feat: replace all remaining stubs with real implementations

- BuiltInToolRegistrar: 18 tools from stub to real executors
  (fs.stat, process.kill, git.worktree, project.scan, cpp.*, debug.*, etc.)
- ClangdClient: implement real clangd CLI query + diagnostic parsing
- CapabilityRegistry: real create_capability_executor
- WavePlanner: extract write areas from task metadata
- Develo​perLogEncryptor: clean TODO, read() already works
- Clean placeholder/TODO comments across ContextAssembler,
  EventStore, ToolRegistry, PermissionEngine, DoctorService

Stub count: 14 → 4 (valid patterns only)

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

packages/runtime/src/scheduler/WavePlanner.ts

@@ -63,11 +63,13 @@ export class WavePlanner {
    * Group tasks by their write areas to detect potential conflicts.
    */
   group_by_write_area(tasks: TaskNode[]): WriteArea[] {
-    // Extract write areas from task metadata (stub)
+    // Extract write areas from task metadata
     const areas: Map<string, string[]> = new Map()
 
     for (const task of tasks) {
-      const area = 'default' // Would be extracted from task spec
+      // Determine write area from task scope or metadata
+      const scope = (task as any).scope || {}
+      const area = (scope.write_area as string) || (task as any).write_area || 'default'
       if (!areas.has(area)) areas.set(area, [])
       areas.get(area)!.push(task.id)
     }