diff --git a/packages/agent-core-v2/src/app/mcpRegistry/mcpRegistryService.ts b/packages/agent-core-v2/src/app/mcpRegistry/mcpRegistryService.ts
index 8b167cb46..c0ceb75e8 100644
--- a/packages/agent-core-v2/src/app/mcpRegistry/mcpRegistryService.ts
+++ b/packages/agent-core-v2/src/app/mcpRegistry/mcpRegistryService.ts
@@ -3,6 +3,7 @@ import { ScopeActivation, registerScopedService } from '#/_base/di/scope';
 
 import { ErrorCodes, Error2 } from '#/errors';
 import { IBootstrapService } from '#/app/bootstrap/bootstrap';
+import { findGitWorkTree } from '#/app/git/workTree';
 import { loadMcpServersDetailed } from '#/app/mcpConfig/configLoader';
 import { IMcpConfigStore } from '#/app/mcpConfig/configStore';
 import { IPluginService } from '#/app/plugin/plugin';
@@ -43,7 +44,8 @@ export class McpRegistryService implements IMcpRegistryService {
         });
       }
     } else {
-      if (!(await readWorkspaceTrust(this.docs, query.cwd))) {
+      const workspaceRoot = (await findGitWorkTree(this.fs, query.cwd))?.root ?? query.cwd;
+      if (!(await readWorkspaceTrust(this.docs, workspaceRoot))) {
         const userEntries = await this.store.list();
         for (const server of userEntries) {
           const { name, ...config } = server;
diff --git a/packages/agent-core-v2/src/mcpCore/oauth/service.ts b/packages/agent-core-v2/src/mcpCore/oauth/service.ts
index c4493ec82..aaa1202a0 100644
--- a/packages/agent-core-v2/src/mcpCore/oauth/service.ts
+++ b/packages/agent-core-v2/src/mcpCore/oauth/service.ts
@@ -474,7 +474,12 @@ export class McpOAuthService {
       now: () => this.scheduler.now(),
       onTokensSaved: (tokens) => {
         this.emit({ type: 'tokens-saved', serverName, serverUrl: canonicalUrl });
-        if (typeof tokens.obtained_at === 'number' && typeof tokens.expires_in === 'number') {
+        if (
+          typeof tokens.obtained_at === 'number' &&
+          typeof tokens.expires_in === 'number' &&
+          typeof tokens.refresh_token === 'string' &&
+          tokens.refresh_token.length > 0
+        ) {
           this.scheduleRefresh(
             serverName,
             canonicalUrl,
diff --git a/packages/agent-core-v2/src/workspace/workspaceTrust/trustRecord.ts b/packages/agent-core-v2/src/workspace/workspaceTrust/trustRecord.ts
index 6c82da784..a917bb1cc 100644
--- a/packages/agent-core-v2/src/workspace/workspaceTrust/trustRecord.ts
+++ b/packages/agent-core-v2/src/workspace/workspaceTrust/trustRecord.ts
@@ -1,4 +1,6 @@
-import { encodeWorkDirKey } from '#/_base/utils/workdir-slug';
+import { normalize } from 'pathe';
+
+import { encodeWorkDirKey, workspaceRootKey } from '#/_base/utils/workdir-slug';
 import type { IAtomicDocumentStore } from '#/persistence/interface/atomicDocumentStore';
 
 const TRUST_SCOPE = 'workspace-trust';
@@ -13,7 +15,7 @@ export async function readWorkspaceTrust(
   root: string,
 ): Promise<boolean> {
   try {
-    return (await docs.get<TrustRecord>(TRUST_SCOPE, encodeWorkDirKey(root))) !== undefined;
+    return (await docs.get<TrustRecord>(TRUST_SCOPE, trustKey(root))) !== undefined;
   } catch {
     return false;
   }
@@ -24,12 +26,16 @@ export function writeWorkspaceTrust(
   root: string,
   trustedAt: number,
 ): Promise<void> {
-  return docs.set(TRUST_SCOPE, encodeWorkDirKey(root), { root, trustedAt });
+  return docs.set(TRUST_SCOPE, trustKey(root), { root, trustedAt });
 }
 
 export function deleteWorkspaceTrust(
   docs: IAtomicDocumentStore,
   root: string,
 ): Promise<void> {
-  return docs.delete(TRUST_SCOPE, encodeWorkDirKey(root));
+  return docs.delete(TRUST_SCOPE, trustKey(root));
+}
+
+function trustKey(root: string): string {
+  return encodeWorkDirKey(workspaceRootKey(normalize(root)));
 }
diff --git a/packages/agent-core-v2/test/app/mcpRegistry/mcpRegistry.test.ts b/packages/agent-core-v2/test/app/mcpRegistry/mcpRegistry.test.ts
index 3f9c0cec7..805cf2ad0 100644
--- a/packages/agent-core-v2/test/app/mcpRegistry/mcpRegistry.test.ts
+++ b/packages/agent-core-v2/test/app/mcpRegistry/mcpRegistry.test.ts
@@ -6,6 +6,7 @@ import { join } from 'pathe';
 import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
 
 import { DisposableStore } from '#/_base/di/lifecycle';
+import { encodeWorkDirKey } from '#/_base/utils/workdir-slug';
 import { createServices } from '#/_base/di/test';
 import { IBootstrapService } from '#/app/bootstrap/bootstrap';
 import {
@@ -49,6 +50,7 @@ describe('McpRegistryService', () => {
   let pluginEntries: PluginMcpServerEntry[];
   let pluginError: Error | undefined;
   let trusted: boolean;
+  let trustedKey: string | undefined;
   let registry: IMcpRegistryService;
 
   beforeEach(() => {
@@ -59,6 +61,7 @@ describe('McpRegistryService', () => {
     pluginEntries = [];
     pluginError = undefined;
     trusted = true;
+    trustedKey = undefined;
     const ix = createServices(disposables, {
       additionalServices: (reg) => {
         reg.defineInstance(IFileSystemStorageService, new InMemoryStorageService());
@@ -72,7 +75,12 @@ describe('McpRegistryService', () => {
         });
         reg.defineInstance(IHostFileSystem, new HostFileSystem());
         reg.definePartialInstance(IAtomicDocumentStore, {
-          get: async <T>() => (trusted ? ({} as T) : undefined),
+          get: async <T>(_scope: string, key: string) => {
+            if (!trusted || (trustedKey !== undefined && key !== encodeWorkDirKey(trustedKey))) {
+              return undefined;
+            }
+            return {} as T;
+          },
         });
         reg.define(IMcpRegistryService, McpRegistryService);
       },
@@ -198,6 +206,18 @@ describe('McpRegistryService', () => {
       ]);
     });
 
+    it('uses the canonical git root when checking trust from a subdirectory', async () => {
+      const { project, sub } = await makeProject();
+      await writeJson(join(project, '.mcp.json'), {
+        mcpServers: { projectOnly: { command: 'project-only' } },
+      });
+      trustedKey = project;
+
+      const entries = await registry.list({ cwd: sub });
+
+      expect(entries.map((entry) => entry.name)).toContain('projectOnly');
+    });
+
     it('exposes plugin servers as read-only entries with their effective config', async () => {
       pluginEntries = [
         pluginEntry('demo', 'finance', {
diff --git a/packages/agent-core-v2/test/mcpCore/oauth/service.test.ts b/packages/agent-core-v2/test/mcpCore/oauth/service.test.ts
index 4a7f8703d..f3a67c893 100644
--- a/packages/agent-core-v2/test/mcpCore/oauth/service.test.ts
+++ b/packages/agent-core-v2/test/mcpCore/oauth/service.test.ts
@@ -762,6 +762,22 @@ describe('McpOAuthService proactive refresh scheduling', () => {
     await fixture.scheduler.advanceBy(10_000);
     expect(refreshSpy).not.toHaveBeenCalled();
   });
+
+  it('does not schedule an expiring grant without a refresh token', async () => {
+    const fixture = makeFixture();
+    cleanups.push(() => fixture.service.dispose());
+    const refreshSpy = vi.spyOn(fixture.service, 'refresh');
+
+    await fixture.service.getProvider(SERVER_NAME, SERVER_URL).saveTokens({
+      access_token: 'a',
+      token_type: 'Bearer',
+      expires_in: 60,
+    });
+
+    await fixture.scheduler.advanceBy(60_000);
+    expect(refreshSpy).not.toHaveBeenCalled();
+    expect(fixture.events.some((event) => event.type === 'refresh-failed')).toBe(false);
+  });
 });
 
 describe('McpOAuthService shutdown', () => {