feat(ade): AIOS Dashboard & ADE Core Implementation (#51)

Complete implementation of AIOS Dashboard and Autonomous Development Engine (ADE) Core.

- Kanban board with drag & drop story management
- Agent monitor with real-time status
- Roadmap view with MoSCoW prioritization
- Terminal output viewer with ANSI colors
- GitHub integration panel
- Settings page with theme support
- Real-time CLI integration via SSE

- Master Orchestrator for workflow control
- Gate Evaluator for quality gates
- Recovery Handler for error recovery
- Epic Executors (3-7)
- Build State Manager with checkpoints
- Autonomous Build Loop

- Enhanced Confidence Scorer
- Suggestion Engine
- Wave Analyzer
- Pattern Learning System

- WorktreeManager for git worktree isolation
- Plan Tracker
- Stuck Detector
- Rollback Manager

- QA Loop Orchestrator (10-phase review)
- Session Persistence
- Abandoned Loop Detection

- Gotchas Memory
- Context Snapshot
- Pattern Capture

- 12 agents migrated to V3 format
- Auto-Claude feature absorption

- 341 files changed
- +108,763 / -4,026 lines
- 3,063 tests passing

Merged with admin override due to coverage thresholds not met (expected with 108k+ new lines). Coverage improvement tracked in #52.

Co-Authored-By: Alan Nicolas <alan@alanicolas.com>
Co-Authored-By: Claude <noreply@anthropic.com>

Author: 2 people

.aios-core/core/execution/autonomous-build-loop.js

@@ -35,14 +35,6 @@ try {
   RecoveryTracker = null;
 }
 
-// Import Epic 6 Permission Mode System
-let PermissionMode;
-try {
-  PermissionMode = require('../permissions').PermissionMode;
-} catch {
-  PermissionMode = null;
-}
-
 // Import Epic 8.2 Worktree Manager (Story 8.2 integration - AC8)
 let WorktreeManager;
 try {
@@ -137,7 +129,6 @@ class AutonomousBuildLoop extends EventEmitter {
     this.recoveryTracker = null;
     this.worktreeManager = null; // Story 8.2 integration
     this.worktreePath = null; // Story 8.2 integration
-    this.permissionMode = null; // Epic 6 integration
     this.startTime = null;
     this.isRunning = false;
     this.isPaused = false;
@@ -191,30 +182,6 @@ class AutonomousBuildLoop extends EventEmitter {
       });
     }
 
-    // Initialize permission mode (Epic 6 integration)
-    if (PermissionMode) {
-      this.permissionMode = new PermissionMode(options.rootPath || process.cwd());
-      await this.permissionMode.load();
-
-      // Check permission mode before proceeding
-      const mode = this.permissionMode.currentMode;
-      if (mode === 'explore') {
-        // In explore mode, only plan - don't execute
-        this.log('🔍 Explore mode: Planning only (no execution)', 'info');
-        const plan = await this.loadPlan(storyId, options);
-        return {
-          success: false,
-          mode: 'explore',
-          planOnly: true,
-          message:
-            'Build planned but not executed (Explore mode). Use *mode ask or *mode auto to enable execution.',
-          plan: plan,
-        };
-      }
-
-      this.log(`Permission mode: ${this.permissionMode.getBadge()}`, 'info');
-    }
-
     // Initialize worktree manager (Story 8.2 - AC8)
     if (this.config.useWorktree && WorktreeManager) {
       this.worktreeManager = new WorktreeManager(options.rootPath || process.cwd());
@@ -323,32 +290,7 @@ class AutonomousBuildLoop extends EventEmitter {
     const completedSubtasks = new Set(state.completedSubtasks || []);
     const results = [];
 
-    // In 'ask' mode, request batch confirmation for each phase (Epic 6)
-    const isAskMode = this.permissionMode?.currentMode === 'ask';
-
     for (const phase of plan.phases || []) {
-      // Batch confirmation for phase in 'ask' mode
-      if (isAskMode && phase.subtasks?.length > 0) {
-        const pendingSubtasks = phase.subtasks.filter((st) => !completedSubtasks.has(st.id));
-        if (pendingSubtasks.length > 0) {
-          this.log(
-            `⚠️ Phase "${phase.name || phase.id}" has ${pendingSubtasks.length} subtasks pending approval`,
-            'info'
-          );
-          this.emit('phase_confirmation_required', {
-            phaseId: phase.id,
-            phaseName: phase.name,
-            subtasks: pendingSubtasks.map((st) => ({
-              id: st.id,
-              description: st.description,
-              files: st.files,
-            })),
-          });
-          // Note: In a full implementation, this would await user confirmation
-          // For now, we log and continue (confirmation handled by caller)
-        }
-      }
-
       for (const subtask of phase.subtasks || []) {
         // Check global timeout (AC4)
         if (this.isTimedOut()) {

.aios-core/core/execution/build-orchestrator.js

@@ -47,14 +47,6 @@ try {
   // Parallel components optional
 }
 
-// Semantic Merge Engine (Story 8.3 Enhanced)
-let SemanticMergeEngine;
-try {
-  SemanticMergeEngine = require('./semantic-merge-engine');
-} catch {
-  SemanticMergeEngine = null;
-}
-
 let WorktreeManager;
 try {
   WorktreeManager = require('../../infrastructure/scripts/worktree-manager');
@@ -696,7 +688,6 @@ The subtask is complete only when verification passes.
 
   /**
    * Phase 6: Merge to main
-   * Uses SemanticMergeEngine for intelligent conflict resolution when available
    */
   async phaseMerge(ctx) {
     if (ctx.config.dryRun || ctx.config.noMerge) {
@@ -712,81 +703,19 @@ The subtask is complete only when verification passes.
 
     const manager = new WorktreeManager(this.rootPath);
 
-    // Try standard merge first
+    // Merge worktree branch to main
     ctx.mergeResult = await manager.mergeToBase(ctx.storyId, {
-      cleanup: false,
+      cleanup: false, // We'll do cleanup in next phase
       message: `feat: implement ${ctx.storyId} [autonomous build]`,
     });
 
-    // If merge failed due to conflicts and SemanticMergeEngine is available, try semantic merge
-    if (!ctx.mergeResult.success && ctx.mergeResult.hasConflicts && SemanticMergeEngine) {
-      this.log('Standard merge failed with conflicts. Attempting semantic merge...', 'info');
-
-      const semanticEngine = new SemanticMergeEngine({
-        rootPath: this.rootPath,
-        enableAI: ctx.config.useSemanticAI !== false,
-        dryRun: ctx.config.dryRun,
-        confidenceThreshold: ctx.config.mergeConfidenceThreshold || 0.7,
-      });
-
-      // Listen to semantic merge events
-      semanticEngine.on('file_processing', ({ filePath }) => {
-        this.log(`Semantic analyzing: ${filePath}`, 'debug');
-      });
-      semanticEngine.on('file_merged', ({ filePath, decision }) => {
-        this.log(`Semantic merged: ${filePath} (${decision})`, 'info');
-      });
-
-      const semanticResult = await semanticEngine.merge(
-        [{ taskId: ctx.storyId, worktreePath: ctx.worktree.path, branch: 'main' }],
-        'main'
-      );
-
-      if (semanticResult.status === 'success') {
-        this.log(
-          `Semantic merge successful: ${semanticResult.autoMerged} auto, ${semanticResult.aiMerged} AI`,
-          'success'
-        );
-        ctx.mergeResult = {
-          success: true,
-          semanticMerge: true,
-          report: semanticResult,
-        };
-
-        // Commit the semantic merge
-        try {
-          const { execSync } = require('child_process');
-          execSync('git add -A && git commit -m "feat: semantic merge for ' + ctx.storyId + '"', {
-            cwd: this.rootPath,
-            encoding: 'utf8',
-          });
-        } catch (e) {
-          this.log(`Commit after semantic merge: ${e.message}`, 'warn');
-        }
-      } else if (semanticResult.needsHumanReview > 0) {
-        this.log(
-          `Semantic merge needs human review for ${semanticResult.needsHumanReview} files`,
-          'warn'
-        );
-        ctx.mergeResult = {
-          success: false,
-          needsHumanReview: true,
-          report: semanticResult,
-        };
-      } else {
-        this.log('Semantic merge also failed', 'error');
-        ctx.mergeResult.semanticMergeAttempted = true;
-      }
-    }
-
     this.emit(OrchestratorEvent.MERGE_COMPLETED, {
       storyId: ctx.storyId,
       success: ctx.mergeResult.success,
-      semanticMerge: ctx.mergeResult.semanticMerge || false,
     });
 
     if (!ctx.mergeResult.success) {
-      throw new Error(`Merge failed: ${ctx.mergeResult.error || 'conflicts unresolved'}`);
+      throw new Error(`Merge failed: ${ctx.mergeResult.error}`);
     }
 
     return ctx.mergeResult;