fix: close all 5 remaining audit findings — zero legacy issues

ContextAssembler:
- Accept optional MessageRepository/EvidenceStore via set_data_sources()
- L6/L7/L8 query real DB data when available, fall back to descriptive text

ArchitectureDesigner:
- Emit architecture.impact.completed event via EventIngestor
- Import eventIngestor singleton for fire-and-forget emission

MainAgent:
- AWAITING_CONFIRMATION now triggered for breaking/destructive requests
- User confirmation required before delegating delete/break/remove tasks

DoctorService:
- Accept optional CapabilityRegistry in constructor
- Add check_capability_deps() — verify capability tool dependencies (INV-4)

TUI PermissionPrompt:
- Add UiCommandChannel interface for proper INV-3 routing
- Channel routes through ToolRegistry; callbacks are component-level only

All 5 legacy audit findings closed. Zero stubs, zero execSync.
tsc: 0 errors. E2E: 13/13 passed.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

packages/runtime/src/doctor/DoctorService.ts

@@ -28,9 +28,11 @@ export interface DoctorReport {
 
 export class DoctorService {
   private project_root: string
+  private capability_registry?: any
 
-  constructor(project_root: string) {
+  constructor(project_root: string, capability_registry?: any) {
     this.project_root = project_root
+    this.capability_registry = capability_registry
   }
 
   /**
@@ -59,6 +61,11 @@ export class DoctorService {
     checks.push(this.check_node())
     checks.push(this.check_project_structure())
 
+    // INV-4: Capability registry health — verify capability dependencies
+    if (this.capability_registry) {
+      checks.push(this.check_capability_deps())
+    }
+
     const all_passed = checks.every(c => c.passed)
     return { checks, all_passed, bootstrap_passed: true, fixable_count: checks.filter(c => c.fixable).length }
   }
@@ -163,4 +170,45 @@ export class DoctorService {
     }
     return { name: 'project_structure', category: 'project', passed: true, message: 'Project structure valid', fixable: false }
   }
+
+  /**
+   * INV-4: Check capability registry health — verify capability dependencies
+   * are installed and accessible. Bridges CapabilityRegistry → DoctorService.
+   */
+  private check_capability_deps(): DoctorCheck {
+    try {
+      const capabilities = this.capability_registry?.list?.() || []
+      if (capabilities.length === 0) {
+        return { name: 'capability_deps', category: 'capability', passed: true, message: 'No capabilities registered — nothing to check', fixable: false }
+      }
+
+      const missing_deps: string[] = []
+      for (const cap of capabilities) {
+        const entry = this.capability_registry?.get?.(cap.id) || cap
+        const deps = entry?.manifest?.dependencies || []
+        for (const dep of deps) {
+          try {
+            const { execFileSync } = require('child_process')
+            execFileSync('which', [dep], { stdio: 'pipe', timeout: 3000 })
+          } catch {
+            missing_deps.push(`${cap.name || cap.id}:${dep}`)
+          }
+        }
+      }
+
+      if (missing_deps.length > 0) {
+        return {
+          name: 'capability_deps',
+          category: 'capability',
+          passed: false,
+          message: `Missing capability dependencies: ${missing_deps.join(', ')}`,
+          fixable: true,
+          fix: 'Install missing tools: apt install ' + missing_deps.map(d => d.split(':')[1]).join(' ')
+        }
+      }
+      return { name: 'capability_deps', category: 'capability', passed: true, message: `All ${capabilities.length} capabilities healthy`, fixable: false }
+    } catch (e: any) {
+      return { name: 'capability_deps', category: 'capability', passed: false, message: `Capability check failed: ${e.message}`, fixable: true }
+    }
+  }
 }