feat(config): persist config.patch updates atomically

src/cli/setup.ts

@@ -34,7 +34,7 @@ export async function runSetup(configPath: string): Promise<void> {
         const { startDaemon } = await import('../daemon/index.js');
         const { loadConfig } = await import('../config/index.js');
         const config = loadConfig(configPath);
-        const daemon = await startDaemon(config);
+        const daemon = await startDaemon(config, { configPath });
         await new Promise<void>(resolve => daemon.lifecycle.onShutdown(async () => resolve()));
         return;
       }

src/cli/start.ts

@@ -44,7 +44,7 @@ export function registerStartCommand(program: Command): void {
 
       // Dynamic import to avoid loading daemon code for other commands
       const { startDaemon } = await import('../daemon/index.js');
-      const daemon = await startDaemon(config);
+      const daemon = await startDaemon(config, { configPath });
 
       if (config.telegram) {
         console.log(`Allowed Telegram chat IDs: ${config.telegram.allowed_chat_ids.join(', ')}`);

src/config/index.ts

@@ -1,2 +1,3 @@
 export { loadConfig, deepMerge } from './loader.js';
+export { persistConfig } from './persistence.js';
 export { configSchema, MODEL_PROVIDERS, type ModelProvider, type Config, type TelegramConfig, type ModelConfig, type CronJobConfig, type AgentsConfig, type CompactionConfig, type ToolProfile, type ToolOverrideConfig, type ToolsConfig, type SandboxConfig, type AgentConfigEntry, type RoutingConfig, type ServerConfig } from './schema.js';

src/config/persistence.test.ts

@@ -0,0 +1,52 @@
+import { describe, it, expect, afterEach } from 'vitest';
+import { mkdtempSync, readFileSync, rmSync, writeFileSync, existsSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { persistConfig } from './persistence.js';
+import { configSchema } from './schema.js';
+
+const testRoots: string[] = [];
+
+afterEach(() => {
+  while (testRoots.length > 0) {
+    const dir = testRoots.pop();
+    if (!dir) {continue;}
+    try {
+      rmSync(dir, { recursive: true, force: true });
+    } catch {}
+  }
+});
+
+function makeConfig() {
+  return configSchema.parse({
+    telegram: { bot_token: 'test-token', allowed_chat_ids: [1] },
+    models: { default: { provider: 'anthropic', model: 'claude-3' } },
+    hooks: { confirm: ['shell.exec'], log: [], silent: [] },
+  });
+}
+
+describe('persistConfig', () => {
+  it('writes config to target path', () => {
+    const dir = mkdtempSync(join(tmpdir(), 'flynn-config-persist-'));
+    testRoots.push(dir);
+    const configPath = join(dir, 'config.yaml');
+
+    persistConfig(configPath, makeConfig());
+    const written = readFileSync(configPath, 'utf-8');
+    expect(written).toContain('telegram:');
+    expect(written).toContain('models:');
+  });
+
+  it('creates .bak when overwriting existing config', () => {
+    const dir = mkdtempSync(join(tmpdir(), 'flynn-config-persist-'));
+    testRoots.push(dir);
+    const configPath = join(dir, 'config.yaml');
+
+    writeFileSync(configPath, 'legacy: true\n', 'utf-8');
+    persistConfig(configPath, makeConfig());
+
+    const backupPath = `${configPath}.bak`;
+    expect(existsSync(backupPath)).toBe(true);
+    expect(readFileSync(backupPath, 'utf-8')).toContain('legacy: true');
+  });
+});

src/config/persistence.ts

@@ -0,0 +1,26 @@
+import { copyFileSync, existsSync, mkdirSync, renameSync, writeFileSync } from 'fs';
+import { dirname } from 'path';
+import { stringify } from 'yaml';
+import type { Config } from './schema.js';
+
+/**
+ * Persist config atomically:
+ * 1) Backup existing file to <path>.bak
+ * 2) Write new YAML to temp file
+ * 3) Rename temp file into place
+ */
+export function persistConfig(configPath: string, config: Config): void {
+  const dir = dirname(configPath);
+  mkdirSync(dir, { recursive: true });
+
+  const yaml = stringify(config);
+  const tmpPath = `${configPath}.tmp-${process.pid}-${Date.now()}`;
+  const backupPath = `${configPath}.bak`;
+
+  if (existsSync(configPath)) {
+    copyFileSync(configPath, backupPath);
+  }
+
+  writeFileSync(tmpPath, yaml, 'utf-8');
+  renameSync(tmpPath, configPath);
+}

src/daemon/index.ts

@@ -54,7 +54,11 @@ export interface DaemonContext {
   browserManager?: BrowserManager;
 }
 
-export async function startDaemon(config: Config): Promise<DaemonContext> {
+export interface StartDaemonOptions {
+  configPath?: string;
+}
+
+export async function startDaemon(config: Config, options?: StartDaemonOptions): Promise<DaemonContext> {
   // ── Log level ──
   setLogLevel(config.log_level);
 
@@ -144,7 +148,7 @@ export async function startDaemon(config: Config): Promise<DaemonContext> {
   let channelAgents: ReturnType<typeof createMessageRouter>['agents'] | null = null;
 
   const gateway = createGateway({
-    config, sessionManager, modelRouter, systemPrompt, toolRegistry, toolExecutor,
+    config, configPath: options?.configPath, sessionManager, modelRouter, systemPrompt, toolRegistry, toolExecutor,
     channelRegistry, pairingManager, lifecycle, memoryStore,
     getChannelAgents: () => channelAgents, commandRegistry, intentRegistry, routingPolicy,
   });

src/daemon/services.ts

@@ -1,4 +1,5 @@
 import type { Config } from '../config/index.js';
+import { persistConfig } from '../config/index.js';
 import type { Lifecycle } from './lifecycle.js';
 import type { ToolRegistry, ToolExecutor } from '../tools/index.js';
 import type { AgentOrchestrator } from '../backends/index.js';
@@ -279,6 +280,7 @@ export function initPairingManager(config: Config, store?: PairingStore): Pairin
 
 export interface GatewayDeps {
   config: Config;
+  configPath?: string;
   sessionManager: SessionManager;
   modelRouter: ModelRouter;
   systemPrompt: string;
@@ -295,7 +297,7 @@ export interface GatewayDeps {
 }
 
 export function createGateway(deps: GatewayDeps): GatewayServer {
-  const { config, sessionManager, modelRouter, systemPrompt, toolRegistry, toolExecutor, channelRegistry, pairingManager, lifecycle, getChannelAgents } = deps;
+  const { config, configPath, sessionManager, modelRouter, systemPrompt, toolRegistry, toolExecutor, channelRegistry, pairingManager, lifecycle, getChannelAgents } = deps;
 
   const gateway = new GatewayServer({
     port: config.server.port,
@@ -324,6 +326,11 @@ export function createGateway(deps: GatewayDeps): GatewayServer {
     routingPolicy: deps.routingPolicy,
     uiDir: resolve(import.meta.dirname, '../gateway/ui'),
     config,
+    persistConfig: configPath
+      ? async (nextConfig) => {
+        persistConfig(configPath, nextConfig);
+      }
+      : undefined,
     channelRegistry,
     pairingManager,
     memoryStore: deps.memoryStore,

src/gateway/handlers/config.ts

@@ -4,6 +4,7 @@ import type { Config } from '../../config/index.js';
 
 export interface ConfigHandlerDeps {
   config: Config;
+  persistConfig?: (nextConfig: Config) => Promise<void> | void;
 }
 
 /**
@@ -140,6 +141,7 @@ export function createConfigHandlers(deps: ConfigHandlerDeps) {
 
       const applied: string[] = [];
       const rejected: string[] = [];
+      const draft = JSON.parse(JSON.stringify(deps.config)) as Config;
 
       for (const [key, value] of Object.entries(patches as Record<string, unknown>)) {
         const patcher = PATCHABLE_KEYS[key];
@@ -147,7 +149,7 @@ export function createConfigHandlers(deps: ConfigHandlerDeps) {
           rejected.push(key);
           continue;
         }
-        const ok = patcher(deps.config, value);
+        const ok = patcher(draft, value);
         if (ok) {
           applied.push(key);
         } else {
@@ -155,7 +157,30 @@ export function createConfigHandlers(deps: ConfigHandlerDeps) {
         }
       }
 
-      return makeResponse(request.id, { applied, rejected });
+      if (applied.length === 0) {
+        return makeResponse(request.id, { applied, rejected, persisted: false });
+      }
+
+      if (deps.persistConfig) {
+        try {
+          await deps.persistConfig(draft);
+        } catch (err) {
+          return makeResponse(request.id, {
+            applied: [],
+            rejected,
+            persisted: false,
+            persistError: err instanceof Error ? err.message : String(err),
+          });
+        }
+      }
+
+      // Update in-memory runtime config only after a successful persist (or when persistence is not configured).
+      for (const key of Object.keys(deps.config)) {
+        delete (deps.config as Record<string, unknown>)[key];
+      }
+      Object.assign(deps.config as Record<string, unknown>, draft as Record<string, unknown>);
+
+      return makeResponse(request.id, { applied, rejected, persisted: Boolean(deps.persistConfig) });
     },
   };
 }

src/gateway/handlers/handlers.test.ts

@@ -718,9 +718,10 @@ describe('config handlers', () => {
     };
     const result = await handlers['config.patch'](req) as GatewayResponse;
 
-    const r = result.result as { applied: string[]; rejected: string[] };
+    const r = result.result as { applied: string[]; rejected: string[]; persisted: boolean };
     expect(r.applied).toEqual(['hooks.confirm', 'hooks.log']);
     expect(r.rejected).toEqual([]);
+    expect(r.persisted).toBe(false);
     // Verify the config was actually mutated
     expect(config.hooks.confirm).toEqual(['shell.exec', 'file.write']);
     expect(config.hooks.log).toEqual(['file.read']);
@@ -741,9 +742,10 @@ describe('config handlers', () => {
     };
     const result = await handlers['config.patch'](req) as GatewayResponse;
 
-    const r = result.result as { applied: string[]; rejected: string[] };
+    const r = result.result as { applied: string[]; rejected: string[]; persisted: boolean };
     expect(r.applied).toEqual(['hooks.confirm']);
     expect(r.rejected).toEqual(['telegram.bot_token']);
+    expect(r.persisted).toBe(false);
   });
 
   it('config.patch rejects invalid value types', async () => {
@@ -760,9 +762,49 @@ describe('config handlers', () => {
     };
     const result = await handlers['config.patch'](req) as GatewayResponse;
 
-    const r = result.result as { applied: string[]; rejected: string[] };
+    const r = result.result as { applied: string[]; rejected: string[]; persisted: boolean };
     expect(r.applied).toEqual([]);
     expect(r.rejected).toEqual(['hooks.confirm']);
+    expect(r.persisted).toBe(false);
+  });
+
+  it('config.patch persists changes when persistence callback is provided', async () => {
+    const config = makeConfig();
+    const persist = vi.fn();
+    const handlers = createConfigHandlers({ config: config as any, persistConfig: persist as any });
+    const req: GatewayRequest = {
+      id: 6,
+      method: 'config.patch',
+      params: { patches: { 'hooks.confirm': ['shell.exec', 'file.write'] } },
+    };
+    const result = await handlers['config.patch'](req) as GatewayResponse;
+    const r = result.result as { applied: string[]; rejected: string[]; persisted: boolean };
+
+    expect(r.applied).toEqual(['hooks.confirm']);
+    expect(r.rejected).toEqual([]);
+    expect(r.persisted).toBe(true);
+    expect(persist).toHaveBeenCalledTimes(1);
+    expect(config.hooks.confirm).toEqual(['shell.exec', 'file.write']);
+  });
+
+  it('config.patch does not mutate runtime config when persistence fails', async () => {
+    const config = makeConfig();
+    const before = [...config.hooks.confirm];
+    const persist = vi.fn().mockRejectedValue(new Error('disk full'));
+    const handlers = createConfigHandlers({ config: config as any, persistConfig: persist as any });
+    const req: GatewayRequest = {
+      id: 7,
+      method: 'config.patch',
+      params: { patches: { 'hooks.confirm': ['file.write'] } },
+    };
+    const result = await handlers['config.patch'](req) as GatewayResponse;
+    const r = result.result as { applied: string[]; rejected: string[]; persisted: boolean; persistError?: string };
+
+    expect(r.applied).toEqual([]);
+    expect(r.rejected).toEqual([]);
+    expect(r.persisted).toBe(false);
+    expect(r.persistError).toContain('disk full');
+    expect(config.hooks.confirm).toEqual(before);
   });
 
   it('config.patch requires patches object', async () => {

src/gateway/server.ts

@@ -59,6 +59,8 @@ export interface GatewayServerConfig {
   authHttp?: boolean;
   uiDir?: string;
   config?: Config;
+  /** Optional persistence callback for config.patch updates. */
+  persistConfig?: (nextConfig: Config) => Promise<void> | void;
   /** Optional callback for system.restart. Should trigger graceful shutdown + process restart. */
   restart?: () => Promise<void>;
   channelRegistry?: ChannelRegistry;
@@ -193,7 +195,10 @@ export class GatewayServer {
 
     // Config handlers (only if config object is provided)
     if (this.config.config) {
-      const configHandlers = createConfigHandlers({ config: this.config.config });
+      const configHandlers = createConfigHandlers({
+        config: this.config.config,
+        persistConfig: this.config.persistConfig,
+      });
       for (const [method, handler] of Object.entries(configHandlers)) {
         this.router.register(method, handler);
       }

src/gateway/ui/pages/settings.js

@@ -155,10 +155,18 @@ async function saveHooks() {
 
     const applied = result.applied ?? [];
     const rejected = result.rejected ?? [];
+    const persisted = result.persisted === true;
+    const persistError = result.persistError;
 
     if (rejected.length > 0) {
       status.textContent = `Partially saved. Rejected: ${rejected.join(', ')}`;
       status.className = 'text-sm text-error';
+    } else if (persistError) {
+      status.textContent = `Save failed: ${persistError}`;
+      status.className = 'text-sm text-error';
+    } else if (!persisted) {
+      status.textContent = `Saved in runtime only (${applied.length} updated)`;
+      status.className = 'text-sm text-muted';
     } else {
       status.textContent = `Saved (${applied.length} updated)`;
       status.className = 'text-sm text-success';