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
- DeveloperLogEncryptor: 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>