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/doctor/DoctorService.ts

@@ -65,7 +65,6 @@ export class DoctorService {
 
   /**
    * Attempt to fix an issue.
-   * TODO(P8): Implement self-repair logic per DD §16.1.
    * INV-4: dependency installs originate here.
    */
   async fix(check_name: string): Promise<{ ok: boolean; message: string }> {