: (config as any).wikiAutoResolveConflicts ?? false,\n      });\n      wiki.initialize();\n\n      const diff = args.diff as string ?? '';\n      if (!diff) return 'diff is required';\n\n      const result = wiki.applyDiff(diff);\n      const lines: string[] = ['\u2713 Wiki diff applied'];\n      if (result.created.length) lines.push(`  Created: ${result.created.join(', ')}`);\n      if (result.updated.length) lines.push(`  Updated: ${result.updated.join(', ')}`);\n      if (result.conflictsResolved.length) lines.push(`  Conflicts auto-resolved: ${result.conflictsResolved.join(', ')}`);\n      if (result.conflictsPending.length) {\n        lines.push(`  \u26A1 Conflicts pending (${result.conflictsPending.length}):`);\n        for (const c of result.conflictsPending) {\n          lines.push(`    ${c.page} \u00A7${c.section}: \"${c.existing}\" vs \"${c.incoming}\" (source: ${c.source})`);\n        }\n      }\n      return lines.join('\\n');\n    }\n\n    case 'kirograph_wiki_search': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const query = args.query as string ?? '';\n      if (!query) return 'query is required';\n      const limit = Math.min(Number(args.limit ?? 5), 20);\n\n      const results = wiki.search(query, limit);\n      if (results.length === 0) return `No wiki pages found for \"${query}\".`;\n\n      const lines = [`Wiki Search: ${query}`, ''];\n      for (const { page, score } of results) {\n        lines.push(`[${page.slug}] ${page.title}  (score: ${score.toFixed(3)})`);\n        // Show first non-heading line as preview\n        const preview = page.content.split('\\n').find(l => l.trim() && !l.startsWith('#'));\n        if (preview) lines.push(`  ${preview.trim().slice(0, 120)}`);\n        lines.push('');\n      }\n      return lines.join('\\n').trim();\n    }\n\n    case 'kirograph_wiki_page': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const slug = args.slug as string ?? '';\n      if (!slug) return 'slug is required';\n\n      const page = wiki.getPage(slug);\n      if (!page) return `Wiki page \"${slug}\" not found. Use kirograph_wiki_list to see available pages.`;\n\n      return page.content;\n    }\n\n    case 'kirograph_wiki_lint': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        typedPages: config.wikiTypedPages,\n      });\n      wiki.initialize();\n\n      const issues = wiki.lint();\n      if (issues.length === 0) return '\u2713 Wiki lint passed \u2014 no issues found.';\n\n      const lines = [`Wiki Lint \u2014 ${issues.length} issue(s)`, ''];\n      for (const issue of issues) {\n        const icon = issue.kind === 'contradiction' ? '\u26A1' : issue.kind === 'orphan' ? '\u25CB' : issue.kind === 'broken_link' ? '\uD83D\uDD17' : issue.kind === 'schema_error' ? '\u2716' : '\u26A0';\n        lines.push(`${icon} [${issue.kind}] ${issue.slug}`);\n        lines.push(`  ${issue.detail}`);\n        lines.push('');\n      }\n      return lines.join('\\n').trim();\n    }\n\n    case 'kirograph_wiki_list': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const pages = wiki.listPages();\n      if (pages.length === 0) return 'Wiki is empty. Use kirograph_wiki_ingest to add pages.';\n\n      const stats = wiki.getStats();\n      const lines = [\n        `Wiki \u2014 ${stats.pageCount} page(s), ${stats.totalSources} total sources`,\n        '',\n      ];\n      for (const page of pages) {\n        const date = new Date(page.updatedAt).toISOString().slice(0, 10);\n        lines.push(`  ${page.slug.padEnd(32)} ${page.title}  (${page.sourceCount} src, ${date})`);\n      }\n      return lines.join('\\n');\n    }\n\n    case 'kirograph_wiki_synthesize': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = args.projectPath as string ?? cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n      if (config.wikiSynthesisMode !== 'local') return 'wikiSynthesisMode is not \"local\". This tool is for local-model synthesis only.';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        autoResolveConflicts: (config as any).wikiAutoResolveConflicts ?? false,\n      });\n      wiki.initialize();\n\n      const queueCount = wiki.getQueueCount();\n      if (queueCount === 0) return 'Wiki queue is empty \u2014 nothing to synthesize.';\n\n      const result = await wiki.synthesize(config.wikiLocalModel, true);\n      const synthLines = [`Wiki synthesis complete \u2014 processed ${result.processed} source(s).`];\n      if (result.created.length) synthLines.push(`Created: ${result.created.join(', ')}`);\n      if (result.updated.length) synthLines.push(`Updated: ${result.updated.join(', ')}`);\n      if (result.errors.length) synthLines.push(`Errors: ${result.errors.join('; ')}`);\n      return synthLines.join('\\n');\n    }\n\n    case 'kirograph_wiki_init': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = args.projectPath as string ?? cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        autoResolveConflicts: (config as any).wikiAutoResolveConflicts ?? false,\n      });\n      wiki.initWiki();\n      return 'Wiki initialized. SCHEMA.md and MANIFEST.md created in .kirograph/wiki/.';\n    }\n\n    case 'kirograph_wiki_reindex': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = args.projectPath as string ?? cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const count = wiki.reindex();\n      return `Reindexed ${count} wiki page(s) from .kirograph/wiki/*.md.`;\n    }\n\n    case 'kirograph_wiki_status': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = args.projectPath as string ?? cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const stats = wiki.getStats();\n      const oldest = stats.oldestPage ? new Date(stats.oldestPage).toISOString().slice(0, 10) : 'n/a';\n      const newest = stats.newestPage ? new Date(stats.newestPage).toISOString().slice(0, 10) : 'n/a';\n      return [\n        'Wiki Status:',\n        `  Pages:         ${stats.pageCount}`,\n        `  Total sources: ${stats.totalSources}`,\n        `  Oldest page:   ${oldest}`,\n        `  Newest page:   ${newest}`,\n        `  Wiki dir:      .kirograph/wiki/`,\n      ].join('\\n');\n    }\n\n    default:\n      return `Unknown tool: ${toolName}`;\n  }\n}\n"],
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+  "sourcesContent": ["import KiroGraph from '../../index';\n\nexport async function handleWiki(toolName: string, args: Record<string, unknown>, cg: KiroGraph): Promise<string> {\n  switch (toolName) {\n    case 'kirograph_wiki_ingest': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        autoResolveConflicts: (config as any).wikiAutoResolveConflicts ?? false,\n      });\n      wiki.initialize();\n\n      const source = args.source as string ?? 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Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        autoResolveConflicts: (config as any).wikiAutoResolveConflicts ?? false,\n      });\n      wiki.initialize();\n\n      const diff = args.diff as string ?? '';\n      if (!diff) return 'diff is required';\n\n      const result = wiki.applyDiff(diff);\n      const lines: string[] = ['\u2713 Wiki diff applied'];\n      if (result.created.length) lines.push(`  Created: ${result.created.join(', ')}`);\n      if (result.updated.length) lines.push(`  Updated: ${result.updated.join(', ')}`);\n      if (result.conflictsResolved.length) lines.push(`  Conflicts auto-resolved: ${result.conflictsResolved.join(', ')}`);\n      if (result.conflictsPending.length) {\n        lines.push(`  \u26A1 Conflicts pending (${result.conflictsPending.length}):`);\n        for (const c of result.conflictsPending) {\n          lines.push(`    ${c.page} \u00A7${c.section}: \"${c.existing}\" vs \"${c.incoming}\" (source: ${c.source})`);\n        }\n      }\n      return lines.join('\\n');\n    }\n\n    case 'kirograph_wiki_search': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const query = args.query as string ?? '';\n      if (!query) return 'query is required';\n      const limit = Math.min(Number(args.limit ?? 5), 20);\n\n      const results = wiki.search(query, limit);\n      if (results.length === 0) return `No wiki pages found for \"${query}\".`;\n\n      const lines = [`Wiki Search: ${query}`, ''];\n      for (const { page, score } of results) {\n        lines.push(`[${page.slug}] ${page.title}  (score: ${score.toFixed(3)})`);\n        // Show first non-heading line as preview\n        const preview = page.content.split('\\n').find(l => l.trim() && !l.startsWith('#'));\n        if (preview) lines.push(`  ${preview.trim().slice(0, 120)}`);\n        lines.push('');\n      }\n      return lines.join('\\n').trim();\n    }\n\n    case 'kirograph_wiki_page': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const slug = args.slug as string ?? '';\n      if (!slug) return 'slug is required';\n\n      const page = wiki.getPage(slug);\n      if (!page) return `Wiki page \"${slug}\" not found. Use kirograph_wiki_list to see available pages.`;\n\n      return page.content;\n    }\n\n    case 'kirograph_wiki_lint': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        wikiContradictionMode: config.wikiContradictionMode,\n        wikiContradictionConfidenceThreshold: config.wikiContradictionConfidenceThreshold,\n        jevApiKey: config.jevApiKey,\n        jevBaseUrl: config.jevBaseUrl,\n        jevModel: config.jevModel,\n        typedPages: config.wikiTypedPages,\n      });\n      wiki.initialize();\n\n      let issues;\n      try {\n        issues = await wiki.lint();\n      } catch (err) {\n        return `Error: ${err instanceof Error ? err.message : String(err)}`;\n      }\n      if (issues.length === 0) return '\u2713 Wiki lint passed \u2014 no issues found.';\n\n      const lines = [`Wiki Lint \u2014 ${issues.length} issue(s)`, ''];\n      for (const issue of issues) {\n        const icon = issue.kind === 'contradiction' ? '\u26A1' : issue.kind === 'orphan' ? '\u25CB' : issue.kind === 'broken_link' ? '\uD83D\uDD17' : issue.kind === 'schema_error' ? '\u2716' : '\u26A0';\n        lines.push(`${icon} [${issue.kind}] ${issue.slug}`);\n        lines.push(`  ${issue.detail}`);\n        lines.push('');\n      }\n      return lines.join('\\n').trim();\n    }\n\n    case 'kirograph_wiki_list': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const pages = wiki.listPages();\n      if (pages.length === 0) return 'Wiki is empty. Use kirograph_wiki_ingest to add pages.';\n\n      const stats = wiki.getStats();\n      const lines = [\n        `Wiki \u2014 ${stats.pageCount} page(s), ${stats.totalSources} total sources`,\n        '',\n      ];\n      for (const page of pages) {\n        const date = new Date(page.updatedAt).toISOString().slice(0, 10);\n        lines.push(`  ${page.slug.padEnd(32)} ${page.title}  (${page.sourceCount} src, ${date})`);\n      }\n      return lines.join('\\n');\n    }\n\n    case 'kirograph_wiki_synthesize': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = args.projectPath as string ?? cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n      if (config.wikiSynthesisMode !== 'local') return 'wikiSynthesisMode is not \"local\". This tool is for local-model synthesis only.';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        autoResolveConflicts: (config as any).wikiAutoResolveConflicts ?? false,\n      });\n      wiki.initialize();\n\n      const queueCount = wiki.getQueueCount();\n      if (queueCount === 0) return 'Wiki queue is empty \u2014 nothing to synthesize.';\n\n      const result = await wiki.synthesize(config.wikiLocalModel, true);\n      const synthLines = [`Wiki synthesis complete \u2014 processed ${result.processed} source(s).`];\n      if (result.created.length) synthLines.push(`Created: ${result.created.join(', ')}`);\n      if (result.updated.length) synthLines.push(`Updated: ${result.updated.join(', ')}`);\n      if (result.errors.length) synthLines.push(`Errors: ${result.errors.join('; ')}`);\n      return synthLines.join('\\n');\n    }\n\n    case 'kirograph_wiki_init': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = args.projectPath as string ?? cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph', {\n        autoResolveConflicts: (config as any).wikiAutoResolveConflicts ?? false,\n      });\n      wiki.initWiki();\n      return 'Wiki initialized. SCHEMA.md and MANIFEST.md created in .kirograph/wiki/.';\n    }\n\n    case 'kirograph_wiki_reindex': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = args.projectPath as string ?? cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const count = wiki.reindex();\n      return `Reindexed ${count} wiki page(s) from .kirograph/wiki/*.md.`;\n    }\n\n    case 'kirograph_wiki_status': {\n      const { loadConfig } = await Promise.resolve().then(() => require('../../config.js'));\n      const projectRoot = args.projectPath as string ?? cg.getProjectRoot();\n      const config = await loadConfig(projectRoot);\n      if (!config.enableWiki) return 'Wiki is not enabled. Set enableWiki: true in .kirograph/config.json';\n\n      const { KiroGraphWiki } = await Promise.resolve().then(() => require('../../wiki/index.js'));\n      const db = cg.getDatabase();\n      db.applyWikiSchema();\n      const wiki = new KiroGraphWiki(db.getRawDb(), projectRoot + '/.kirograph');\n      wiki.initialize();\n\n      const stats = wiki.getStats();\n      const oldest = stats.oldestPage ? new Date(stats.oldestPage).toISOString().slice(0, 10) : 'n/a';\n      const newest = stats.newestPage ? new Date(stats.newestPage).toISOString().slice(0, 10) : 'n/a';\n      return [\n        'Wiki Status:',\n        `  Pages:         ${stats.pageCount}`,\n        `  Total sources: ${stats.totalSources}`,\n        `  Oldest page:   ${oldest}`,\n        `  Newest page:   ${newest}`,\n        `  Wiki dir:      .kirograph/wiki/`,\n      ].join('\\n');\n    }\n\n    default:\n      return `Unknown tool: ${toolName}`;\n  }\n}\n"],
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   "names": []
 }

package/dist/mcp/tools.js

@@ -881,19 +881,19 @@ const tools = [
   },
   {
     name: "kirograph_mem_compare",
-    description: "Establish a typed relation between two observations (supersedes, conflicts_with, compatible, scoped, related, not_conflict). Accepts observation IDs or topic_key values.",
+    description: 'Establish a typed relation between two observations (supersedes, conflicts_with, compatible, scoped, related, not_conflict). Accepts observation IDs or topic_key values. When memoryRelationMode is "jev", omit `relation` to have it classified automatically instead of reasoning it out yourself.',
     inputSchema: {
       type: "object",
       properties: {
         observationA: { type: "string", description: "First observation ID or topic_key" },
         observationB: { type: "string", description: "Second observation ID or topic_key" },
-        relation: { type: "string", enum: ["supersedes", "conflicts_with", "compatible", "scoped", "related", "not_conflict"], description: "Relation type" },
-        confidence: { type: "number", description: "Confidence 0.0\u20131.0 (default: 1.0)" },
+        relation: { type: "string", enum: ["supersedes", "conflicts_with", "compatible", "scoped", "related", "not_conflict"], description: 'Relation type. Required unless memoryRelationMode is "jev", in which case omitting it classifies the relation automatically.' },
+        confidence: { type: "number", description: "Confidence 0.0\u20131.0 (default: 1.0). Ignored when relation is omitted in jev mode \u2014 jev supplies its own calibrated confidence." },
         reason: { type: "string", description: "Explanation of the relation" },
         evidence: { type: "string", description: "Supporting evidence text" },
         projectPath: { type: "string" }
       },
-      required: ["observationA", "observationB", "relation"]
+      required: ["observationA", "observationB"]
     }
   },
   {