SynkraAI
diff --git a/‎.aios-core/core/execution/semantic-merge-engine.js‎
Lines changed: 12 additions & 14 deletions b/‎.aios-core/core/execution/semantic-merge-engine.js‎
Lines changed: 12 additions & 14 deletions
diff --git a/‎.aios-core/core/memory/file-evolution-tracker.js‎
Lines changed: 10 additions & 23 deletions b/‎.aios-core/core/memory/file-evolution-tracker.js‎
Lines changed: 10 additions & 23 deletions
diff --git a/‎.aios-core/core/memory/timeline-manager.js‎
Lines changed: 4 additions & 4 deletions b/‎.aios-core/core/memory/timeline-manager.js‎
Lines changed: 4 additions & 4 deletions
diff --git a/‎.aios-core/core/permissions/__tests__/permission-mode.test.js‎
Lines changed: 2 additions & 2 deletions b/‎.aios-core/core/permissions/__tests__/permission-mode.test.js‎
Lines changed: 2 additions & 2 deletions
diff --git a/‎.aios-core/core/permissions/permission-mode.js‎
Lines changed: 1 addition & 1 deletion b/‎.aios-core/core/permissions/permission-mode.js‎
Lines changed: 1 addition & 1 deletion
diff --git a/‎.aios-core/core/quality-gates/layer2-pr-automation.js‎
Lines changed: 6 additions & 8 deletions b/‎.aios-core/core/quality-gates/layer2-pr-automation.js‎
Lines changed: 6 additions & 8 deletions
diff --git a/‎.aios-core/development/agents/aios-master.md‎
Lines changed: 4 additions & 0 deletions b/‎.aios-core/development/agents/aios-master.md‎
Lines changed: 4 additions & 0 deletions
diff --git a/‎.aios-core/development/agents/data-engineer.md‎
Lines changed: 9 additions & 16 deletions b/‎.aios-core/development/agents/data-engineer.md‎
Lines changed: 9 additions & 16 deletions
diff --git a/‎.aios-core/development/agents/devops.md‎
Lines changed: 9 additions & 16 deletions b/‎.aios-core/development/agents/devops.md‎
Lines changed: 9 additions & 16 deletions
diff --git a/‎.aios-core/development/agents/po.md‎
Lines changed: 4 additions & 6 deletions b/‎.aios-core/development/agents/po.md‎
Lines changed: 4 additions & 6 deletions
@@ -16,7 +16,7 @@
  * Based on Auto-Claude's merge system architecture.
  */
 
-const { execSync, execFileSync } = require('child_process');
+const { execSync } = require('child_process');
 const fs = require('fs');
 const path = require('path');
 const EventEmitter = require('events');
@@ -240,7 +240,7 @@ class SemanticAnalyzer {
   /**
    * Compute semantic changes between two element sets
    */
-  computeChanges(before, after, _language) {
+  computeChanges(before, after, language) {
     const changes = [];
 
     // Compare imports
@@ -474,7 +474,7 @@ class ConflictDetector {
           analysisA.changes,
           taskB,
           analysisB.changes,
-          analysisA.filePath,
+          analysisA.filePath
         );
 
         conflicts.push(...taskConflicts);
@@ -670,12 +670,12 @@ class AutoMerger {
     // This is a simplified version - real implementation would parse AST
     let mergedContent = baseContent;
 
-    for (const [_taskId, content] of Object.entries(taskContents)) {
+    for (const [taskId, content] of Object.entries(taskContents)) {
       for (const funcName of functionNames) {
         // Check if function exists in this task's content but not in merged
         const funcRegex = new RegExp(
           `(?:export\\s+)?(?:async\\s+)?function\\s+${funcName}\\s*\\([^)]*\\)\\s*\\{[^}]*\\}`,
-          'g',
+          'g'
         );
 
         const match = content.match(funcRegex);
@@ -811,20 +811,18 @@ Provide ONLY the merged code in a code block. No explanations outside the code b
 
   /**
    * Call Claude CLI for merge resolution
-   * Uses execFileSync with args array to prevent command injection
    */
   async callClaude(prompt) {
     return new Promise((resolve, reject) => {
       try {
-        // Use Claude CLI in print mode with safe argument passing (no shell interpolation)
-        const result = execFileSync(
-          'claude',
-          ['--print', '--dangerously-skip-permissions', '-p', prompt],
+        // Use Claude CLI in print mode
+        const result = execSync(
+          `claude --print --dangerously-skip-permissions -p "${prompt.replace(/"/g, '\\"').replace(/\n/g, '\\n')}"`,
           {
             encoding: 'utf8',
             maxBuffer: 10 * 1024 * 1024,
             timeout: 120000,
-          },
+          }
         );
         resolve(result);
       } catch (error) {
@@ -1378,7 +1376,7 @@ class SemanticMergeEngine extends EventEmitter {
           filePath,
           baseContent,
           taskContent,
-          taskId,
+          taskId
         );
         taskContents[taskId] = taskContent;
       }
@@ -1450,7 +1448,7 @@ class SemanticMergeEngine extends EventEmitter {
         const aiResult = await this.aiResolver.resolveConflict(
           conflict,
           baseContent,
-          taskSnapshots,
+          taskSnapshots
         );
         results.push({
           conflict,
@@ -1700,7 +1698,7 @@ class SemanticMergeEngine extends EventEmitter {
 
     const reportPath = path.join(
       this.storageDir,
-      `merge-report-${new Date().toISOString().replace(/[:.]/g, '-')}.json`,
+      `merge-report-${new Date().toISOString().replace(/[:.]/g, '-')}.json`
     );
 
     fs.writeFileSync(reportPath, JSON.stringify(report, null, 2));
 
@@ -419,20 +419,20 @@ class FileEvolutionTracker {
 
     if (analysis.overallSeverity === DriftSeverity.CRITICAL) {
       recommendations.push(
-        'CRITICAL: Multiple tasks modified the same functions/classes. Manual review required.',
+        'CRITICAL: Multiple tasks modified the same functions/classes. Manual review required.'
       );
       recommendations.push('Consider rebasing one task onto the other before merging.');
     }
 
     if (analysis.overallSeverity === DriftSeverity.HIGH) {
       recommendations.push(
-        'HIGH: Overlapping changes detected. Use Semantic Merge Engine for AI-assisted resolution.',
+        'HIGH: Overlapping changes detected. Use Semantic Merge Engine for AI-assisted resolution.'
       );
     }
 
     if (analysis.overallSeverity === DriftSeverity.MEDIUM) {
       recommendations.push(
-        'MEDIUM: Same files modified but different sections. Auto-merge likely to succeed.',
+        'MEDIUM: Same files modified but different sections. Auto-merge likely to succeed.'
       );
     }
 
@@ -443,7 +443,7 @@ class FileEvolutionTracker {
         conflict.severity === DriftSeverity.CRITICAL
       ) {
         recommendations.push(
-          `Review ${conflict.filePath}: ${conflict.tasks.join(', ')} both modified this file.`,
+          `Review ${conflict.filePath}: ${conflict.tasks.join(', ')} both modified this file.`
         );
       }
     }
@@ -832,7 +832,6 @@ class FileEvolutionTracker {
 
   /**
    * Compute diff summary between two versions
-   * Uses the actual commit/hash for the diff instead of hardcoded HEAD~1
    * @private
    */
   _computeDiffSummary(filePath, oldHash, newHash) {
@@ -841,24 +840,12 @@ class FileEvolutionTracker {
     }
 
     try {
-      // Try to get diff stats from git using the actual base reference
-      // Use oldHash if it's a valid commit reference, otherwise fall back to working tree diff
-      let diffOutput;
-      if (oldHash && oldHash.length >= 7) {
-        // oldHash looks like a commit hash, use it as base
-        diffOutput = execSync(`git diff --stat ${oldHash} -- "${filePath}"`, {
-          cwd: this.rootPath,
-          encoding: 'utf-8',
-          stdio: ['pipe', 'pipe', 'pipe'],
-        });
-      } else {
-        // Fall back to unstaged diff (current working tree vs index)
-        diffOutput = execSync(`git diff --stat -- "${filePath}"`, {
-          cwd: this.rootPath,
-          encoding: 'utf-8',
-          stdio: ['pipe', 'pipe', 'pipe'],
-        });
-      }
+      // Try to get diff stats from git
+      const diffOutput = execSync(`git diff --stat HEAD~1 -- "${filePath}"`, {
+        cwd: this.rootPath,
+        encoding: 'utf-8',
+        stdio: ['pipe', 'pipe', 'pipe'],
+      });
 
       // Parse diff output
       const match = diffOutput.match(/(\d+) insertion.+?(\d+) deletion/);
 
@@ -222,7 +222,7 @@ class TimelineManager {
    * Parse build log entry
    * @private
    */
-  _parseLogEntry(logLine, _storyId) {
+  _parseLogEntry(logLine, storyId) {
     // Format: [timestamp] [storyId] [subtaskId] action: {json}
     const match = logLine.match(/\[(.*?)\] \[(.*?)\] \[(.*?)\] (\w+): (.*)/);
     if (!match) return null;
@@ -471,7 +471,7 @@ class TimelineManager {
 
     // Activity patterns
     const peakHour = analysis.activityHeatmap.byHour.indexOf(
-      Math.max(...analysis.activityHeatmap.byHour),
+      Math.max(...analysis.activityHeatmap.byHour)
     );
     insights.push({
       type: 'activity_pattern',
@@ -483,7 +483,7 @@ class TimelineManager {
     // Failure rate (if we have build events)
     const failures = timeline.filter((e) => e.eventType === 'failure').length;
     const totalBuildEvents = timeline.filter(
-      (e) => e.source === TimelineEventSource.BUILD_STATE,
+      (e) => e.source === TimelineEventSource.BUILD_STATE
     ).length;
     if (totalBuildEvents > 0) {
       const failureRate = ((failures / totalBuildEvents) * 100).toFixed(1);
@@ -575,7 +575,7 @@ class TimelineManager {
           entries: timeline,
         },
         null,
-        2,
+        2
       );
     } else if (format === 'csv') {
       const headers = ['timestamp', 'source', 'eventType', 'taskId', 'filePath', 'summary'];
 
@@ -40,7 +40,7 @@ describe('PermissionMode', () => {
     it('should load mode from config file', async () => {
       await fs.writeFile(
         path.join(tempDir, '.aios', 'config.yaml'),
-        'permissions:\n  mode: auto\n',
+        'permissions:\n  mode: auto\n'
       );
 
       const result = await mode.load();
@@ -50,7 +50,7 @@ describe('PermissionMode', () => {
     it('should fallback to "ask" for invalid mode in config', async () => {
       await fs.writeFile(
         path.join(tempDir, '.aios', 'config.yaml'),
-        'permissions:\n  mode: invalid_mode\n',
+        'permissions:\n  mode: invalid_mode\n'
       );
 
       const result = await mode.load();
 
@@ -90,7 +90,7 @@ class PermissionMode {
         console.warn(`Invalid mode "${this.currentMode}" in config, defaulting to "ask"`);
         this.currentMode = 'ask';
       }
-    } catch (_error) {
+    } catch (error) {
       // Config doesn't exist or is invalid, use default
       this.currentMode = 'ask';
     }
 
@@ -75,7 +75,7 @@ class Layer2PRAutomation extends BaseLayer {
       const summary = this.getSummary();
       const icon = summary.pass ? '✅' : '⚠️';
       console.log(
-        `\n${icon} Layer 2 ${summary.pass ? 'PASSED' : 'HAS ISSUES'} (${this.formatDuration(summary.duration)})`,
+        `\n${icon} Layer 2 ${summary.pass ? 'PASSED' : 'HAS ISSUES'} (${this.formatDuration(summary.duration)})`
       );
     }
 
@@ -97,11 +97,9 @@ class Layer2PRAutomation extends BaseLayer {
 
     try {
       // Check if CodeRabbit is available
-      // Resolve PROJECT_ROOT from environment or use cwd (prevents shell injection)
-      const projectRoot = process.env.AIOS_PROJECT_ROOT || process.env.PROJECT_ROOT || process.cwd();
       const command =
         this.coderabbit.command ||
-        `wsl bash -c 'cd ${projectRoot} && ~/.local/bin/coderabbit --prompt-only -t uncommitted'`;
+        "wsl bash -c 'cd ${PROJECT_ROOT} && ~/.local/bin/coderabbit --prompt-only -t uncommitted'";
 
       const result = await this.runCommand(command, timeout);
 
@@ -139,7 +137,7 @@ class Layer2PRAutomation extends BaseLayer {
       if (verbose) {
         const icon = pass ? '✓' : '⚠️';
         console.log(
-          `  ${icon} CodeRabbit: ${criticalCount} CRITICAL, ${highCount} HIGH, ${mediumCount} MEDIUM`,
+          `  ${icon} CodeRabbit: ${criticalCount} CRITICAL, ${highCount} HIGH, ${mediumCount} MEDIUM`
         );
       }
 
@@ -215,7 +213,7 @@ class Layer2PRAutomation extends BaseLayer {
       const suggestions = await this.generateQuinnSuggestions(context);
 
       const blockingSuggestions = suggestions.filter((s) =>
-        this.quinn.severity?.block?.includes(s.severity),
+        this.quinn.severity?.block?.includes(s.severity)
       );
 
       const pass = blockingSuggestions.length === 0;
@@ -234,7 +232,7 @@ class Layer2PRAutomation extends BaseLayer {
       if (verbose) {
         const icon = pass ? '✓' : '⚠️';
         console.log(
-          `  ${icon} Quinn: ${suggestions.length} suggestions, ${blockingSuggestions.length} blocking`,
+          `  ${icon} Quinn: ${suggestions.length} suggestions, ${blockingSuggestions.length} blocking`
         );
       }
 
@@ -255,7 +253,7 @@ class Layer2PRAutomation extends BaseLayer {
    * @param {Object} context - Execution context
    * @returns {Promise<Array>} Suggestions
    */
-  async generateQuinnSuggestions(_context = {}) {
+  async generateQuinnSuggestions(context = {}) {
     // This would integrate with the QA agent for automated review
     // For now, return empty suggestions - full integration in Story 2.11
     return [];
 
@@ -289,6 +289,10 @@ dependencies:
     - po-master-checklist.md
     - story-dod-checklist.md
     - story-draft-checklist.md
+
+autoClaude:
+  version: '3.0'
+  migratedAt: '2026-01-29T02:24:00.000Z'
 ```
 
 ---
 
@@ -23,23 +23,16 @@ activation-instructions:
   - STEP 2: Adopt the persona defined in the 'agent' and 'persona' sections below
 
   - STEP 3: |
-      Generate greeting by executing unified greeting generator:
-
-      1. Execute: node .aios-core/development/scripts/generate-greeting.js data-engineer
-      2. Capture the complete output
-      3. Display the greeting exactly as returned
-
-      If execution fails or times out:
-      - Fallback to simple greeting: "🗄️ data-engineer Agent ready"
-      - Show: "Type *help to see available commands"
-
-      Do NOT modify or interpret the greeting output.
-      Display it exactly as received.
-
-  - STEP 4: Display the greeting you generated in STEP 3
-
+      Build intelligent greeting using .aios-core/development/scripts/greeting-builder.js
+      The buildGreeting(agentDefinition, conversationHistory) method:
+        - Detects session type (new/existing/workflow) via context analysis
+        - Checks git configuration status (with 5min cache)
+        - Loads project status automatically
+        - Filters commands by visibility metadata (full/quick/key)
+        - Suggests workflow next steps if in recurring pattern
+        - Formats adaptive greeting automatically
+  - STEP 4: Display the greeting returned by GreetingBuilder
   - STEP 5: HALT and await user input
-
   - IMPORTANT: Do NOT improvise or add explanatory text beyond what is specified in greeting_levels and Quick Commands section
   - DO NOT: Load any other agent files during activation
   - ONLY load dependency files when user selects them for execution via command or request of a task
 
@@ -19,23 +19,16 @@ activation-instructions:
   - STEP 2: Adopt the persona defined in the 'agent' and 'persona' sections below
 
   - STEP 3: |
-      Generate greeting by executing unified greeting generator:
-
-      1. Execute: node .aios-core/development/scripts/generate-greeting.js devops
-      2. Capture the complete output
-      3. Display the greeting exactly as returned
-
-      If execution fails or times out:
-      - Fallback to simple greeting: "🚀 devops Agent ready"
-      - Show: "Type *help to see available commands"
-
-      Do NOT modify or interpret the greeting output.
-      Display it exactly as received.
-
-  - STEP 4: Display the greeting you generated in STEP 3
-
+      Build intelligent greeting using .aios-core/development/scripts/greeting-builder.js
+      The buildGreeting(agentDefinition, conversationHistory) method:
+        - Detects session type (new/existing/workflow) via context analysis
+        - Checks git configuration status (with 5min cache)
+        - Loads project status automatically
+        - Filters commands by visibility metadata (full/quick/key)
+        - Suggests workflow next steps if in recurring pattern
+        - Formats adaptive greeting automatically
+  - STEP 4: Display the greeting returned by GreetingBuilder
   - STEP 5: HALT and await user input
-
   - IMPORTANT: Do NOT improvise or add explanatory text beyond what is specified in greeting_levels and Quick Commands section
   - DO NOT: Load any other agent files during activation
   - ONLY load dependency files when user selects them for execution via command or request of a task
 
@@ -115,12 +115,10 @@ commands:
     description: 'Regenerate story index from docs/stories/'
 
   # Story Management
-  - name: create-epic
-    visibility: [full]
-    description: 'Create epic for brownfield projects'
-  - name: create-story
-    visibility: [full, quick]
-    description: 'Create user story from requirements'
+  # NOTE: create-epic and create-story removed - delegated to @pm and @sm respectively
+  # See: docs/architecture/command-authority-matrix.md
+  # For epic creation → Delegate to @pm using *create-epic
+  # For story creation → Delegate to @sm using *draft
   - name: validate-story-draft
     visibility: [full, quick, key]
     description: 'Validate story quality and completeness'
Original file line number	Diff line number	Diff line change
`@@ -90,7 +90,7 @@ class PermissionMode {`
`90`	`90`	console.warn(`Invalid mode "${this.currentMode}" in config, defaulting to "ask"`);
`91`	`91`	`this.currentMode = 'ask';`
`92`	`92`	`}`
`93`		`- } catch (_error) {`
	`93`	`+ } catch (error) {`
`94`	`94`	`// Config doesn't exist or is invalid, use default`
`95`	`95`	`this.currentMode = 'ask';`
`96`	`96`	`}`