@triedotdev/mcp 1.0.138 → 1.0.140

package/dist/{issue-store-BO5OWLJW.js → issue-store-LZWZIGM7.js}

@@ -10,7 +10,7 @@ import {
   resolveGoalViolation,
   searchIssues,
   storeIssues
-} from "./chunk-Z2P4WST6.js";
+} from "./chunk-62POBLFC.js";
 import "./chunk-4MJ52WBH.js";
 import "./chunk-43X6JBEM.js";
 import "./chunk-SH7H3WRU.js";
@@ -29,4 +29,4 @@ export {
   searchIssues,
   storeIssues
 };
-//# sourceMappingURL=issue-store-BO5OWLJW.js.map
+//# sourceMappingURL=issue-store-LZWZIGM7.js.map

package/dist/linear-ingester-JRDQAIAA.js

@@ -0,0 +1,11 @@
+import {
+  LinearIngester
+} from "./chunk-LD7ZEFNY.js";
+import "./chunk-NKHO34UZ.js";
+import "./chunk-SH7H3WRU.js";
+import "./chunk-APMV77PU.js";
+import "./chunk-DGUM43GV.js";
+export {
+  LinearIngester
+};
+//# sourceMappingURL=linear-ingester-JRDQAIAA.js.map

package/dist/linear-ingester-JRDQAIAA.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":[],"sourcesContent":[],"mappings":"","names":[]}

package/dist/{trie-agent-XMSGMD7E.js → trie-agent-M6PHM6UD.js}

@@ -1,21 +1,21 @@
 import {
   TrieAgent,
   getTrieAgent
-} from "./chunk-YOKQ25IW.js";
-import "./chunk-FOCXXIXY.js";
-import "./chunk-67GSG2ST.js";
+} from "./chunk-OQ4A3RDY.js";
+import "./chunk-YEIJW6X6.js";
+import "./chunk-XTTZAQWJ.js";
 import "./chunk-3MUCUZ46.js";
-import "./chunk-6LLH3TBZ.js";
-import "./chunk-Y32FM3MR.js";
+import "./chunk-UOSTOLU7.js";
+import "./chunk-FH335WL5.js";
+import "./chunk-FPEMP54L.js";
 import "./chunk-LT6VUZG2.js";
+import "./chunk-62POBLFC.js";
+import "./chunk-4MJ52WBH.js";
+import "./chunk-43X6JBEM.js";
 import "./chunk-F4NJ4CBP.js";
 import "./chunk-IXO4G4D3.js";
 import "./chunk-6NLHFIYA.js";
 import "./chunk-FG467PDD.js";
-import "./chunk-QSWUPSLK.js";
-import "./chunk-Z2P4WST6.js";
-import "./chunk-4MJ52WBH.js";
-import "./chunk-43X6JBEM.js";
 import "./chunk-SH7H3WRU.js";
 import "./chunk-APMV77PU.js";
 import "./chunk-DGUM43GV.js";
@@ -23,4 +23,4 @@ export {
   TrieAgent,
   getTrieAgent
 };
-//# sourceMappingURL=trie-agent-XMSGMD7E.js.map
+//# sourceMappingURL=trie-agent-M6PHM6UD.js.map

package/dist/trie-agent-M6PHM6UD.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":[],"sourcesContent":[],"mappings":"","names":[]}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@triedotdev/mcp",
-  "version": "1.0.138",
-  "description": "Trainable AI Agent for Maintaining AI-Generated Codebases",
+  "version": "1.0.140",
+  "description": "Trainable AI agent with a cryptographic governance ledger and portable context for AI-generated codebases.",
   "main": "dist/index.js",
   "type": "module",
   "bin": {
@@ -25,17 +25,24 @@
     "prepublishOnly": "npm run build"
   },
   "keywords": [
+    "governance",
+    "ledger",
     "ai",
+    "agent",
+    "mcp",
+    "cursor",
+    "claude",
     "code-review",
     "security",
-    "mcp",
-    "agent",
     "orchestration",
+    "decision-memory",
+    "incident-tracking",
+    "linear",
+    "github",
     "trie",
-    "pdf",
-    "document-to-agent",
-    "custom-agents",
-    "knowledge-base"
+    "custom-agent",
+    "knowledge-base",
+    "blockchain"
   ],
   "author": "Trie Team",
   "license": "MIT",

package/dist/chunk-67GSG2ST.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/agent/hypothesis.ts"],"sourcesContent":["/**\n * Hypothesis System - Self-improving hypothesis generation and validation\n * \n * Features:\n * - Generate hypotheses from patterns\n * - Track evidence for/against hypotheses\n * - Auto-validate/invalidate based on evidence\n * - Adjust confidence over time\n * - Learn from hypothesis outcomes\n */\n\nimport type { Hypothesis } from './project-state.js';\nimport { getProjectState } from './project-state.js';\nimport { getInsightStore, type Insight } from './insight-store.js';\nimport { searchIssues } from '../memory/issue-store.js';\nimport { dirname } from 'path';\n\n// ============================================================================\n// Types\n// ============================================================================\n\n/**\n * Hypothesis template for auto-generation\n */\nexport interface HypothesisTemplate {\n  category: 'timing' | 'pattern' | 'team' | 'code' | 'general';\n  statement: string;\n  testCriteria: string;\n  minConfidence: number;\n  dataRequired: string[];\n}\n\n/**\n * Evidence for a hypothesis\n */\nexport interface HypothesisEvidence {\n  type: 'supporting' | 'contradicting';\n  description: string;\n  weight: number; // 0-1\n  timestamp: string;\n}\n\n/**\n * Hypothesis analysis result\n */\nexport interface HypothesisAnalysis {\n  hypothesis: Hypothesis;\n  recentEvidence: HypothesisEvidence[];\n  confidenceChange: number;\n  statusChange?: 'validated' | 'invalidated';\n  actionRequired: boolean;\n}\n\n// ============================================================================\n// Hypothesis Templates\n// ============================================================================\n\nconst HYPOTHESIS_TEMPLATES: HypothesisTemplate[] = [\n  {\n    category: 'timing',\n    statement: 'Issues spike after weekend deployments',\n    testCriteria: 'Compare Monday issue counts to other days',\n    minConfidence: 0.3,\n    dataRequired: ['issue_timestamps', 'deployment_data'],\n  },\n  {\n    category: 'timing',\n    statement: 'Code quality declines on Fridays',\n    testCriteria: 'Compare Friday issue introduction rate to weekly average',\n    minConfidence: 0.3,\n    dataRequired: ['issue_timestamps'],\n  },\n  {\n    category: 'pattern',\n    statement: 'Auth-related code has the highest incident rate',\n    testCriteria: 'Compare auth/ issue count to other directories',\n    minConfidence: 0.4,\n    dataRequired: ['issue_files'],\n  },\n  {\n    category: 'pattern',\n    statement: 'Security issues cluster in specific directories',\n    testCriteria: 'Check if security issues are concentrated (>50% in <3 dirs)',\n    minConfidence: 0.4,\n    dataRequired: ['issue_files', 'issue_agents'],\n  },\n  {\n    category: 'code',\n    statement: 'Files with multiple authors have more issues',\n    testCriteria: 'Correlate file author count with issue count',\n    minConfidence: 0.4,\n    dataRequired: ['issue_files', 'git_blame'],\n  },\n  {\n    category: 'code',\n    statement: 'Recently modified files are more likely to have issues',\n    testCriteria: 'Compare issue rate for recent vs old files',\n    minConfidence: 0.3,\n    dataRequired: ['issue_timestamps', 'file_modification_times'],\n  },\n  {\n    category: 'pattern',\n    statement: 'Critical issues often come in clusters',\n    testCriteria: 'Check temporal clustering of critical issues',\n    minConfidence: 0.3,\n    dataRequired: ['issue_timestamps', 'issue_severities'],\n  },\n];\n\n// ============================================================================\n// HypothesisEngine Class\n// ============================================================================\n\n/**\n * Engine for generating and validating hypotheses\n */\nexport class HypothesisEngine {\n  private projectPath: string;\n  private projectState;\n  private insightStore;\n  \n  constructor(projectPath: string) {\n    this.projectPath = projectPath;\n    this.projectState = getProjectState(projectPath);\n    this.insightStore = getInsightStore(projectPath);\n  }\n  \n  /**\n   * Create a new hypothesis\n   */\n  async createHypothesis(statement: string, options?: {\n    category?: Hypothesis['category'];\n    testCriteria?: string;\n    initialConfidence?: number;\n    autoGenerated?: boolean;\n  }): Promise<Hypothesis> {\n    const hypothesis: Hypothesis = {\n      id: `hyp-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`,\n      statement,\n      confidence: options?.initialConfidence ?? 0,\n      status: 'proposed',\n      evidence: [],\n      createdAt: new Date().toISOString(),\n      updatedAt: new Date().toISOString(),\n      testCriteria: options?.testCriteria,\n      category: options?.category ?? 'general',\n      autoGenerated: options?.autoGenerated ?? false,\n    };\n    \n    await this.projectState.addHypothesis(hypothesis);\n    \n    return hypothesis;\n  }\n  \n  /**\n   * Auto-generate hypotheses based on detected patterns\n   */\n  async autoGenerateHypotheses(): Promise<Hypothesis[]> {\n    const generated: Hypothesis[] = [];\n    \n    try {\n      // Get existing hypotheses to avoid duplicates\n      await this.projectState.load();\n      const existing = this.projectState.getAllHypotheses();\n      const existingStatements = new Set(existing.map(h => h.statement.toLowerCase()));\n      \n      // Get data for pattern detection\n      const issues = await searchIssues('', {\n        workDir: this.projectPath,\n        limit: 500,\n        includeResolved: true,\n      });\n      \n      if (issues.length < 10) {\n        return generated; // Not enough data\n      }\n      \n      // Check each template for applicability\n      for (const template of HYPOTHESIS_TEMPLATES) {\n        // Skip if already have similar hypothesis\n        if (existingStatements.has(template.statement.toLowerCase())) {\n          continue;\n        }\n        \n        // Check if we have enough evidence to propose this hypothesis\n        const evidence = await this.gatherInitialEvidence(template, issues);\n        \n        if (evidence.length > 0 && evidence[0]!.weight >= template.minConfidence) {\n          const hypothesis = await this.createHypothesis(template.statement, {\n            category: template.category,\n            testCriteria: template.testCriteria,\n            initialConfidence: evidence[0]!.weight,\n            autoGenerated: true,\n          });\n          \n          // Add initial evidence\n          for (const e of evidence) {\n            await this.projectState.addEvidence(hypothesis.id, e);\n          }\n          \n          generated.push(hypothesis);\n          \n          // Limit to 2 new hypotheses per run\n          if (generated.length >= 2) break;\n        }\n      }\n      \n    } catch (error) {\n      console.error('Failed to auto-generate hypotheses:', error);\n    }\n    \n    return generated;\n  }\n  \n  /**\n   * Use Claude AI to generate novel hypotheses from observed patterns\n   * This enables fully agentic hypothesis creation based on actual codebase observations\n   */\n  async generateHypothesesWithAI(context: {\n    recentIssues?: any[];\n    patterns?: string[];\n    observations?: string[];\n  }): Promise<Hypothesis[]> {\n    const { isAIAvailable, runAIAnalysis } = await import('../ai/client.js');\n    \n    if (!isAIAvailable()) {\n      return []; // Fall back to template-based generation\n    }\n    \n    const generated: Hypothesis[] = [];\n    \n    try {\n      // Get existing hypotheses to avoid duplicates\n      await this.projectState.load();\n      const existing = this.projectState.getAllHypotheses();\n      const existingStatements = existing.map(h => h.statement);\n      \n      // Get recent issue data\n      const issues = context.recentIssues || await searchIssues('', {\n        workDir: this.projectPath,\n        limit: 100,\n        includeResolved: true,\n      });\n      \n      if (issues.length < 5) {\n        return generated; // Not enough data for AI\n      }\n      \n      // Build context for Claude\n      const issuesSummary = this.summarizeIssuesForAI(issues);\n      const patternsSummary = context.patterns?.join('\\n') || 'No explicit patterns provided';\n      const observationsSummary = context.observations?.join('\\n') || 'No explicit observations provided';\n      \n      const prompt = `You are an AI agent observing a codebase over time. Based on the patterns below, generate 1-3 testable hypotheses about this codebase's quality patterns.\n\n## Recent Issues Summary\n${issuesSummary}\n\n## Observed Patterns\n${patternsSummary}\n\n## Additional Observations\n${observationsSummary}\n\n## Existing Hypotheses (avoid duplicates)\n${existingStatements.length > 0 ? existingStatements.map(s => `- ${s}`).join('\\n') : 'None yet'}\n\nGenerate hypotheses that are:\n1. Specific and testable (can be validated with data)\n2. Actionable (if validated, can guide improvements)\n3. Novel (not duplicates of existing hypotheses)\n4. Based on real patterns in the data above\n\nReturn ONLY a JSON array of hypotheses. Each hypothesis must have:\n- \"statement\": Clear, concise hypothesis statement\n- \"category\": One of: \"timing\", \"pattern\", \"team\", \"code\", \"general\"\n- \"testCriteria\": How to test this hypothesis\n- \"confidence\": Initial confidence (0-1)\n- \"reasoning\": Why you think this hypothesis is worth testing\n\nExample format:\n[\n  {\n    \"statement\": \"Authentication code changes correlate with security issues\",\n    \"category\": \"pattern\",\n    \"testCriteria\": \"Track auth file changes and subsequent security issue rates\",\n    \"confidence\": 0.6,\n    \"reasoning\": \"65% of security issues occur in files modified in the past week\"\n  }\n]\n\nReturn empty array [] if no novel hypotheses can be generated from the data.`;\n      \n      const result = await runAIAnalysis({\n        systemPrompt: 'You are an expert code quality analyst who identifies patterns and generates testable hypotheses.',\n        userPrompt: prompt,\n        maxTokens: 1024,\n        temperature: 0.7, // Higher temperature for creative hypothesis generation\n      });\n      \n      if (!result.success || !result.content.trim()) {\n        return generated;\n      }\n      \n      // Parse AI response\n      let aiHypotheses: Array<{\n        statement: string;\n        category: Hypothesis['category'];\n        testCriteria: string;\n        confidence: number;\n        reasoning: string;\n      }> = [];\n      \n      try {\n        const cleaned = result.content.replace(/```json?\\n?|\\n?```/g, '').trim();\n        aiHypotheses = JSON.parse(cleaned);\n        if (!Array.isArray(aiHypotheses)) aiHypotheses = [];\n      } catch {\n        return generated; // AI response wasn't valid JSON\n      }\n      \n      // Create hypotheses from AI suggestions\n      for (const aiHypo of aiHypotheses.slice(0, 3)) {\n        // Check for duplicates\n        const isDuplicate = existingStatements.some(existing => \n          existing.toLowerCase().includes(aiHypo.statement.toLowerCase().slice(0, 30))\n        );\n        \n        if (isDuplicate) continue;\n        \n        const hypothesis = await this.createHypothesis(aiHypo.statement, {\n          category: aiHypo.category,\n          testCriteria: aiHypo.testCriteria,\n          initialConfidence: Math.max(0.3, Math.min(0.7, aiHypo.confidence)),\n          autoGenerated: true,\n        });\n        \n        // Add AI reasoning as initial evidence\n        await this.projectState.addEvidence(hypothesis.id, {\n          type: 'supporting',\n          description: `AI observed: ${aiHypo.reasoning}`,\n          weight: aiHypo.confidence,\n        });\n        \n        generated.push(hypothesis);\n      }\n      \n    } catch (error) {\n      console.error('Failed to generate hypotheses with AI:', error);\n    }\n    \n    return generated;\n  }\n  \n  /**\n   * Summarize issues for AI context\n   */\n  private summarizeIssuesForAI(issues: Array<{ issue: any; score: number }>): string {\n    const totalIssues = issues.length;\n    \n    // Severity breakdown\n    const severityCounts: Record<string, number> = {};\n    for (const { issue } of issues) {\n      severityCounts[issue.severity] = (severityCounts[issue.severity] || 0) + 1;\n    }\n    \n    // Agent breakdown\n    const agentCounts: Record<string, number> = {};\n    for (const { issue } of issues) {\n      agentCounts[issue.agent] = (agentCounts[issue.agent] || 0) + 1;\n    }\n    \n    // File/directory patterns\n    const fileCounts: Record<string, number> = {};\n    for (const { issue } of issues) {\n      const dir = dirname(issue.file);\n      fileCounts[dir] = (fileCounts[dir] || 0) + 1;\n    }\n    \n    // Time patterns\n    const dayOfWeekCounts: Record<number, number> = {};\n    for (const { issue } of issues) {\n      const date = new Date(issue.timestamp);\n      const day = date.getDay();\n      dayOfWeekCounts[day] = (dayOfWeekCounts[day] || 0) + 1;\n    }\n    \n    const dayNames = ['Sun', 'Mon', 'Tue', 'Wed', 'Thu', 'Fri', 'Sat'];\n    const dayDistribution = Object.entries(dayOfWeekCounts)\n      .sort(([a], [b]) => Number(a) - Number(b))\n      .map(([day, count]) => `${dayNames[Number(day)]}: ${count}`)\n      .join(', ');\n    \n    const topDirs = Object.entries(fileCounts)\n      .sort(([, a], [, b]) => b - a)\n      .slice(0, 5)\n      .map(([dir, count]) => `${dir}: ${count}`)\n      .join(', ');\n    \n    const topAgents = Object.entries(agentCounts)\n      .sort(([, a], [, b]) => b - a)\n      .slice(0, 5)\n      .map(([agent, count]) => `${agent}: ${count}`)\n      .join(', ');\n    \n    return `Total Issues: ${totalIssues}\nSeverities: ${Object.entries(severityCounts).map(([s, c]) => `${s}=${c}`).join(', ')}\nTop Agents: ${topAgents}\nTop Directories: ${topDirs}\nDay Distribution: ${dayDistribution}`;\n  }\n  \n  /**\n   * Gather initial evidence for a hypothesis template\n   */\n  private async gatherInitialEvidence(\n    template: HypothesisTemplate,\n    issues: Array<{ issue: any; score: number }>\n  ): Promise<HypothesisEvidence[]> {\n    const evidence: HypothesisEvidence[] = [];\n    \n    switch (template.category) {\n      case 'timing':\n        evidence.push(...this.analyzeTimingPatterns(template, issues));\n        break;\n      case 'pattern':\n        evidence.push(...this.analyzeLocationPatterns(template, issues));\n        break;\n      case 'code':\n        evidence.push(...this.analyzeCodePatterns(template, issues));\n        break;\n    }\n    \n    return evidence;\n  }\n  \n  /**\n   * Analyze timing patterns in issues\n   */\n  private analyzeTimingPatterns(\n    template: HypothesisTemplate,\n    issues: Array<{ issue: any; score: number }>\n  ): HypothesisEvidence[] {\n    const evidence: HypothesisEvidence[] = [];\n    \n    // Analyze day-of-week patterns\n    const dayOfWeekCounts: Record<number, number> = {};\n    for (const { issue } of issues) {\n      const date = new Date(issue.timestamp);\n      const day = date.getDay();\n      dayOfWeekCounts[day] = (dayOfWeekCounts[day] || 0) + 1;\n    }\n    \n    // Check for Friday pattern\n    if (template.statement.includes('Friday')) {\n      const fridayCount = dayOfWeekCounts[5] || 0;\n      const avgOtherDays = (Object.values(dayOfWeekCounts).reduce((a, b) => a + b, 0) - fridayCount) / 4;\n      \n      if (fridayCount > avgOtherDays * 1.5) {\n        evidence.push({\n          type: 'supporting',\n          description: `Friday has ${((fridayCount / avgOtherDays - 1) * 100).toFixed(0)}% more issues than average`,\n          weight: Math.min(0.8, 0.3 + (fridayCount / avgOtherDays - 1) * 0.2),\n          timestamp: new Date().toISOString(),\n        });\n      } else {\n        evidence.push({\n          type: 'contradicting',\n          description: 'Friday issue count is not significantly higher',\n          weight: 0.3,\n          timestamp: new Date().toISOString(),\n        });\n      }\n    }\n    \n    // Check for Monday/weekend pattern\n    if (template.statement.includes('weekend') || template.statement.includes('Monday')) {\n      const mondayCount = dayOfWeekCounts[1] || 0;\n      const avgOtherDays = (Object.values(dayOfWeekCounts).reduce((a, b) => a + b, 0) - mondayCount) / 4;\n      \n      if (mondayCount > avgOtherDays * 1.5) {\n        evidence.push({\n          type: 'supporting',\n          description: `Monday has ${((mondayCount / avgOtherDays - 1) * 100).toFixed(0)}% more issues than average`,\n          weight: Math.min(0.8, 0.3 + (mondayCount / avgOtherDays - 1) * 0.2),\n          timestamp: new Date().toISOString(),\n        });\n      }\n    }\n    \n    return evidence;\n  }\n  \n  /**\n   * Analyze location patterns in issues\n   */\n  private analyzeLocationPatterns(\n    template: HypothesisTemplate,\n    issues: Array<{ issue: any; score: number }>\n  ): HypothesisEvidence[] {\n    const evidence: HypothesisEvidence[] = [];\n    \n    // Analyze directory distribution\n    const dirCounts: Record<string, number> = {};\n    for (const { issue } of issues) {\n      const dir = dirname(issue.file);\n      dirCounts[dir] = (dirCounts[dir] || 0) + 1;\n    }\n    \n    const sortedDirs = Object.entries(dirCounts)\n      .sort(([, a], [, b]) => b - a);\n    \n    // Check for auth pattern\n    if (template.statement.includes('Auth')) {\n      const authDirs = sortedDirs.filter(([dir]) => \n        dir.toLowerCase().includes('auth') || \n        dir.toLowerCase().includes('login') ||\n        dir.toLowerCase().includes('session')\n      );\n      \n      const authCount = authDirs.reduce((sum, [, count]) => sum + count, 0);\n      const percentage = (authCount / issues.length) * 100;\n      \n      if (percentage >= 20) {\n        evidence.push({\n          type: 'supporting',\n          description: `Auth-related code has ${percentage.toFixed(0)}% of issues`,\n          weight: Math.min(0.85, 0.4 + percentage / 100),\n          timestamp: new Date().toISOString(),\n        });\n      }\n    }\n    \n    // Check for clustering pattern\n    if (template.statement.includes('cluster')) {\n      const topThreeDirs = sortedDirs.slice(0, 3);\n      const topThreeCount = topThreeDirs.reduce((sum, [, count]) => sum + count, 0);\n      const percentage = (topThreeCount / issues.length) * 100;\n      \n      if (percentage >= 50) {\n        evidence.push({\n          type: 'supporting',\n          description: `Top 3 directories have ${percentage.toFixed(0)}% of issues`,\n          weight: Math.min(0.8, 0.3 + percentage / 100),\n          timestamp: new Date().toISOString(),\n        });\n      }\n    }\n    \n    return evidence;\n  }\n  \n  /**\n   * Analyze code patterns\n   */\n  private analyzeCodePatterns(\n    template: HypothesisTemplate,\n    issues: Array<{ issue: any; score: number }>\n  ): HypothesisEvidence[] {\n    const evidence: HypothesisEvidence[] = [];\n    \n    // Analyze temporal clustering (critical issues in bursts)\n    if (template.statement.includes('cluster')) {\n      const criticalIssues = issues.filter(r => r.issue.severity === 'critical');\n      \n      if (criticalIssues.length >= 3) {\n        // Check if critical issues are clustered in time\n        const timestamps = criticalIssues\n          .map(r => new Date(r.issue.timestamp).getTime())\n          .sort((a, b) => a - b);\n        \n        let clusteredCount = 0;\n        for (let i = 1; i < timestamps.length; i++) {\n          // If within 24 hours of previous\n          if (timestamps[i]! - timestamps[i - 1]! < 24 * 60 * 60 * 1000) {\n            clusteredCount++;\n          }\n        }\n        \n        const clusterRatio = clusteredCount / (timestamps.length - 1);\n        \n        if (clusterRatio >= 0.5) {\n          evidence.push({\n            type: 'supporting',\n            description: `${(clusterRatio * 100).toFixed(0)}% of critical issues occur within 24h of another`,\n            weight: Math.min(0.75, 0.3 + clusterRatio * 0.4),\n            timestamp: new Date().toISOString(),\n          });\n        }\n      }\n    }\n    \n    return evidence;\n  }\n  \n  /**\n   * Update confidence scores based on new data\n   */\n  async updateConfidenceFromOutcomes(): Promise<HypothesisAnalysis[]> {\n    const analyses: HypothesisAnalysis[] = [];\n    \n    try {\n      await this.projectState.load();\n      const activeHypotheses = this.projectState.getActiveHypotheses();\n      \n      for (const hypothesis of activeHypotheses) {\n        const analysis = await this.analyzeHypothesis(hypothesis);\n        analyses.push(analysis);\n        \n        // Create insight if hypothesis was validated or invalidated\n        if (analysis.statusChange && this.insightStore.canCreateInsight('hypothesis-update')) {\n          const insight = this.createHypothesisInsight(analysis);\n          await this.insightStore.addInsight(insight);\n          await this.insightStore.markInsightCreated('hypothesis-update');\n        }\n      }\n      \n      // Update hypothesis accuracy metric\n      await this.projectState.updateHypothesisAccuracy();\n      \n    } catch (error) {\n      console.error('Failed to update hypothesis confidence:', error);\n    }\n    \n    return analyses;\n  }\n  \n  /**\n   * Analyze a single hypothesis\n   */\n  private async analyzeHypothesis(hypothesis: Hypothesis): Promise<HypothesisAnalysis> {\n    // Get recent issues for new evidence\n    const issues = await searchIssues('', {\n      workDir: this.projectPath,\n      limit: 100,\n      includeResolved: false,\n    });\n    \n    // Find the matching template\n    const template = HYPOTHESIS_TEMPLATES.find(t => \n      t.statement.toLowerCase() === hypothesis.statement.toLowerCase()\n    );\n    \n    const recentEvidence: HypothesisEvidence[] = [];\n    \n    if (template) {\n      recentEvidence.push(...await this.gatherInitialEvidence(template, issues));\n    } else {\n      // For user-created hypotheses, use semantic evidence gathering\n      recentEvidence.push(...this.gatherSemanticEvidence(hypothesis, issues));\n    }\n    \n    // Calculate confidence change\n    const oldConfidence = hypothesis.confidence;\n    let newConfidence = oldConfidence;\n    \n    for (const evidence of recentEvidence) {\n      if (evidence.type === 'supporting') {\n        newConfidence = Math.min(1, newConfidence + evidence.weight * 0.1);\n      } else {\n        newConfidence = Math.max(0, newConfidence - evidence.weight * 0.1);\n      }\n    }\n    \n    // Determine status change\n    let statusChange: 'validated' | 'invalidated' | undefined;\n    \n    if (newConfidence >= 0.8 && hypothesis.evidence.length >= 3) {\n      statusChange = 'validated';\n      await this.projectState.updateHypothesis(hypothesis.id, {\n        status: 'validated',\n        confidence: newConfidence,\n        validatedAt: new Date().toISOString(),\n      });\n    } else if (newConfidence <= 0.2 && hypothesis.evidence.length >= 3) {\n      statusChange = 'invalidated';\n      await this.projectState.updateHypothesis(hypothesis.id, {\n        status: 'invalidated',\n        confidence: newConfidence,\n      });\n    } else {\n      // Just update confidence\n      await this.projectState.updateHypothesis(hypothesis.id, {\n        confidence: newConfidence,\n      });\n    }\n    \n    // Add new evidence\n    for (const evidence of recentEvidence) {\n      await this.projectState.addEvidence(hypothesis.id, evidence);\n    }\n    \n    const analysis: HypothesisAnalysis = {\n      hypothesis: { ...hypothesis, confidence: newConfidence },\n      recentEvidence,\n      confidenceChange: newConfidence - oldConfidence,\n      actionRequired: statusChange !== undefined,\n    };\n    \n    if (statusChange) {\n      analysis.statusChange = statusChange;\n    }\n    \n    return analysis;\n  }\n  \n  /**\n   * Gather evidence for user-created hypotheses using semantic matching\n   * \n   * This enables agentic tracking for natural language hypotheses like:\n   * - \"Mondays have more bugs than Fridays\"\n   * - \"Code reviews reduce bug rate\"\n   * - \"Security issues cluster in auth code\"\n   */\n  private gatherSemanticEvidence(\n    hypothesis: Hypothesis,\n    issues: Array<{ issue: any; score: number }>\n  ): HypothesisEvidence[] {\n    const evidence: HypothesisEvidence[] = [];\n    const stmt = hypothesis.statement.toLowerCase();\n    \n    // Time-based hypotheses (days of week patterns)\n    if (stmt.includes('monday') || stmt.includes('friday') || stmt.includes('weekend') ||\n        stmt.includes('morning') || stmt.includes('afternoon')) {\n      const dayNames = ['sunday', 'monday', 'tuesday', 'wednesday', 'thursday', 'friday', 'saturday'];\n      const dayOfWeekCounts: Record<number, number> = { 0: 0, 1: 0, 2: 0, 3: 0, 4: 0, 5: 0, 6: 0 };\n      \n      for (const { issue } of issues) {\n        const date = new Date(issue.timestamp);\n        const day = date.getDay();\n        dayOfWeekCounts[day] = (dayOfWeekCounts[day] || 0) + 1;\n      }\n      \n      const totalIssues = Object.values(dayOfWeekCounts).reduce((a, b) => a + b, 0);\n      const avgPerDay = totalIssues / 7;\n      \n      // Check each day mentioned\n      for (let dayIdx = 0; dayIdx < 7; dayIdx++) {\n        const dayName = dayNames[dayIdx]!;\n        if (stmt.includes(dayName)) {\n          const dayCount = dayOfWeekCounts[dayIdx] || 0;\n          \n          if (stmt.includes('more') || stmt.includes('higher') || stmt.includes('spike')) {\n            // Testing if this day has MORE issues\n            if (dayCount > avgPerDay * 1.3) {\n              evidence.push({\n                type: 'supporting',\n                description: `${dayName.charAt(0).toUpperCase() + dayName.slice(1)} has ${dayCount} issues (${((dayCount/avgPerDay - 1) * 100).toFixed(0)}% above average)`,\n                weight: Math.min(0.7, 0.3 + (dayCount / avgPerDay - 1) * 0.3),\n                timestamp: new Date().toISOString(),\n              });\n            } else {\n              evidence.push({\n                type: 'contradicting',\n                description: `${dayName.charAt(0).toUpperCase() + dayName.slice(1)} has average or below average issue count`,\n                weight: 0.3,\n                timestamp: new Date().toISOString(),\n              });\n            }\n          } else if (stmt.includes('fewer') || stmt.includes('less') || stmt.includes('reduce')) {\n            // Testing if this day has FEWER issues\n            if (dayCount < avgPerDay * 0.7) {\n              evidence.push({\n                type: 'supporting',\n                description: `${dayName.charAt(0).toUpperCase() + dayName.slice(1)} has ${dayCount} issues (${((1 - dayCount/avgPerDay) * 100).toFixed(0)}% below average)`,\n                weight: Math.min(0.7, 0.3 + (1 - dayCount / avgPerDay) * 0.3),\n                timestamp: new Date().toISOString(),\n              });\n            }\n          }\n        }\n      }\n    }\n    \n    // Code review hypotheses\n    if (stmt.includes('review') || stmt.includes('pr') || stmt.includes('pull request')) {\n      // Look for patterns in reviewed vs unreviewed code (approximated by commit patterns)\n      const recentIssues = issues.slice(0, 30); // Most recent\n      const olderIssues = issues.slice(30); // Older\n      \n      if (recentIssues.length >= 10 && olderIssues.length >= 10) {\n        const recentRate = recentIssues.length;\n        const olderRate = olderIssues.length;\n        \n        if (stmt.includes('reduce') || stmt.includes('fewer') || stmt.includes('less')) {\n          if (recentRate < olderRate) {\n            evidence.push({\n              type: 'supporting',\n              description: `Recent period has ${((1 - recentRate/olderRate) * 100).toFixed(0)}% fewer issues`,\n              weight: Math.min(0.6, 0.3 + (1 - recentRate/olderRate) * 0.3),\n              timestamp: new Date().toISOString(),\n            });\n          } else {\n            evidence.push({\n              type: 'contradicting',\n              description: `Issue rate has not decreased recently`,\n              weight: 0.2,\n              timestamp: new Date().toISOString(),\n            });\n          }\n        }\n      }\n    }\n    \n    // Directory/location clustering hypotheses\n    if (stmt.includes('cluster') || stmt.includes('concentrate') || stmt.includes('auth') ||\n        stmt.includes('specific') || stmt.includes('certain files')) {\n      const dirCounts: Record<string, number> = {};\n      for (const { issue } of issues) {\n        const dir = dirname(issue.file);\n        dirCounts[dir] = (dirCounts[dir] || 0) + 1;\n      }\n      \n      const sortedDirs = Object.entries(dirCounts).sort(([, a], [, b]) => b - a);\n      const topThreeCount = sortedDirs.slice(0, 3).reduce((sum, [, count]) => sum + count, 0);\n      const totalCount = issues.length;\n      const concentration = topThreeCount / totalCount;\n      \n      if (concentration >= 0.5) {\n        evidence.push({\n          type: 'supporting',\n          description: `Top 3 directories have ${(concentration * 100).toFixed(0)}% of issues (concentrated)`,\n          weight: Math.min(0.7, 0.3 + concentration * 0.4),\n          timestamp: new Date().toISOString(),\n        });\n      } else {\n        evidence.push({\n          type: 'contradicting',\n          description: `Issues are distributed across many directories`,\n          weight: 0.3,\n          timestamp: new Date().toISOString(),\n        });\n      }\n    }\n    \n    // Severity trend hypotheses\n    if (stmt.includes('critical') || stmt.includes('security') || stmt.includes('severity')) {\n      const criticalCount = issues.filter(r => r.issue.severity === 'critical').length;\n      const seriousCount = issues.filter(r => r.issue.severity === 'serious').length;\n      const highSeverityRatio = (criticalCount + seriousCount) / issues.length;\n      \n      if (stmt.includes('increase') || stmt.includes('more') || stmt.includes('rise')) {\n        if (highSeverityRatio > 0.3) {\n          evidence.push({\n            type: 'supporting',\n            description: `${(highSeverityRatio * 100).toFixed(0)}% of issues are high severity`,\n            weight: Math.min(0.7, 0.3 + highSeverityRatio),\n            timestamp: new Date().toISOString(),\n          });\n        }\n      } else if (stmt.includes('decrease') || stmt.includes('fewer') || stmt.includes('reduce')) {\n        if (highSeverityRatio < 0.2) {\n          evidence.push({\n            type: 'supporting',\n            description: `Only ${(highSeverityRatio * 100).toFixed(0)}% of issues are high severity`,\n            weight: 0.5,\n            timestamp: new Date().toISOString(),\n          });\n        }\n      }\n    }\n    \n    // Agent/skill specific hypotheses\n    const agents = ['security', 'performance', 'accessibility', 'test', 'typecheck', 'bug-finding'];\n    for (const agent of agents) {\n      if (stmt.includes(agent) || stmt.includes(agent.replace('-', ' '))) {\n        const agentIssues = issues.filter(r => r.issue.agent === agent);\n        const agentRatio = agentIssues.length / issues.length;\n        \n        if (stmt.includes('most') || stmt.includes('majority') || stmt.includes('main')) {\n          if (agentRatio > 0.4) {\n            evidence.push({\n              type: 'supporting',\n              description: `${agent} accounts for ${(agentRatio * 100).toFixed(0)}% of issues`,\n              weight: Math.min(0.7, 0.3 + agentRatio),\n              timestamp: new Date().toISOString(),\n            });\n          } else {\n            evidence.push({\n              type: 'contradicting',\n              description: `${agent} only accounts for ${(agentRatio * 100).toFixed(0)}% of issues`,\n              weight: 0.3,\n              timestamp: new Date().toISOString(),\n            });\n          }\n        }\n      }\n    }\n    \n    return evidence;\n  }\n  \n  /**\n   * Create an insight for hypothesis status change\n   */\n  private createHypothesisInsight(analysis: HypothesisAnalysis): Insight {\n    const isValidated = analysis.statusChange === 'validated';\n    \n    return {\n      id: `insight-hyp-${analysis.hypothesis.id}`,\n      type: isValidated ? 'celebration' : 'observation',\n      message: isValidated\n        ? `Hypothesis confirmed: \"${analysis.hypothesis.statement}\"`\n        : `Hypothesis disproven: \"${analysis.hypothesis.statement}\"`,\n      context: `Confidence: ${(analysis.hypothesis.confidence * 100).toFixed(0)}%. ${analysis.recentEvidence.length} evidence points analyzed.`,\n      relatedIssues: [],\n      priority: 5,\n      timestamp: Date.now(),\n      dismissed: false,\n      category: 'pattern',\n      details: {\n        examples: analysis.recentEvidence.map(e => `${e.type}: ${e.description}`),\n      },\n    };\n  }\n  \n  /**\n   * Get hypothesis by ID\n   */\n  async getHypothesis(hypothesisId: string): Promise<Hypothesis | undefined> {\n    await this.projectState.load();\n    return this.projectState.getHypothesis(hypothesisId);\n  }\n  \n  /**\n   * Get all hypotheses\n   */\n  async getAllHypotheses(): Promise<Hypothesis[]> {\n    await this.projectState.load();\n    return this.projectState.getAllHypotheses();\n  }\n  \n  /**\n   * Get validated hypotheses\n   */\n  async getValidatedHypotheses(): Promise<Hypothesis[]> {\n    await this.projectState.load();\n    return this.projectState.getValidatedHypotheses();\n  }\n  \n  /**\n   * Get hypothesis accuracy stats\n   */\n  getAccuracy(): number {\n    const metrics = this.projectState.getMetrics();\n    return metrics.hypothesisAccuracy;\n  }\n}\n\n// ============================================================================\n// Singleton Management\n// ============================================================================\n\nconst hypothesisEngines: Map<string, HypothesisEngine> = new Map();\n\n/**\n * Get the HypothesisEngine for a project (singleton per project)\n */\nexport function getHypothesisEngine(projectPath: string): HypothesisEngine {\n  let engine = hypothesisEngines.get(projectPath);\n  if (!engine) {\n    engine = new HypothesisEngine(projectPath);\n    hypothesisEngines.set(projectPath, engine);\n  }\n  return engine;\n}\n\n/**\n * Clear all HypothesisEngine instances (for testing)\n */\nexport function clearHypothesisEngines(): void {\n  hypothesisEngines.clear();\n}\n\n/**\n * Gather evidence for a specific hypothesis (manual check from UI)\n */\nexport async function gatherEvidenceForHypothesis(\n  hypothesisId: string,\n  projectPath: string\n): Promise<Array<{ supports: boolean; description: string; weight: number }>> {\n  const engine = getHypothesisEngine(projectPath);\n  const projectState = getProjectState(projectPath);\n  await projectState.load();\n  \n  const hypothesis = projectState.getAllHypotheses().find(h => h.id === hypothesisId);\n  if (!hypothesis) {\n    throw new Error(`Hypothesis ${hypothesisId} not found`);\n  }\n  \n  // Get the analysis - access private method via bracket notation\n  const analysis = await (engine as any).analyzeHypothesis(hypothesis);\n  \n  // Convert evidence to simpler format\n  return analysis.recentEvidence.map((e: HypothesisEvidence) => ({\n    supports: e.type === 'supporting',\n    description: e.description,\n    weight: e.weight,\n  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package/dist/chunk-D3AS5LY7.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/utils/project-info.ts","../src/utils/context-state.ts","../src/config/loader.ts","../src/config/validation.ts","../src/bootstrap/stack-detector.ts","../src/bootstrap/files.ts","../src/ingest/linear-ingester.ts"],"sourcesContent":["/**\n * Project Info Manager\n * \n * Manages the .trie/PROJECT.md file that stores user-defined project context.\n * Unlike AGENTS.md (auto-generated), PROJECT.md is fully user-controlled.\n */\n\nimport { readFile, writeFile, mkdir } from 'fs/promises';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\nimport { getWorkingDirectory, getTrieDirectory } from './workspace.js';\n\nconst PROJECT_MD_PATH = 'PROJECT.md';\n\n/**\n * Default PROJECT.md template\n */\nexport function getProjectTemplate(): string {\n  return `# Project Information\n\n> This file stores important project context for AI assistants.\n> Edit freely - this file is yours, not auto-generated.\n> Available via MCP resource: \\`trie://project\\`\n\n---\n\n## Project Overview\n\n<!-- Describe your project's purpose and goals -->\n\n[Add project description here]\n\n---\n\n## Technology Stack\n\n<!-- List frameworks, languages, databases, cloud services, etc. -->\n\n- **Language:** \n- **Framework:** \n- **Database:** \n- **Hosting:** \n\n---\n\n## Architecture\n\n<!-- Key patterns, architectural decisions, and system design -->\n\n[Describe your architecture here]\n\n---\n\n## Coding Conventions\n\n<!-- Style guidelines, naming conventions, patterns to follow -->\n\n- \n- \n- \n\n---\n\n## Environment\n\n<!-- URLs, API endpoints, deployment info -->\n\n| Environment | URL | Notes |\n|-------------|-----|-------|\n| Development | | |\n| Staging | | |\n| Production | | |\n\n---\n\n## Team\n\n<!-- Ownership, contacts, responsibilities -->\n\n- **Owner:** \n- **Team:** \n\n---\n\n## Compliance\n\n<!-- HIPAA, SOC2, GDPR, PCI-DSS requirements if applicable -->\n\n- [ ] GDPR\n- [ ] SOC2\n- [ ] HIPAA\n- [ ] PCI-DSS\n\n---\n\n## AI Instructions\n\n<!-- Special instructions for AI assistants working on this project -->\n\nWhen working on this project, AI assistants should:\n\n1. \n2. \n3. \n\n---\n\n*This file is read by Trie agents and exposed via \\`trie://project\\` MCP resource.*\n*Edit this file to provide context to Claude Code, Cursor, GitHub Actions, and other AI tools.*\n`;\n}\n\n/**\n * Check if PROJECT.md exists\n */\nexport function projectInfoExists(workDir?: string): boolean {\n  const dir = workDir || getWorkingDirectory(undefined, true);\n  const projectPath = join(getTrieDirectory(dir), PROJECT_MD_PATH);\n  return existsSync(projectPath);\n}\n\n/**\n * Load PROJECT.md content\n */\nexport async function loadProjectInfo(workDir?: string): Promise<string | null> {\n  const dir = workDir || getWorkingDirectory(undefined, true);\n  const projectPath = join(getTrieDirectory(dir), PROJECT_MD_PATH);\n  \n  try {\n    if (!existsSync(projectPath)) {\n      return null;\n    }\n    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} from '../types/index.js';\nimport type { SkillRecord } from '../types/external-skill.js';\nimport { loadProjectInfo, projectInfoExists } from './project-info.js';\nimport { storeIssues, autoResolveIssues, getIssueHash } from '../memory/issue-store.js';\nimport { recordToGlobalMemory, updateGlobalMemoryMd } from '../memory/global-memory.js';\nimport { atomicWriteJSON, atomicWriteFile } from './atomic-write.js';\n\nexport interface ScanSummary {\n  timestamp: string;\n  agents: string[];\n  filesScanned: number;\n  issues: {\n    critical: number;\n    serious: number;\n    moderate: number;\n    low: number;\n    total: number;\n  };\n  duration: number;\n  hotFiles: Array<{ file: string; issueCount: number }>;\n}\n\nexport interface ContextState {\n  lastScan: ScanSummary | null;\n  activePriorities: string[];\n  contextSignals: Record<string, boolean>;\n  agentStatus: Record<string, {\n    lastRun: string | null;\n    issuesFound: number;\n    skillsApplied?: string[];\n  }>;\n  scanHistory: ScanSummary[];\n  customAgents: string[];\n  skills: Record<string, SkillRecord>;\n  environment?: string;\n}\n\nconst AGENTS_MD_PATH = 'AGENTS.md';\nconst STATE_JSON_PATH = 'state.json';\n\n/**\n * Load current context state\n */\nexport async function loadContextState(): Promise<ContextState> {\n  const workDir = getWorkingDirectory(undefined, true);\n  const statePath = join(getTrieDirectory(workDir), STATE_JSON_PATH);\n  const defaults = getDefaultState();\n  \n  try {\n    if (existsSync(statePath)) {\n      const content = await readFile(statePath, 'utf-8');\n      const loaded = JSON.parse(content);\n      const { healthScore: _dropped, ...loadedRest } = loaded;\n      // Merge with defaults to ensure new fields exist (omit legacy healthScore)\n      return {\n        ...defaults,\n        ...loadedRest,\n        skills: loaded.skills || defaults.skills,\n      };\n    }\n  } catch {\n    // Return default state\n  }\n  \n  return defaults;\n}\n\n/**\n * Save context state using atomic write\n */\nexport async function saveContextState(state: ContextState): Promise<void> {\n  const workDir = getWorkingDirectory(undefined, true);\n  const trieDir = getTrieDirectory(workDir);\n  const statePath = join(trieDir, STATE_JSON_PATH);\n  \n  // Ensure directory exists\n  await mkdir(trieDir, { recursive: true });\n  \n  // Use atomic write to prevent corruption\n  await atomicWriteJSON(statePath, state);\n}\n\n/**\n * Update context state after a scan\n */\nexport async function updateContextAfterScan(\n  results: AgentResult[],\n  filesScanned: number,\n  contextSignals: Record<string, boolean>,\n  duration: number,\n  scannedFiles?: string[]\n): Promise<void> {\n  const state = await loadContextState();\n  const workDir = getWorkingDirectory(undefined, true);\n  const now = new Date().toISOString();\n  \n  // Calculate issue counts\n  const allIssues = results.flatMap(r => r.issues);\n  const issueCounts = {\n    critical: allIssues.filter(i => i.severity === 'critical').length,\n    serious: allIssues.filter(i => i.severity === 'serious').length,\n    moderate: allIssues.filter(i => i.severity === 'moderate').length,\n    low: allIssues.filter(i => i.severity === 'low').length,\n    total: allIssues.length,\n  };\n  \n  // Find hot files\n  const fileIssueMap = new Map<string, number>();\n  for (const issue of allIssues) {\n    const count = fileIssueMap.get(issue.file) || 0;\n    fileIssueMap.set(issue.file, count + 1);\n  }\n  const hotFiles = Array.from(fileIssueMap.entries())\n    .sort((a, b) => b[1] - a[1])\n    .slice(0, 10)\n    .map(([file, issueCount]) => ({ file, issueCount }));\n  \n  // Create scan summary\n  const scanSummary: ScanSummary = {\n    timestamp: now,\n    agents: results.map(r => r.agent),\n    filesScanned,\n    issues: issueCounts,\n    duration,\n    hotFiles,\n  };\n  \n  // Update agent status\n  for (const result of results) {\n    state.agentStatus[result.agent] = {\n      lastRun: now,\n      issuesFound: result.issues.length,\n    };\n  }\n  \n  // Update priorities based on issues\n  state.activePriorities = generatePriorities(issueCounts, contextSignals);\n  \n  // Update context signals\n  state.contextSignals = { ...state.contextSignals, ...contextSignals };\n  \n  // Update scan history (keep last 20)\n  state.scanHistory = [scanSummary, ...state.scanHistory.slice(0, 19)];\n  state.lastScan = scanSummary;\n  \n  // Save state\n  await saveContextState(state);\n  \n  // Update AGENTS.md\n  await updateAgentsMd(state);\n  \n  // Store issues to memory\n  const projectName = basename(workDir);\n  if (allIssues.length > 0) {\n    try {\n      await storeIssues(allIssues, projectName, workDir);\n      await recordToGlobalMemory(allIssues, projectName, workDir);\n      await updateGlobalMemoryMd();\n    } catch {\n      // Memory storage is non-critical, don't fail the scan\n    }\n  }\n  \n  // Auto-resolve issues that are no longer detected in scanned files\n  if (scannedFiles && scannedFiles.length > 0) {\n    try {\n      // Build set of hashes from current scan\n      const currentHashes = new Set(allIssues.map(issue => getIssueHash(issue)));\n      const { resolved } = await autoResolveIssues(currentHashes, scannedFiles, workDir);\n      if (resolved > 0) {\n        // Log auto-resolution in non-interactive mode\n        const { isInteractiveMode } = await import('./progress.js');\n        if (!isInteractiveMode()) {\n          console.error(`   ✓ Auto-resolved ${resolved} issue${resolved > 1 ? 's' : ''} no longer detected`);\n        }\n      }\n    } catch {\n      // Auto-resolution is non-critical\n    }\n  }\n}\n\n/**\n * Update the AGENTS.md file with current state\n */\nasync function updateAgentsMd(state: ContextState): Promise<void> {\n  const workDir = getWorkingDirectory(undefined, true);\n  const mdPath = join(getTrieDirectory(workDir), AGENTS_MD_PATH);\n  \n  let content: string;\n  try {\n    content = await readFile(mdPath, 'utf-8');\n  } catch {\n    // Use template if file doesn't exist\n    content = getAgentsMdTemplate();\n  }\n  \n  // Update sections\n  content = updateSection(content, 'Project State', generateProjectStateTable(state));\n  content = updateSection(content, 'Active Priorities', generatePrioritiesList(state));\n  content = updateSection(content, 'Agent Status', generateAgentStatusTable(state));\n  content = updateSection(content, 'Recent Scan History', generateScanHistoryTable(state));\n  content = updateSection(content, 'Context Signals Detected', generateContextSignals(state));\n  content = updateSection(content, 'Risk Assessment', generateRiskAssessment(state));\n  content = updateSection(content, 'Hot Files', generateHotFilesSection(state));\n  \n  // Update last updated timestamp\n  content = content.replace(\n    /Last updated:.*$/m,\n    `Last updated: ${new Date().toISOString()}`\n  );\n  \n  // Use atomic write to prevent corruption\n  await atomicWriteFile(mdPath, content);\n}\n\n/**\n * Update a specific section in the markdown\n */\nfunction updateSection(content: string, sectionName: string, newContent: string): string {\n  // Look for the section header and replace content until the next section\n  const sectionRegex = new RegExp(\n    `(### ${sectionName}[\\\\s\\\\S]*?)(?=###|---|\\n## |$)`,\n    'g'\n  );\n  \n  const replacement = `### ${sectionName}\\n${newContent}\\n\\n`;\n  \n  if (content.match(sectionRegex)) {\n    return content.replace(sectionRegex, replacement);\n  }\n  \n  // Section doesn't exist, don't add it\n  return content;\n}\n\n/**\n * Generate the project state table\n */\nfunction generateProjectStateTable(state: ContextState): string {\n  const lastScan = state.lastScan;\n  const lastScanDate = lastScan ? new Date(lastScan.timestamp).toLocaleString() : 'Never';\n  const criticalCount = lastScan?.issues.critical ?? 0;\n  const totalTasks = lastScan?.issues.total ?? 0;\n  \n  return `| Metric | Value | Updated |\n|--------|-------|---------|\n| Last Scan | ${lastScanDate} | ${lastScan ? 'Auto' : '-'} |\n| Critical Issues | ${criticalCount} | ${lastScan ? 'Auto' : '-'} |\n| Open Tasks | ${totalTasks} | ${lastScan ? 'Auto' : '-'} |`;\n}\n\n/**\n * Generate priorities list\n */\nfunction generatePrioritiesList(state: ContextState): string {\n  if (state.activePriorities.length === 0) {\n    return '_No active priorities. Run a scan to identify issues._';\n  }\n  \n  return state.activePriorities\n    .map((p, i) => `${i + 1}. ${p}`)\n    .join('\\n');\n}\n\n/**\n * Generate priorities based on scan results\n */\nfunction generatePriorities(\n  issues: { critical: number; serious: number; moderate: number; low: number },\n  contextSignals: Record<string, boolean>\n): string[] {\n  const priorities: string[] = [];\n  \n  if (issues.critical > 0) {\n    priorities.push(`Fix ${issues.critical} critical security issue${issues.critical > 1 ? 's' : ''} immediately`);\n  }\n  \n  if (issues.serious > 0) {\n    priorities.push(`Address ${issues.serious} serious issue${issues.serious > 1 ? 's' : ''} before deployment`);\n  }\n  \n  if (contextSignals.touchesAuth && issues.critical === 0) {\n    priorities.push('Auth code reviewed - continue monitoring');\n  }\n  \n  if (contextSignals.touchesPayments) {\n    priorities.push('💳 Payment code detected - ensure PCI compliance');\n  }\n  \n  if (issues.moderate > 5) {\n    priorities.push(`Schedule time to address ${issues.moderate} moderate issues`);\n  }\n  \n  if (priorities.length === 0) {\n    priorities.push('No critical issues - focus on feature development');\n  }\n  \n  return priorities.slice(0, 5);\n}\n\n/**\n * Generate agent status table\n */\nfunction generateAgentStatusTable(state: ContextState): string {\n  const builtInAgents = [\n    'security', 'legal', 'accessibility', 'bugs',\n    'design', 'architecture', 'performance', 'devops', 'soc2',\n    'e2e', 'typecheck', 'visual-qa', 'data-flow'\n  ];\n  \n  let table = `| Agent | Status | Last Run | Issues Found |\n|-------|--------|----------|--------------|`;\n  \n  for (const agent of builtInAgents) {\n    const status = state.agentStatus[agent];\n    const lastRun = status?.lastRun \n      ? new Date(status.lastRun).toLocaleDateString()\n      : 'Never';\n    const issues = status?.issuesFound ?? '-';\n    const statusEmoji = status ? '✅' : '⏸️';\n    \n    table += `\\n| ${agent} | ${statusEmoji} Ready | ${lastRun} | ${issues} |`;\n  }\n  \n  return table;\n}\n\n/**\n * Generate scan history table\n */\nfunction generateScanHistoryTable(state: ContextState): string {\n  if (state.scanHistory.length === 0) {\n    return `| Date | Agents | Files | Issues | Duration |\n|------|--------|-------|--------|----------|\n| - | - | - | - | - |`;\n  }\n  \n  let table = `| Date | Agents | Files | Issues | Duration |\n|------|--------|-------|--------|----------|`;\n  \n  for (const scan of state.scanHistory.slice(0, 10)) {\n    const date = new Date(scan.timestamp).toLocaleDateString();\n    const agents = scan.agents.slice(0, 3).join(', ') + (scan.agents.length > 3 ? '...' : '');\n    const duration = `${(scan.duration / 1000).toFixed(1)}s`;\n    \n    table += `\\n| ${date} | ${agents} | ${scan.filesScanned} | ${scan.issues.total} | ${duration} |`;\n  }\n  \n  return table;\n}\n\n/**\n * Generate context signals section\n */\nfunction generateContextSignals(state: ContextState): string {\n  const signals = [\n    'touchesAuth',\n    'touchesPayments', \n    'touchesUserData',\n    'touchesAPI',\n    'touchesDatabase',\n    'touchesCrypto'\n  ];\n  \n  return signals\n    .map(s => {\n      const value = state.contextSignals[s];\n      const emoji = value === true ? '✅' : value === false ? '❌' : '❓';\n      return `- \\`${s}\\`: ${emoji} ${value === undefined ? 'Unknown' : value ? 'Yes' : 'No'}`;\n    })\n    .join('\\n');\n}\n\n/**\n * Generate risk assessment section\n */\nfunction generateRiskAssessment(state: ContextState): string {\n  if (state.lastScan === null) {\n    return `- Overall Risk: Unknown\n- Confidence: 0%`;\n  }\n\n  const { critical, serious, total } = state.lastScan.issues;\n  let riskLevel: string;\n  let confidence: number;\n\n  if (critical > 0) {\n    riskLevel = '🔴 Critical';\n    confidence = 90;\n  } else if (serious > 2 || total > 20) {\n    riskLevel = '🟠 High';\n    confidence = 80;\n  } else if (serious > 0 || total > 10) {\n    riskLevel = '🟡 Medium';\n    confidence = 85;\n  } else {\n    riskLevel = '🟢 Low';\n    confidence = 95;\n  }\n\n  return `- Overall Risk: ${riskLevel}\n- Confidence: ${confidence}%`;\n}\n\n/**\n * Generate hot files section\n */\nfunction generateHotFilesSection(state: ContextState): string {\n  if (!state.lastScan || state.lastScan.hotFiles.length === 0) {\n    return '_Run a scan to identify hot files._';\n  }\n  \n  return state.lastScan.hotFiles\n    .map(f => `- \\`${f.file}\\` - ${f.issueCount} issue${f.issueCount > 1 ? 's' : ''}`)\n    .join('\\n');\n}\n\n/**\n * Get default state\n */\nfunction getDefaultState(): ContextState {\n  return {\n    lastScan: null,\n    activePriorities: [\n      'Initial setup required - run first scan with `trie scan`',\n      'Configure agents in `.trie/config.json`',\n      'Set up CI/CD integration'\n    ],\n    contextSignals: {},\n    agentStatus: {},\n    scanHistory: [],\n    customAgents: [],\n    skills: {},\n    environment: detectEnvironment(),\n  };\n}\n\n/**\n * Detect the current execution environment\n */\nexport function detectEnvironment(): string {\n  if (process.env.GITHUB_ACTIONS) return 'github-actions';\n  if (process.env.GITLAB_CI) return 'gitlab-ci';\n  if (process.env.CI) return 'ci';\n  const parent = process.env._ || '';\n  if (parent.includes('cursor')) return 'cursor';\n  if (parent.includes('claude')) return 'claude-code';\n  return 'cli';\n}\n\n/**\n * Record skill installation in context state\n */\nexport async function recordSkillInstalled(params: {\n  name: string;\n  source: string;\n}): Promise<void> {\n  const state = await loadContextState();\n  state.skills[params.name] = {\n    source: params.source,\n    installedAt: new Date().toISOString(),\n    timesApplied: 0,\n    appliedBy: [],\n  };\n  await saveContextState(state);\n}\n\n/**\n * Record skill usage by an agent\n */\nexport async function recordSkillUsage(params: {\n  skillNames: string[];\n  agentName: string;\n}): Promise<void> {\n  const state = await loadContextState();\n  const now = new Date().toISOString();\n  \n  for (const skillName of params.skillNames) {\n    const skillRecord = state.skills[skillName];\n    if (skillRecord) {\n      skillRecord.timesApplied++;\n      skillRecord.lastApplied = now;\n      if (!skillRecord.appliedBy.includes(params.agentName)) {\n        skillRecord.appliedBy.push(params.agentName);\n      }\n    }\n  }\n  \n  const agentStatus = state.agentStatus[params.agentName];\n  if (agentStatus) {\n    agentStatus.skillsApplied = params.skillNames;\n  }\n  \n  await saveContextState(state);\n}\n\n/**\n * Get the AGENTS.md template\n */\nfunction getAgentsMdTemplate(): string {\n  return `# Trie Agent Context\n\n> **Auto-generated file** - Updated automatically when agents run.\n> Last updated: Never (initial state)\n\nThis file provides prioritized context for all AI coding assistants working with this codebase.\nAgents should read this file first and update it after completing scans.\n\n---\n\n## Quick Context (Read First)\n\n### Project State\n| Metric | Value | Updated |\n|--------|-------|---------|\n| Last Scan | Never | - |\n| Critical Issues | 0 | - |\n| Open Tasks | 0 | - |\n| Health Score | Unknown | - |\n\n### Active Priorities\n1. Initial setup required - run first scan with \\`trie scan\\`\n2. Configure agents in \\`.trie/config.json\\`\n3. Set up CI/CD integration\n\n### Hot Files\n_Run a scan to identify hot files._\n\n---\n\n## Agent Status\n\n### Agent Status\n| Agent | Status | Last Run | Issues Found |\n|-------|--------|----------|--------------|\n| security | Ready | Never | - |\n| bugs | Ready | Never | - |\n\n### Recent Scan History\n| Date | Agents | Files | Issues | Duration |\n|------|--------|-------|--------|----------|\n| - | - | - | - | - |\n\n---\n\n## Context Analysis\n\n### Context Signals Detected\n- \\`touchesAuth\\`: Unknown\n- \\`touchesPayments\\`: Unknown\n- \\`touchesUserData\\`: Unknown\n- \\`touchesAPI\\`: Unknown\n- \\`touchesDatabase\\`: Unknown\n- \\`touchesCrypto\\`: Unknown\n\n### Risk Assessment\n- Overall Risk: Unknown\n- Confidence: 0%\n\n---\n\n*This file is maintained by Trie agents. Manual edits will be preserved in non-auto sections.*\n`;\n}\n\n/**\n * Add custom skill to context state\n */\nexport async function addCustomAgentToContext(agentName: string): Promise<void> {\n  const state = await loadContextState();\n  \n  if (!state.customAgents.includes(agentName)) {\n    state.customAgents.push(agentName);\n    await saveContextState(state);\n  }\n}\n\n/**\n * Get context state for AI assistants (formatted summary)\n */\nexport async function getContextForAI(): Promise<string> {\n  const state = await loadContextState();\n  const workDir = getWorkingDirectory(undefined, true);\n  \n  const lines: string[] = [];\n  \n  // Include PROJECT.md content first (user-defined context takes priority)\n  if (projectInfoExists(workDir)) {\n    const projectInfo = await loadProjectInfo(workDir);\n    if (projectInfo) {\n      lines.push(projectInfo);\n      lines.push('');\n      lines.push('---');\n      lines.push('');\n    }\n  }\n  \n  // Add Trie scan context\n  lines.push(\n    '## Trie Scan Context',\n    '',\n    `**Last Scan:** ${state.lastScan ? new Date(state.lastScan.timestamp).toLocaleString() : 'Never'}`,\n    '',\n    '**Active Priorities:**',\n    ...state.activePriorities.map(p => `- ${p}`),\n    ''\n  );\n  \n  if (state.lastScan) {\n    lines.push(\n      '**Recent Issues:**',\n      `- Critical: ${state.lastScan.issues.critical}`,\n      `- Serious: ${state.lastScan.issues.serious}`,\n      `- Moderate: ${state.lastScan.issues.moderate}`,\n      `- Low: ${state.lastScan.issues.low}`,\n      ''\n    );\n    \n    if (state.lastScan.hotFiles.length > 0) {\n      lines.push(\n        '**Hot Files (most issues):**',\n        ...state.lastScan.hotFiles.slice(0, 5).map(f => `- ${f.file}: ${f.issueCount} issues`),\n        ''\n      );\n    }\n  }\n  \n  return lines.join('\\n');\n}\n","import { readFile, writeFile, mkdir } from 'fs/promises';\nimport { existsSync } from 'fs';\nimport { join, dirname } from 'path';\nimport { ConfigValidator, DEFAULT_CONFIG, type TrieConfig } from './validation.js';\nimport { getWorkingDirectory, getTrieDirectory } from '../utils/workspace.js';\nimport { isInteractiveMode } from '../utils/progress.js';\n\nexport async function loadConfig(): Promise<TrieConfig> {\n  const validator = new ConfigValidator();\n  const configPath = join(getTrieDirectory(getWorkingDirectory(undefined, true)), 'config.json');\n\n  try {\n    // Look for config in .trie/config.json\n    if (!existsSync(configPath)) {\n      return DEFAULT_CONFIG;\n    }\n\n    const configFile = await readFile(configPath, 'utf-8');\n    const userConfig = JSON.parse(configFile) as Record<string, unknown>;\n\n    // Deep merge with defaults\n    const merged = mergeConfig(DEFAULT_CONFIG, userConfig);\n\n    // Validate merged config\n    const result = validator.validateConfig(merged);\n    if (!result.success) {\n      // Suppress console output in interactive mode (TUI handles display)\n      if (!isInteractiveMode()) {\n        console.error('Configuration validation failed:');\n        for (const error of result.errors) {\n          console.error(`  - ${error}`);\n        }\n      }\n      return DEFAULT_CONFIG;\n    }\n\n    // Environment validation warnings (skip in interactive mode)\n    if (!isInteractiveMode()) {\n      const envValidation = validator.validateEnvironment();\n      for (const warning of envValidation.warnings) {\n        console.warn(warning);\n      }\n      for (const error of envValidation.errors) {\n        console.error(error);\n      }\n    }\n\n    return result.data;\n  } catch (error) {\n    // If no config found, return defaults (suppress in interactive mode)\n    if (!isInteractiveMode()) {\n      console.error('Failed to load config, using defaults:', error);\n    }\n    return DEFAULT_CONFIG;\n  }\n}\n\nexport async function saveConfig(config: TrieConfig): Promise<void> {\n  const configPath = join(getTrieDirectory(getWorkingDirectory(undefined, true)), 'config.json');\n  const dir = dirname(configPath);\n\n  if (!existsSync(dir)) {\n    await mkdir(dir, { recursive: true });\n  }\n\n  await writeFile(configPath, JSON.stringify(config, null, 2), 'utf-8');\n}\n\nfunction mergeConfig<T extends Record<string, unknown>>(defaults: T, user: Record<string, unknown>): T {\n  if (typeof user !== 'object' || user === null || Array.isArray(user)) {\n    return { ...defaults };\n  }\n\n  const result = { ...defaults } as T;\n\n  for (const [key, value] of Object.entries(user)) {\n    const defaultValue = defaults[key as keyof T];\n    if (typeof value === 'object' && value !== null && !Array.isArray(value) && typeof defaultValue === 'object' && defaultValue !== null) {\n      result[key as keyof T] = mergeConfig(defaultValue as Record<string, unknown>, value as Record<string, unknown>) as T[keyof T];\n    } else {\n      result[key as keyof T] = value as T[keyof T];\n    }\n  }\n\n  return result;\n}","import { z } from 'zod';\nimport { existsSync, readFileSync, mkdirSync } from 'fs';\nimport { resolve, join } from 'path';\nimport { getWorkingDirectory, getTrieDirectory } from '../utils/workspace.js';\n\n// API key validation patterns\nconst API_KEY_PATTERNS = {\n  anthropic: /^sk-ant-api\\d{2}-[\\w-]{95}$/,\n  openai: /^sk-[\\w]{48}$/,\n  github: /^ghp_[\\w]{36}$/,\n  vercel: /^[\\w]{24}$/,\n  linear: /^lin_api_[\\w]{40,60}$/,\n} as const;\n\n// Configuration schemas\nconst ApiKeysSchema = z.object({\n  anthropic: z.string().regex(API_KEY_PATTERNS.anthropic, 'Invalid Anthropic API key format').optional(),\n  openai: z.string().regex(API_KEY_PATTERNS.openai, 'Invalid OpenAI API key format').optional(),\n  github: z.string().regex(API_KEY_PATTERNS.github, 'Invalid GitHub token format').optional(),\n  vercel: z.string().regex(API_KEY_PATTERNS.vercel, 'Invalid Vercel token format').optional(),\n  linear: z.string().optional(), // Linear keys can vary, so we'll be flexible but allow storage\n});\n\nconst AgentConfigSchema = z.object({\n  enabled: z.array(z.string()).optional().default([]),\n  disabled: z.array(z.string()).optional().default([]),\n  parallel: z.boolean().optional().default(true),\n  maxConcurrency: z.number().int().min(1).max(20).optional().default(4),\n  timeout: z.number().int().min(1000).max(300000).optional().default(120000), // 2 minutes\n  cache: z.boolean().optional().default(true),\n});\n\nconst ComplianceSchema = z.object({\n  standards: z.array(z.enum(['SOC2', 'GDPR', 'HIPAA', 'CCPA', 'PCI-DSS'])).optional().default(['SOC2']),\n  enforceCompliance: z.boolean().optional().default(false),\n  reportFormat: z.enum(['json', 'sarif', 'csv', 'html']).optional().default('json'),\n});\n\nconst OutputSchema = z.object({\n  format: z.enum(['console', 'json', 'sarif', 'junit']).optional().default('console'),\n  level: z.enum(['critical', 'serious', 'moderate', 'low', 'all']).optional().default('all'),\n  interactive: z.boolean().optional().default(false),\n  streaming: z.boolean().optional().default(true),\n  colors: z.boolean().optional().default(true),\n});\n\nconst PathsSchema = z.object({\n  include: z.array(z.string()).optional().default([]),\n  exclude: z.array(z.string()).optional().default(['node_modules', 'dist', 'build', '.git']),\n  configDir: z.string().optional().default('.trie'),\n  outputDir: z.string().optional().default('trie-reports'),\n});\n\nconst IntegrationsSchema = z.object({\n  github: z.object({\n    enabled: z.boolean().optional().default(false),\n    token: z.string().optional(),\n    webhook: z.string().url().optional(),\n  }).optional(),\n  slack: z.object({\n    enabled: z.boolean().optional().default(false),\n    webhook: z.string().url().optional(),\n    channel: z.string().optional(),\n  }).optional(),\n  jira: z.object({\n    enabled: z.boolean().optional().default(false),\n    url: z.string().url().optional(),\n    token: z.string().optional(),\n    project: z.string().optional(),\n  }).optional(),\n});\n\n// User identity for attribution tracking\nconst UserSchema = z.object({\n  name: z.string().min(1).optional(),\n  email: z.string().email().optional(),\n  role: z.enum([\n    'developer',\n    'designer', \n    'qa',\n    'devops',\n    'security',\n    'architect',\n    'manager',\n    'contributor'\n  ]).optional().default('developer'),\n  github: z.string().optional(),  // GitHub username\n  url: z.string().url().optional(), // Personal/portfolio URL\n});\n\nexport const TrieConfigSchema = z.object({\n  version: z.string().optional().default('1.0.0'),\n  apiKeys: ApiKeysSchema.optional(),\n  agents: AgentConfigSchema.optional(),\n  compliance: ComplianceSchema.optional(),\n  output: OutputSchema.optional(),\n  paths: PathsSchema.optional(),\n  integrations: IntegrationsSchema.optional(),\n  user: UserSchema.optional(),  // User identity for attribution\n});\n\nexport type TrieConfig = z.infer<typeof TrieConfigSchema>;\nexport type ApiKeys = z.infer<typeof ApiKeysSchema>;\nexport type AgentConfig = z.infer<typeof AgentConfigSchema>;\n\n/**\n * Configuration validator with detailed error reporting\n */\nexport class ConfigValidator {\n  /**\n   * Validate configuration object\n   */\n  validateConfig(config: unknown): { success: true; data: TrieConfig } | { success: false; errors: string[] } {\n    try {\n      const validated = TrieConfigSchema.parse(config);\n\n      // Additional business logic validation\n      const businessErrors = this.validateBusinessLogic(validated);\n      if (businessErrors.length > 0) {\n        return { success: false, errors: businessErrors };\n      }\n\n      return { success: true, data: validated };\n    } catch (error) {\n      if (error instanceof z.ZodError) {\n        const errors = error.errors.map(err =>\n          `${err.path.join('.')}: ${err.message}`\n        );\n        return { success: false, errors };\n      }\n\n      return {\n        success: false,\n        errors: [`Configuration validation failed: ${error instanceof Error ? error.message : 'Unknown error'}`]\n      };\n    }\n  }\n\n  /**\n   * Validate environment variables for API keys\n   */\n  validateEnvironment(): { valid: boolean; warnings: string[]; errors: string[] } {\n    const warnings: string[] = [];\n    const errors: string[] = [];\n\n    // Check for potentially exposed secrets\n    const exposedPatterns = [\n      'NEXT_PUBLIC_ANTHROPIC',\n      'REACT_APP_ANTHROPIC',\n      'VITE_ANTHROPIC',\n      'PUBLIC_ANTHROPIC'\n    ];\n\n    for (const pattern of exposedPatterns) {\n      const envVars = Object.keys(process.env).filter(key => key.includes(pattern));\n      for (const envVar of envVars) {\n        errors.push(`[!] Security risk: API key in client-side environment variable: ${envVar}`);\n      }\n    }\n\n    // Check API key format if present (check env var first, then config)\n    let anthropicKey = process.env.ANTHROPIC_API_KEY;\n    \n    // Also check config file if available (for validation purposes)\n    // Note: This is a read-only check for validation, actual usage goes through isAIAvailable()\n    if (!anthropicKey) {\n      try {\n        const configPath = join(getTrieDirectory(getWorkingDirectory(undefined, true)), 'config.json');\n        if (existsSync(configPath)) {\n          const config = JSON.parse(readFileSync(configPath, 'utf-8'));\n          anthropicKey = config.apiKeys?.anthropic;\n        }\n      } catch {\n        // Config file check failed, continue with env var only\n      }\n    }\n    \n    if (anthropicKey && !API_KEY_PATTERNS.anthropic.test(anthropicKey)) {\n      errors.push('ANTHROPIC_API_KEY does not match expected format');\n    }\n\n    // Warnings for missing optional keys\n    if (!anthropicKey) {\n      warnings.push('ANTHROPIC_API_KEY not set - AI features will be disabled. Set in environment, .trie/config.json, or .env file');\n    }\n\n    if (!process.env.GITHUB_TOKEN && process.env.CI) {\n      warnings.push('GITHUB_TOKEN not set - GitHub integration disabled');\n    }\n\n    return {\n      valid: errors.length === 0,\n      warnings,\n      errors\n    };\n  }\n\n  /**\n   * Validate file paths in configuration\n   */\n  validatePaths(paths: z.infer<typeof PathsSchema>): { valid: boolean; errors: string[] } {\n    const errors: string[] = [];\n\n    if (paths?.include) {\n      for (const path of paths.include) {\n        const resolvedPath = resolve(path);\n        if (!existsSync(resolvedPath)) {\n          errors.push(`Include path does not exist: ${path}`);\n        }\n      }\n    }\n\n    if (paths?.configDir) {\n      const configPath = resolve(paths.configDir);\n      if (!existsSync(configPath)) {\n        try {\n          // Try to create the directory\n          mkdirSync(configPath, { recursive: true });\n        } catch {\n          errors.push(`Cannot create config directory: ${paths.configDir}`);\n        }\n      }\n    }\n\n    return {\n      valid: errors.length === 0,\n      errors\n    };\n  }\n\n  /**\n   * Validate integration configurations\n   */\n  validateIntegrations(integrations: z.infer<typeof IntegrationsSchema>): { valid: boolean; errors: string[] } {\n    const errors: string[] = [];\n\n    // GitHub integration\n    if (integrations?.github?.enabled) {\n      if (!integrations.github.token) {\n        errors.push('GitHub integration enabled but no token provided');\n      }\n    }\n\n    // Slack integration\n    if (integrations?.slack?.enabled) {\n      if (!integrations.slack.webhook) {\n        errors.push('Slack integration enabled but no webhook URL provided');\n      }\n    }\n\n    // JIRA integration\n    if (integrations?.jira?.enabled) {\n      if (!integrations.jira.url || !integrations.jira.token || !integrations.jira.project) {\n        errors.push('JIRA integration enabled but missing required fields (url, token, project)');\n      }\n    }\n\n    return {\n      valid: errors.length === 0,\n      errors\n    };\n  }\n\n  /**\n   * Business logic validation\n   */\n  private validateBusinessLogic(config: TrieConfig): string[] {\n    const errors: string[] = [];\n\n    // Agent configuration validation\n    if (config.agents?.enabled && config.agents?.disabled) {\n      const overlap = config.agents.enabled.filter(agent =>\n        config.agents?.disabled?.includes(agent)\n      );\n      if (overlap.length > 0) {\n        errors.push(`Agents cannot be both enabled and disabled: ${overlap.join(', ')}`);\n      }\n    }\n\n    // Concurrency validation\n    if (config.agents?.maxConcurrency && config.agents.maxConcurrency > 10) {\n      errors.push('maxConcurrency should not exceed 10 for optimal performance');\n    }\n\n    // Compliance standards validation\n    if (config.compliance?.standards) {\n      const invalidStandards = config.compliance.standards.filter(standard =>\n        !['SOC2', 'GDPR', 'HIPAA', 'CCPA', 'PCI-DSS'].includes(standard)\n      );\n      if (invalidStandards.length > 0) {\n        errors.push(`Invalid compliance standards: ${invalidStandards.join(', ')}`);\n      }\n    }\n\n    // Path validation\n    if (config.paths) {\n      const pathValidation = this.validatePaths(config.paths);\n      errors.push(...pathValidation.errors);\n    }\n\n    // Integration validation\n    if (config.integrations) {\n      const integrationValidation = this.validateIntegrations(config.integrations);\n      errors.push(...integrationValidation.errors);\n    }\n\n    return errors;\n  }\n\n  /**\n   * Generate configuration template\n   */\n  generateTemplate(): TrieConfig {\n    return {\n      version: '1.0.0',\n      agents: {\n        enabled: ['security', 'bugs', 'types'],\n        disabled: [],\n        parallel: true,\n        maxConcurrency: 4,\n        timeout: 120000,\n        cache: true\n      },\n      compliance: {\n        standards: ['SOC2'],\n        enforceCompliance: false,\n        reportFormat: 'json'\n      },\n      output: {\n        format: 'console',\n        level: 'all',\n        interactive: false,\n        streaming: true,\n        colors: true\n      },\n      paths: {\n        include: [],\n        exclude: ['node_modules', 'dist', 'build', '.git'],\n        configDir: '.trie',\n        outputDir: 'trie-reports'\n      }\n    };\n  }\n\n  /**\n   * Validate and provide suggestions for improvement\n   */\n  analyze(config: TrieConfig): {\n    score: number;\n    suggestions: string[];\n    securityIssues: string[];\n    optimizations: string[];\n  } {\n    const suggestions: string[] = [];\n    const securityIssues: string[] = [];\n    const optimizations: string[] = [];\n    let score = 100;\n\n    // Check for AI enhancement (check config, env var, and .env files)\n    let hasApiKey = Boolean(config.apiKeys?.anthropic || process.env.ANTHROPIC_API_KEY);\n    if (!hasApiKey) {\n      // Check .env files as well\n      try {\n        const workDir = getWorkingDirectory(undefined, true);\n        const envFiles = ['.env', '.env.local', '.env.production'];\n        for (const envFile of envFiles) {\n          const envPath = join(workDir, envFile);\n          if (existsSync(envPath)) {\n            const envContent = readFileSync(envPath, 'utf-8');\n            if (envContent.includes('ANTHROPIC_API_KEY=')) {\n              hasApiKey = true;\n              break;\n            }\n          }\n        }\n      } catch {\n        // .env check failed, continue\n      }\n    }\n    \n    if (!hasApiKey) {\n      suggestions.push('Add ANTHROPIC_API_KEY to enable AI-powered analysis for better issue detection. Set in environment, .trie/config.json, or .env file');\n      score -= 10;\n    }\n\n    // Check parallel execution\n    if (config.agents?.parallel === false) {\n      optimizations.push('Enable parallel agent execution for 3-5x faster scans');\n      score -= 15;\n    }\n\n    // Check caching\n    if (config.agents?.cache === false) {\n      optimizations.push('Enable result caching to speed up repeated scans');\n      score -= 10;\n    }\n\n    // Check compliance standards\n    if (!config.compliance?.standards || config.compliance.standards.length === 0) {\n      suggestions.push('Configure compliance standards (SOC2, GDPR, etc.) for regulatory requirements');\n      score -= 5;\n    }\n\n    // Check integrations for team collaboration\n    const hasIntegrations = config.integrations && (\n      config.integrations.github?.enabled ||\n      config.integrations.slack?.enabled ||\n      config.integrations.jira?.enabled\n    );\n    if (!hasIntegrations) {\n      suggestions.push('Consider enabling GitHub/Slack/JIRA integrations for better team collaboration');\n      score -= 5;\n    }\n\n    // Security checks\n    if (config.apiKeys) {\n      securityIssues.push('API keys in config file - consider using environment variables instead');\n      score -= 20;\n    }\n\n    return {\n      score: Math.max(0, score),\n      suggestions,\n      securityIssues,\n      optimizations\n    };\n  }\n}\n\n/**\n * Default configuration with security best practices\n */\nexport const DEFAULT_CONFIG: TrieConfig = {\n  version: '1.0.0',\n  agents: {\n    enabled: [],\n    disabled: [],\n    parallel: true,\n    maxConcurrency: 4,\n    timeout: 120000,\n    cache: true,\n  },\n  compliance: {\n    standards: ['SOC2'],\n    enforceCompliance: false,\n    reportFormat: 'json',\n  },\n  output: {\n    format: 'console',\n    level: 'all',\n    interactive: false,\n    streaming: true,\n    colors: true,\n  },\n  paths: {\n    include: [],\n    exclude: ['node_modules', 'dist', 'build', '.git', '.next', '.nuxt', 'coverage'],\n    configDir: '.trie',\n    outputDir: 'trie-reports',\n  },\n};\n\n/**\n * Validate startup configuration\n */\nexport function validateStartupConfig(): {\n  valid: boolean;\n  config: TrieConfig;\n  warnings: string[];\n  errors: string[];\n} {\n  const validator = new ConfigValidator();\n\n  // Validate environment\n  const envValidation = validator.validateEnvironment();\n\n  // Use default config as base\n  const configResult = validator.validateConfig(DEFAULT_CONFIG);\n\n  if (!configResult.success) {\n    return {\n      valid: false,\n      config: DEFAULT_CONFIG,\n      warnings: envValidation.warnings,\n      errors: [...envValidation.errors, ...configResult.errors]\n    };\n  }\n\n  return {\n    valid: envValidation.valid,\n    config: configResult.data,\n    warnings: envValidation.warnings,\n    errors: envValidation.errors\n  };\n}","/**\n * Stack Detector\n * \n * Detects project technology stack from config files.\n * Used by bootstrap system to suggest skills and agents.\n * \n * Skills data sourced from:\n * - https://skills.sh (leaderboard)\n * - https://github.com/anthropics/skills\n * - Partner repositories (Expo, Stripe, Supabase, etc.)\n */\n\nimport { readFile } from 'fs/promises';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\n\nexport interface DetectedStack {\n  framework?: string;\n  language?: string;\n  database?: string;\n  auth?: string;\n  packageManager?: string;\n  suggestedSkills: string[];\n  suggestedAgents: string[];\n  dependencies: Set<string>;\n}\n\n/**\n * Comprehensive dependency-to-skill mappings\n * Format: dependency name -> array of skill identifiers\n */\nconst SKILL_MAPPINGS: Record<string, string[]> = {\n  // Frontend Frameworks - React/Next.js\n  'next': [\n    'vercel-labs/agent-skills vercel-react-best-practices',\n    'vercel-labs/agent-skills web-design-guidelines',\n    'anthropics/skills frontend-design',\n    'wshobson/agents nextjs-app-router-patterns',\n  ],\n  'react': [\n    'vercel-labs/agent-skills vercel-react-best-practices',\n    'anthropics/skills frontend-design',\n    'wshobson/agents react-state-management',\n  ],\n\n  // Vue/Nuxt Ecosystem\n  'vue': [\n    'hyf0/vue-skills vue-best-practices',\n    'hyf0/vue-skills pinia-best-practices',\n    'hyf0/vue-skills vueuse-best-practices',\n    'onmax/nuxt-skills vue',\n  ],\n  'nuxt': [\n    'onmax/nuxt-skills nuxt',\n    'onmax/nuxt-skills nuxt-ui',\n    'onmax/nuxt-skills nuxt-content',\n    'onmax/nuxt-skills nuxt-modules',\n    'onmax/nuxt-skills nuxt-better-auth',\n    'onmax/nuxt-skills nuxthub',\n  ],\n  'pinia': [\n    'hyf0/vue-skills pinia-best-practices',\n  ],\n  '@vueuse/core': [\n    'hyf0/vue-skills vueuse-best-practices',\n    'onmax/nuxt-skills vueuse',\n  ],\n\n  // Mobile - Expo\n  'expo': [\n    'expo/skills building-native-ui',\n    'expo/skills upgrading-expo',\n    'expo/skills native-data-fetching',\n    'expo/skills expo-dev-client',\n    'expo/skills expo-deployment',\n    'expo/skills expo-api-routes',\n    'expo/skills expo-tailwind-setup',\n    'expo/skills expo-cicd-workflows',\n    'expo/skills use-dom',\n  ],\n\n  // Mobile - React Native\n  'react-native': [\n    'callstackincubator/agent-skills react-native-best-practices',\n    'wshobson/agents react-native-architecture',\n  ],\n\n  // Backend Frameworks\n  '@nestjs/core': [\n    'kadajett/agent-nestjs-skills nestjs-best-practices',\n  ],\n  'nestjs': [\n    'kadajett/agent-nestjs-skills nestjs-best-practices',\n  ],\n  'elysia': [\n    'elysiajs/skills elysiajs',\n  ],\n  'hono': [\n    'elysiajs/skills elysiajs',\n  ],\n\n  // Database/BaaS\n  '@supabase/supabase-js': [\n    'supabase/agent-skills supabase-postgres-best-practices',\n  ],\n  'convex': [\n    'waynesutton/convexskills convex-best-practices',\n  ],\n  'pg': [\n    'wshobson/agents postgresql-table-design',\n  ],\n  'postgres': [\n    'wshobson/agents postgresql-table-design',\n  ],\n\n  // Auth\n  'better-auth': [\n    'better-auth/skills better-auth-best-practices',\n    'better-auth/skills create-auth-skill',\n  ],\n\n  // Payments\n  'stripe': [\n    'stripe/ai stripe-best-practices',\n  ],\n  '@stripe/stripe-js': [\n    'stripe/ai stripe-best-practices',\n  ],\n\n  // Media/Graphics\n  'remotion': [\n    'remotion-dev/skills remotion-best-practices',\n  ],\n  'three': [\n    'cloudai-x/threejs-skills threejs-fundamentals',\n    'cloudai-x/threejs-skills threejs-animation',\n    'cloudai-x/threejs-skills threejs-materials',\n    'cloudai-x/threejs-skills threejs-shaders',\n    'cloudai-x/threejs-skills threejs-lighting',\n    'cloudai-x/threejs-skills threejs-geometry',\n    'cloudai-x/threejs-skills threejs-textures',\n    'cloudai-x/threejs-skills threejs-loaders',\n    'cloudai-x/threejs-skills threejs-interaction',\n    'cloudai-x/threejs-skills threejs-postprocessing',\n  ],\n\n  // UI Libraries\n  'tailwindcss': [\n    'wshobson/agents tailwind-design-system',\n    'jezweb/claude-skills tailwind-v4-shadcn',\n    'wshobson/agents responsive-design',\n  ],\n  '@shadcn/ui': [\n    'giuseppe-trisciuoglio/developer-kit shadcn-ui',\n  ],\n  'shadcn': [\n    'giuseppe-trisciuoglio/developer-kit shadcn-ui',\n  ],\n  '@radix-ui/react-slot': [\n    'onmax/nuxt-skills reka-ui',\n  ],\n\n  // State Management\n  '@tanstack/react-query': [\n    'jezweb/claude-skills tanstack-query',\n  ],\n\n  // Testing\n  'playwright': [\n    'anthropics/skills webapp-testing',\n    'wshobson/agents e2e-testing-patterns',\n  ],\n  'puppeteer': [\n    'anthropics/skills webapp-testing',\n  ],\n  'vitest': [\n    'wshobson/agents e2e-testing-patterns',\n  ],\n  'jest': [\n    'wshobson/agents e2e-testing-patterns',\n  ],\n\n  // DevTools/MCP\n  '@modelcontextprotocol/sdk': [\n    'anthropics/skills mcp-builder',\n  ],\n\n  // Security\n  'semgrep': [\n    'trailofbits/skills semgrep',\n  ],\n\n  // Monorepos\n  'turbo': [\n    'wshobson/agents monorepo-management',\n  ],\n  'nx': [\n    'wshobson/agents monorepo-management',\n  ],\n  'lerna': [\n    'wshobson/agents monorepo-management',\n  ],\n\n  // TypeScript (handled separately based on tsconfig.json)\n  'typescript': [\n    'wshobson/agents typescript-advanced-types',\n  ],\n};\n\n/**\n * Skills categories for user opt-in browsing\n */\nexport const SKILL_CATEGORIES: Record<string, string[]> = {\n  documents: [\n    'anthropics/skills pdf',\n    'anthropics/skills xlsx',\n    'anthropics/skills pptx',\n    'anthropics/skills docx',\n    'anthropics/skills doc-coauthoring',\n  ],\n  design: [\n    'anthropics/skills canvas-design',\n    'anthropics/skills theme-factory',\n    'anthropics/skills web-artifacts-builder',\n    'anthropics/skills algorithmic-art',\n    'anthropics/skills brand-guidelines',\n    'anthropics/skills slack-gif-creator',\n    'nextlevelbuilder/ui-ux-pro-max ui-ux-pro-max',\n    'superdesigndev/superdesign-skill superdesign',\n    'wshobson/agents design-system-patterns',\n  ],\n  marketing: [\n    'coreyhaines31/marketingskills seo-audit',\n    'coreyhaines31/marketingskills copywriting',\n    'coreyhaines31/marketingskills marketing-psychology',\n    'coreyhaines31/marketingskills programmatic-seo',\n    'coreyhaines31/marketingskills marketing-ideas',\n    'coreyhaines31/marketingskills copy-editing',\n    'coreyhaines31/marketingskills pricing-strategy',\n    'coreyhaines31/marketingskills social-content',\n    'coreyhaines31/marketingskills launch-strategy',\n    'coreyhaines31/marketingskills page-cro',\n    'coreyhaines31/marketingskills competitor-alternatives',\n    'coreyhaines31/marketingskills analytics-tracking',\n    'coreyhaines31/marketingskills schema-markup',\n    'coreyhaines31/marketingskills onboarding-cro',\n    'coreyhaines31/marketingskills email-sequence',\n    'coreyhaines31/marketingskills paid-ads',\n    'coreyhaines31/marketingskills signup-flow-cro',\n    'coreyhaines31/marketingskills free-tool-strategy',\n    'coreyhaines31/marketingskills form-cro',\n    'coreyhaines31/marketingskills paywall-upgrade-cro',\n    'coreyhaines31/marketingskills referral-program',\n    'coreyhaines31/marketingskills popup-cro',\n    'coreyhaines31/marketingskills ab-test-setup',\n  ],\n  development: [\n    'obra/superpowers brainstorming',\n    'obra/superpowers test-driven-development',\n    'obra/superpowers systematic-debugging',\n    'obra/superpowers writing-plans',\n    'obra/superpowers executing-plans',\n    'obra/superpowers verification-before-completion',\n    'obra/superpowers using-superpowers',\n    'obra/superpowers subagent-driven-development',\n    'obra/superpowers requesting-code-review',\n    'obra/superpowers writing-skills',\n    'obra/superpowers dispatching-parallel-agents',\n    'obra/superpowers receiving-code-review',\n    'obra/superpowers using-git-worktrees',\n    'obra/superpowers finishing-a-development-branch',\n    'wshobson/agents code-review-excellence',\n    'wshobson/agents api-design-principles',\n    'wshobson/agents architecture-patterns',\n    'wshobson/agents error-handling-patterns',\n    'wshobson/agents nodejs-backend-patterns',\n    'wshobson/agents microservices-patterns',\n    'wshobson/agents modern-javascript-patterns',\n    'wshobson/agents web-component-design',\n    'wshobson/agents async-python-patterns',\n    'wshobson/agents python-testing-patterns',\n    'boristane/agent-skills logging-best-practices',\n  ],\n  productivity: [\n    'softaworks/agent-toolkit daily-meeting-update',\n    'softaworks/agent-toolkit agent-md-refactor',\n    'softaworks/agent-toolkit session-handoff',\n    'softaworks/agent-toolkit meme-factory',\n    'softaworks/agent-toolkit qa-test-planner',\n    'softaworks/agent-toolkit writing-clearly-and-concisely',\n    'softaworks/agent-toolkit commit-work',\n    'softaworks/agent-toolkit mermaid-diagrams',\n    'softaworks/agent-toolkit dependency-updater',\n    'softaworks/agent-toolkit crafting-effective-readmes',\n    'softaworks/agent-toolkit reducing-entropy',\n    'softaworks/agent-toolkit feedback-mastery',\n    'softaworks/agent-toolkit marp-slide',\n    'softaworks/agent-toolkit professional-communication',\n    'softaworks/agent-toolkit difficult-workplace-conversations',\n    'anthropics/skills internal-comms',\n    'othmanadi/planning-with-files planning-with-files',\n  ],\n  security: [\n    'trailofbits/skills semgrep',\n    'trailofbits/skills secure-workflow-guide',\n    'trailofbits/skills codeql',\n    'trailofbits/skills property-based-testing',\n    'trailofbits/skills variant-analysis',\n    'trailofbits/skills guidelines-advisor',\n    'trailofbits/skills sharp-edges',\n    'trailofbits/skills differential-review',\n    'trailofbits/skills ask-questions-if-underspecified',\n    'squirrelscan/skills audit-website',\n  ],\n  mobile: [\n    'wshobson/agents mobile-ios-design',\n    'wshobson/agents mobile-android-design',\n    'dimillian/skills swiftui-ui-patterns',\n    'dimillian/skills swiftui-liquid-glass',\n  ],\n  obsidian: [\n    'kepano/obsidian-skills obsidian-markdown',\n    'kepano/obsidian-skills obsidian-bases',\n    'kepano/obsidian-skills json-canvas',\n  ],\n  prompts: [\n    'f/awesome-chatgpt-prompts skill-lookup',\n    'f/awesome-chatgpt-prompts prompt-lookup',\n    'wshobson/agents prompt-engineering-patterns',\n  ],\n  browser: [\n    'vercel-labs/agent-browser agent-browser',\n  ],\n  content: [\n    'op7418/humanizer-zh humanizer-zh',\n    'blader/humanizer humanizer',\n    'op7418/youtube-clipper-skill youtube-clipper',\n    'jimliu/baoyu-skills baoyu-slide-deck',\n    'jimliu/baoyu-skills baoyu-article-illustrator',\n    'jimliu/baoyu-skills baoyu-cover-image',\n    'jimliu/baoyu-skills baoyu-comic',\n    'jimliu/baoyu-skills baoyu-infographic',\n    'jimliu/baoyu-skills baoyu-image-gen',\n  ],\n  integrations: [\n    'intellectronica/agent-skills context7',\n    'softaworks/agent-toolkit gemini',\n    'softaworks/agent-toolkit codex',\n  ],\n};\n\nexport async function detectStack(projectDir: string): Promise<DetectedStack> {\n  const stack: DetectedStack = {\n    suggestedSkills: [],\n    suggestedAgents: ['security', 'bugs'],\n    dependencies: new Set(),\n  };\n\n  // Detect language\n  if (existsSync(join(projectDir, 'tsconfig.json'))) {\n    stack.language = 'TypeScript';\n    stack.suggestedSkills.push('wshobson/agents typescript-advanced-types');\n  } else if (existsSync(join(projectDir, 'package.json'))) {\n    stack.language = 'JavaScript';\n  } else if (existsSync(join(projectDir, 'requirements.txt')) || existsSync(join(projectDir, 'pyproject.toml'))) {\n    stack.language = 'Python';\n  } else if (existsSync(join(projectDir, 'go.mod'))) {\n    stack.language = 'Go';\n  } else if (existsSync(join(projectDir, 'Cargo.toml'))) {\n    stack.language = 'Rust';\n  }\n\n  // Detect Swift/iOS projects\n  if (existsSync(join(projectDir, 'Package.swift')) || \n      existsSync(join(projectDir, 'project.pbxproj')) ||\n      existsSync(join(projectDir, '*.xcodeproj'))) {\n    stack.language = 'Swift';\n    stack.suggestedSkills.push('dimillian/skills swiftui-ui-patterns');\n    stack.suggestedSkills.push('dimillian/skills swiftui-liquid-glass');\n  }\n\n  // Detect package manager\n  if (existsSync(join(projectDir, 'pnpm-lock.yaml'))) {\n    stack.packageManager = 'pnpm';\n  } else if (existsSync(join(projectDir, 'yarn.lock'))) {\n    stack.packageManager = 'yarn';\n  } else if (existsSync(join(projectDir, 'bun.lockb'))) {\n    stack.packageManager = 'bun';\n  } else if (existsSync(join(projectDir, 'package-lock.json'))) {\n    stack.packageManager = 'npm';\n  }\n\n  // Check for GitHub Actions\n  if (existsSync(join(projectDir, '.github', 'workflows'))) {\n    stack.suggestedSkills.push('wshobson/agents github-actions-templates');\n  }\n\n  // Parse package.json for framework detection\n  try {\n    const pkgPath = join(projectDir, 'package.json');\n    if (existsSync(pkgPath)) {\n      const pkgContent = await readFile(pkgPath, 'utf-8');\n      const pkg = JSON.parse(pkgContent);\n      const deps = { ...pkg.dependencies, ...pkg.devDependencies };\n\n      // Store all dependencies\n      for (const dep of Object.keys(deps)) {\n        stack.dependencies.add(dep);\n      }\n\n      // Add skills based on dependency mappings\n      for (const dep of Object.keys(deps)) {\n        const skills = SKILL_MAPPINGS[dep];\n        if (skills) {\n          stack.suggestedSkills.push(...skills);\n        }\n      }\n\n      // Framework detection (for display purposes)\n      if (deps['next']) {\n        stack.framework = `Next.js ${deps['next'].replace('^', '')}`;\n        stack.suggestedAgents.push('accessibility', 'design');\n      } else if (deps['react']) {\n        stack.framework = `React ${deps['react'].replace('^', '')}`;\n        stack.suggestedAgents.push('accessibility');\n      } else if (deps['vue']) {\n        stack.framework = `Vue ${deps['vue'].replace('^', '')}`;\n      } else if (deps['nuxt']) {\n        stack.framework = `Nuxt ${deps['nuxt'].replace('^', '')}`;\n      } else if (deps['svelte']) {\n        stack.framework = 'Svelte';\n      } else if (deps['express']) {\n        stack.framework = 'Express.js';\n      } else if (deps['fastify']) {\n        stack.framework = 'Fastify';\n      } else if (deps['hono']) {\n        stack.framework = 'Hono';\n      } else if (deps['elysia']) {\n        stack.framework = 'Elysia';\n      } else if (deps['@nestjs/core']) {\n        stack.framework = 'NestJS';\n      }\n\n      // Auth detection\n      if (deps['next-auth'] || deps['@auth/core']) {\n        stack.auth = 'NextAuth.js';\n      } else if (deps['passport']) {\n        stack.auth = 'Passport.js';\n      } else if (deps['@clerk/nextjs'] || deps['@clerk/clerk-react']) {\n        stack.auth = 'Clerk';\n      } else if (deps['better-auth']) {\n        stack.auth = 'Better Auth';\n      }\n\n      // Database detection\n      if (deps['prisma'] || deps['@prisma/client']) {\n        stack.database = 'Prisma ORM';\n      } else if (deps['drizzle-orm']) {\n        stack.database = 'Drizzle ORM';\n      } else if (deps['@supabase/supabase-js']) {\n        stack.database = 'Supabase';\n      } else if (deps['mongoose']) {\n        stack.database = 'MongoDB (Mongoose)';\n      } else if (deps['pg']) {\n        stack.database = 'PostgreSQL';\n      } else if (deps['convex']) {\n        stack.database = 'Convex';\n      }\n\n    }\n  } catch {\n    // package.json parsing failed\n  }\n\n  // Database from other sources\n  if (!stack.database) {\n    if (existsSync(join(projectDir, 'prisma', 'schema.prisma'))) {\n      stack.database = 'Prisma ORM';\n    } else if (existsSync(join(projectDir, 'drizzle.config.ts'))) {\n      stack.database = 'Drizzle ORM';\n    }\n  }\n\n  // Deduplicate\n  stack.suggestedSkills = [...new Set(stack.suggestedSkills)];\n  stack.suggestedAgents = [...new Set(stack.suggestedAgents)];\n\n  return stack;\n}\n\n/**\n * Get skills for a specific category\n */\nexport function getSkillsByCategory(category: string): string[] {\n  return SKILL_CATEGORIES[category] || [];\n}\n\n/**\n * Get all available skill categories\n */\nexport function getSkillCategories(): { name: string; count: number }[] {\n  return Object.entries(SKILL_CATEGORIES).map(([name, skills]) => ({\n    name,\n    count: skills.length,\n  }));\n}\n\n/**\n * Get project dependencies from package.json\n */\nexport async function getProjectDependencies(projectDir: string): Promise<Set<string>> {\n  try {\n    const pkgPath = join(projectDir, 'package.json');\n    if (!existsSync(pkgPath)) {\n      return new Set();\n    }\n    \n    const pkg = JSON.parse(await readFile(pkgPath, 'utf-8'));\n    return new Set([\n      ...Object.keys(pkg.dependencies || {}),\n      ...Object.keys(pkg.devDependencies || {}),\n    ]);\n  } catch {\n    return new Set();\n  }\n}\n","/**\n * Bootstrap File System\n * \n * Manages workspace files that inject context at scan start.\n * Files: BOOTSTRAP.md, RULES.md, TEAM.md\n */\n\nimport { readFile, writeFile, unlink, mkdir } from 'fs/promises';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\nimport { getWorkingDirectory, getTrieDirectory } from '../utils/workspace.js';\nimport { detectStack, type DetectedStack } from './stack-detector.js';\n\nexport interface BootstrapFile {\n  name: string;\n  path: string;\n  type: 'user' | 'auto' | 'one-time';\n  exists: boolean;\n  content?: string;\n}\n\nexport interface BootstrapContext {\n  files: BootstrapFile[];\n  injectedContent: string;\n  needsBootstrap: boolean;\n}\n\ninterface BootstrapFileSpec {\n  name: string;\n  type: 'user' | 'auto' | 'one-time';\n  description: string;\n}\n\nconst BOOTSTRAP_FILES: BootstrapFileSpec[] = [\n  { name: 'PROJECT.md', type: 'user', description: 'Project overview and conventions' },\n  { name: 'RULES.md', type: 'user', description: 'Coding standards agents enforce' },\n  { name: 'TEAM.md', type: 'user', description: 'Team ownership and escalation' },\n  { name: 'BOOTSTRAP.md', type: 'one-time', description: 'First-run setup (deleted after)' },\n  { name: 'AGENTS.md', type: 'auto', description: 'Auto-generated scan context' },\n];\n\n/**\n * Load bootstrap files and inject into agent context\n */\nexport async function loadBootstrapContext(workDir?: string): Promise<BootstrapContext> {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const trieDir = getTrieDirectory(projectDir);\n  const files: BootstrapFile[] = [];\n  const contentParts: string[] = [];\n  let needsBootstrap = false;\n\n  for (const file of BOOTSTRAP_FILES) {\n    const filePath = join(trieDir, file.name);\n    const exists = existsSync(filePath);\n    \n    if (file.name === 'BOOTSTRAP.md' && exists) {\n      needsBootstrap = true;\n    }\n    \n    let content: string | undefined;\n    if (exists) {\n      try {\n        content = await readFile(filePath, 'utf-8');\n        if (content.trim() && file.type !== 'one-time') {\n          contentParts.push(`<!-- ${file.name} -->\\n${content}`);\n        }\n      } catch {\n        // Skip files that can't be read\n      }\n    }\n\n    const fileEntry: BootstrapFile = {\n      name: file.name,\n      path: filePath,\n      type: file.type,\n      exists,\n    };\n    if (content) fileEntry.content = content;\n    files.push(fileEntry);\n  }\n\n  return {\n    files,\n    injectedContent: contentParts.join('\\n\\n---\\n\\n'),\n    needsBootstrap,\n  };\n}\n\n/**\n * Initialize bootstrap files for a new project\n */\nexport async function initializeBootstrapFiles(options: {\n  workDir?: string;\n  force?: boolean;\n  skipBootstrap?: boolean;\n} = {}): Promise<{ created: string[]; skipped: string[]; stack: DetectedStack }> {\n  const projectDir = options.workDir || getWorkingDirectory(undefined, true);\n  const trieDir = getTrieDirectory(projectDir);\n  await mkdir(trieDir, { recursive: true });\n\n  const created: string[] = [];\n  const skipped: string[] = [];\n\n  const stack = await detectStack(projectDir);\n\n  for (const file of BOOTSTRAP_FILES) {\n    const filePath = join(trieDir, file.name);\n    const exists = existsSync(filePath);\n\n    if (exists && !options.force) {\n      skipped.push(file.name);\n      continue;\n    }\n\n    if (file.name === 'BOOTSTRAP.md' && options.skipBootstrap) {\n      skipped.push(file.name);\n      continue;\n    }\n\n    if (file.name === 'AGENTS.md') {\n      skipped.push(file.name);\n      continue;\n    }\n\n    const template = getFileTemplate(file.name, stack);\n    if (template) {\n      await writeFile(filePath, template);\n      created.push(file.name);\n    }\n  }\n\n  return { created, skipped, stack };\n}\n\n/**\n * Mark bootstrap as complete (delete BOOTSTRAP.md)\n */\nexport async function completeBootstrap(workDir?: string): Promise<boolean> {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const bootstrapPath = join(getTrieDirectory(projectDir), 'BOOTSTRAP.md');\n\n  try {\n    await unlink(bootstrapPath);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Check if bootstrap is needed (BOOTSTRAP.md exists)\n */\nexport function needsBootstrap(workDir?: string): boolean {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const bootstrapPath = join(getTrieDirectory(projectDir), 'BOOTSTRAP.md');\n  return existsSync(bootstrapPath);\n}\n\n/**\n * Get rules from RULES.md\n */\nexport async function loadRules(workDir?: string): Promise<string | null> {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const rulesPath = join(getTrieDirectory(projectDir), 'RULES.md');\n  \n  try {\n    if (existsSync(rulesPath)) {\n      return await readFile(rulesPath, 'utf-8');\n    }\n  } catch {\n    // Rules file doesn't exist or can't be read\n  }\n  \n  return null;\n}\n\n/**\n * Get team info from TEAM.md\n */\nexport async function loadTeamInfo(workDir?: string): Promise<string | null> {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const teamPath = join(getTrieDirectory(projectDir), 'TEAM.md');\n  \n  try {\n    if (existsSync(teamPath)) {\n      return await readFile(teamPath, 'utf-8');\n    }\n  } catch {\n    // Team file doesn't exist or can't be read\n  }\n  \n  return null;\n}\n\nfunction getFileTemplate(fileName: string, stack: DetectedStack): string | null {\n  switch (fileName) {\n    case 'PROJECT.md':\n      return getProjectTemplate(stack);\n    case 'RULES.md':\n      return getRulesTemplate(stack);\n    case 'TEAM.md':\n      return getTeamTemplate();\n    case 'BOOTSTRAP.md':\n      return getBootstrapTemplate(stack);\n    default:\n      return null;\n  }\n}\n\nfunction getProjectTemplate(stack: DetectedStack): string {\n  const lines: string[] = ['# Project Overview', '', '> Define your project context here. AI assistants read this first.', ''];\n  \n  lines.push('## Description', '', '[Describe what this project does and who it\\'s for]', '');\n  \n  lines.push('## Technology Stack', '');\n  if (stack.framework) lines.push(`- **Framework:** ${stack.framework}`);\n  if (stack.language) lines.push(`- **Language:** ${stack.language}`);\n  if (stack.database) lines.push(`- **Database:** ${stack.database}`);\n  if (stack.auth) lines.push(`- **Auth:** ${stack.auth}`);\n  if (!stack.framework && !stack.language && !stack.database) {\n    lines.push('[Add your technology stack]');\n  }\n  lines.push('');\n  \n  lines.push('## Architecture', '', '[Key patterns and design decisions]', '');\n  lines.push('## Coding Conventions', '', '[Style rules agents should follow]', '');\n  lines.push('## AI Instructions', '', 'When working on this project:', '1. [Instruction 1]', '2. [Instruction 2]', '3. [Instruction 3]', '');\n  lines.push('---', '', '*Edit this file to provide project context to AI assistants.*');\n  \n  return lines.join('\\n');\n}\n\nfunction getRulesTemplate(stack: DetectedStack): string {\n  const packageManager = stack.packageManager || 'npm';\n  \n  return `# Project Rules\n\n> These rules are enforced by Trie agents during scans.\n> Violations appear as issues with [RULES] prefix.\n\n## Code Style\n\n1. Use named exports, not default exports\n2. Prefer \\`${packageManager}\\` for package management\n3. Maximum file length: 300 lines\n4. Use TypeScript strict mode\n\n## Testing Requirements\n\n1. Critical paths require unit tests\n2. API endpoints require integration tests\n3. Minimum coverage: 70%\n\n## Security Rules\n\n1. Never log sensitive data (passwords, tokens, PII)\n2. All API routes require authentication\n3. Rate limiting required on public endpoints\n4. SQL queries must use parameterized statements\n\n## Review Requirements\n\n1. All PRs require at least 1 reviewer\n2. Security-sensitive changes require security review\n3. Database migrations require review\n\n---\n\n*Edit this file to define your project's coding standards.*\n`;\n}\n\nfunction getTeamTemplate(): string {\n  return `# Team Structure\n\n## Code Ownership\n\n| Area | Owner | Backup | Review Required |\n|------|-------|--------|-----------------|\n| \\`/src/api/\\` | @backend-team | - | 1 approver |\n| \\`/src/ui/\\` | @frontend-team | - | 1 approver |\n| \\`/src/auth/\\` | @security-team | - | Security review |\n\n## Escalation\n\n| Severity | First Contact | Escalate To | SLA |\n|----------|--------------|-------------|-----|\n| Critical | Team lead | CTO | 1 hour |\n| Serious | PR reviewer | Team lead | 4 hours |\n| Moderate | Self-serve | - | 1 day |\n\n## Contacts\n\n- **Security:** [email/slack]\n- **Privacy:** [email/slack]\n- **Emergencies:** [phone/pager]\n\n---\n\n*Edit this file to define your team structure.*\n`;\n}\n\nfunction getBootstrapTemplate(stack: DetectedStack): string {\n  const skillCommands = stack.suggestedSkills\n    .map(s => `trie skills add ${s}`)\n    .join('\\n');\n\n  const agentList = stack.suggestedAgents.join(', ');\n\n  const lines: string[] = [\n    '# Trie Bootstrap Checklist',\n    '',\n    'This file guides your first scan setup. **Delete when complete.**',\n    '',\n    '## Auto-Detected Stack',\n    '',\n    'Based on your project, Trie detected:',\n  ];\n  \n  if (stack.framework) lines.push(`- **Framework:** ${stack.framework}`);\n  if (stack.language) lines.push(`- **Language:** ${stack.language}`);\n  if (stack.database) lines.push(`- **Database:** ${stack.database}`);\n  if (stack.auth) lines.push(`- **Auth:** ${stack.auth}`);\n  \n  lines.push('', '## Recommended Actions', '', '### 1. Skills to Install', 'Based on your stack, consider installing:', '```bash');\n  lines.push(skillCommands || '# No specific skills detected - browse https://skills.sh');\n  lines.push('```', '', '### 2. Agents to Enable', `Your stack suggests these agents: ${agentList || 'security, bugs'}`, '');\n  lines.push('### 3. Configure Rules', 'Add your coding standards to `.trie/RULES.md`.', '');\n  lines.push('### 4. Run First Scan', '```bash', 'trie scan', '```', '');\n  lines.push('---', '', '**Delete this file after completing setup.** Run:', '```bash', 'rm .trie/BOOTSTRAP.md', '```');\n  \n  return lines.join('\\n');\n}\n","import { loadConfig } from '../config/loader.js';\nimport { ContextGraph } from '../context/graph.js';\nimport type { LinearTicketNodeData } from '../context/nodes.js';\n\nexport interface LinearTicket {\n  id: string;\n  identifier: string;\n  title: string;\n  description: string;\n  priority: number;\n  status: { name: string };\n  assignee?: { name: string };\n  labels: { nodes: { name: string }[] };\n  createdAt: string;\n  updatedAt: string;\n}\n\nexport class LinearIngester {\n  private readonly graph: ContextGraph;\n\n  constructor(_projectPath: string, graph: ContextGraph) {\n    this.graph = graph;\n  }\n\n  async syncTickets(): Promise<void> {\n    const apiKey = await this.getApiKey();\n    if (!apiKey) {\n      console.warn('Linear API key not found. Run \"trie linear auth <key>\" to enable ticket sync.');\n      return;\n    }\n\n    const tickets = await this.fetchActiveTickets(apiKey);\n    for (const ticket of tickets) {\n      await this.ingestTicket(ticket);\n    }\n  }\n\n  private async getApiKey(): Promise<string | null> {\n    const config = await loadConfig();\n    return (config.apiKeys as any)?.linear || process.env.LINEAR_API_KEY || null;\n  }\n\n  private async fetchActiveTickets(apiKey: string): Promise<LinearTicket[]> {\n    const query = `\n      query {\n        issues(filter: { state: { type: { in: [\"started\", \"unstarted\"] } } }) {\n          nodes {\n            id\n            identifier\n            title\n            description\n            priority\n            status {\n              name\n            }\n            assignee {\n              name\n            }\n            labels {\n              nodes {\n                name\n              }\n            }\n            createdAt\n            updatedAt\n          }\n        }\n      }\n    `;\n\n    const response = await fetch('https://api.linear.app/graphql', {\n      method: 'POST',\n      headers: {\n        'Content-Type': 'application/json',\n        'Authorization': apiKey,\n      },\n      body: JSON.stringify({ query }),\n    });\n\n    if (!response.ok) {\n      throw new Error(`Linear API error: ${response.statusText}`);\n    }\n\n    const data = (await response.json()) as any;\n    return data.data.issues.nodes as LinearTicket[];\n  }\n\n  private async ingestTicket(ticket: LinearTicket): Promise<void> {\n    const labels = ticket.labels.nodes.map(l => l.name);\n    const intentVibe = this.extractIntentVibes(ticket.title, ticket.description, labels);\n    \n    // Attempt to find linked files in description or via labels (heuristic)\n    const linkedFiles = this.extractLinkedFiles(ticket.description);\n\n    const data: LinearTicketNodeData = {\n      ticketId: ticket.identifier,\n      title: ticket.title,\n      description: ticket.description || '',\n      priority: this.mapPriority(ticket.priority),\n      labels,\n      intentVibe,\n      linkedFiles,\n      status: ticket.status.name,\n      assignee: ticket.assignee?.name || null,\n      createdAt: ticket.createdAt,\n      updatedAt: ticket.updatedAt,\n    };\n\n    await this.graph.addNode('linear-ticket', data);\n\n    // Link to files if found\n    for (const file of linkedFiles) {\n      const fileNode = await this.graph.getNode('file', file); // Use ID (path)\n      if (fileNode) {\n        await this.graph.addEdge(`linear:${ticket.identifier}`, fileNode.id, 'relatedTo');\n      }\n    }\n  }\n\n  private extractIntentVibes(title: string, description: string, labels: string[]): string[] {\n    const vibes = new Set<string>();\n    const text = (title + ' ' + (description || '') + ' ' + labels.join(' ')).toLowerCase();\n\n    if (text.includes('performance') || text.includes('slow') || text.includes('optimize')) vibes.add('performance');\n    if (text.includes('security') || text.includes('auth') || text.includes('vulnerability')) vibes.add('security');\n    if (text.includes('refactor') || text.includes('cleanup') || text.includes('debt')) vibes.add('refactor');\n    if (text.includes('feature') || text.includes('new')) vibes.add('feature');\n    if (text.includes('bug') || text.includes('fix') || text.includes('broken')) vibes.add('bug');\n    if (text.includes('breaking') || text.includes('major change')) vibes.add('breaking-change');\n\n    return Array.from(vibes);\n  }\n\n  private extractLinkedFiles(description: string): string[] {\n    if (!description) return [];\n    const matches = description.match(/[\\\\w./_-]+\\\\.(ts|tsx|js|jsx|mjs|cjs|py|go|rs)/gi);\n    if (!matches) return [];\n    return Array.from(new Set(matches.map(m => m.replace(/^\\.\\/+/, ''))));\n  }\n\n  private mapPriority(priority: number): string {\n    switch (priority) {\n      case 1: return 'urgent';\n      case 2: return 'high';\n      case 3: return 'medium';\n      case 4: return 'low';\n      default: return 'none';\n    }\n  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