fix(init): stop advertising a memory path the runtime ignores (#4392)

ruflo init wrote memory.persistPath: .claude-flow/data into .claude-flow/config.yaml, but getMemoryRoot() only reads the JSON config candidates (claude-flow.config.json and .claude-flow/config.json) and otherwise uses .swarm. The YAML key was dead text: editing it moved nothing and could mislead users into thinking a new store location was active (#3193 part b).\n\nRemove the ignored key and point the YAML at the JSON key that actually controls the store. Add an init regression test that fails on the old YAML and asserts the generated file no longer advertises persistPath.

v3/@claude-flow/cli/__tests__/init-dual-native-2636-2637.test.ts

@@ -82,6 +82,21 @@ describe('native dual initialization (#2636)', () => {
   });
 });
 
+describe('generated runtime config (#3193)', () => {
+  it('does not advertise a memory.persistPath that getMemoryRoot ignores', async () => {
+    const options = structuredClone(MINIMAL_INIT_OPTIONS);
+    options.targetDir = projectPath;
+    options.skipGlobalClaudeMd = true;
+
+    const result = await executeInit(options);
+
+    expect(result.success).toBe(true);
+    const cfg = readFileSync(join(projectPath, '.claude-flow', 'config.yaml'), 'utf8');
+    expect(cfg).not.toMatch(/^\s*persistPath:/m);
+    expect(cfg).toContain('claude-flow.config.json');
+  });
+});
+
 describe('root secret ignore (#2637)', () => {
   it('appends secret/runtime entries without replacing existing project rules', async () => {
     writeFileSync(join(projectPath, '.gitignore'), 'dist/\n', 'utf8');

v3/@claude-flow/cli/src/init/executor.ts

@@ -1587,7 +1587,8 @@ swarm:
 memory:
   backend: ${options.runtime.memoryBackend}
   enableHNSW: ${options.runtime.enableHNSW}
-  persistPath: .claude-flow/data
+  # Store location is read from claude-flow.config.json (memory.persistPath);
+  # this YAML file is runtime/daemon configuration only.
   cacheSize: 100
   # ADR-049: Self-Learning Memory
   learningBridge: