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/test/regression/tool-stubs.test.ts

@@ -51,8 +51,8 @@ describe('C7: MVP tool registrations', () => {
     }
   })
 
-  it('create_stub_definitions and create_stub_executor exist', () => {
+  it('create_stub_definitions and create_real_executor exist', () => {
     expect(typeof (BuiltInToolRegistrar.prototype as any).create_stub_definitions).toBe('function')
-    expect(typeof (BuiltInToolRegistrar.prototype as any).create_stub_executor).toBe('function')
+    expect(typeof (BuiltInToolRegistrar.prototype as any).create_real_executor).toBe('function')
   })
 })