feat(atlas): enforce 4-phase critical QA with mandatory hands-on verification

Rewrite Atlas GPT verification from a checklist to a 4-phase protocol:
Phase 1 (Read Code First), Phase 2 (Automated Checks), Phase 3 (Hands-On QA),
Phase 4 (Gate Decision). Hands-on QA is now mandatory for user-facing changes,
not 'if applicable'. Hook message reinforces subagent distrust and requires
actually running deliverables before proceeding to next task.

src/cli/run/runner.ts

@@ -91,6 +91,9 @@ export async function run(options: RunOptions): Promise<number> {
         path: { id: sessionID },
         body: {
           agent: resolvedAgent,
+          tools: {
+            question: false,
+          },
           parts: [{ type: "text", text: message }],
         },
         query: { directory },