feat(manager): add per-step passthrough flags via config

Adds `manager.flags.{discuss,plan,execute}` config keys so users can
configure flags that /gsd:manager passes to each step when dispatching.
For example, `manager.flags.discuss: "--auto --analyze"` makes every
discuss dispatched from the manager include those flags.

Closes #1400

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

tests/init-manager.test.cjs

@@ -413,4 +413,44 @@ describe('init manager', () => {
     // macOS resolves /var → /private/var; normalize both sides
     assert.strictEqual(fs.realpathSync(output.project_root), fs.realpathSync(tmpDir));
   });
+
+  test('output includes manager_flags defaults when not configured', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [{ number: '1', name: 'Test' }]);
+
+    const result = runGsdTools('init manager', tmpDir);
+    const output = JSON.parse(result.output);
+
+    assert.ok(output.manager_flags, 'should include manager_flags');
+    assert.strictEqual(output.manager_flags.discuss, '');
+    assert.strictEqual(output.manager_flags.plan, '');
+    assert.strictEqual(output.manager_flags.execute, '');
+  });
+
+  test('output includes manager_flags from config when set', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [{ number: '1', name: 'Test' }]);
+
+    // Write config with manager flags
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({
+        manager: {
+          flags: {
+            discuss: '--auto --analyze',
+            plan: '--skip-research',
+            execute: '--interactive',
+          }
+        }
+      })
+    );
+
+    const result = runGsdTools('init manager', tmpDir);
+    const output = JSON.parse(result.output);
+
+    assert.ok(output.manager_flags, 'should include manager_flags');
+    assert.strictEqual(output.manager_flags.discuss, '--auto --analyze');
+    assert.strictEqual(output.manager_flags.plan, '--skip-research');
+    assert.strictEqual(output.manager_flags.execute, '--interactive');
+  });
 });