diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index 258e58ea35..6b3980eeea 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -3340,20 +3340,10 @@ export class Config implements McpContext, AgentLoopContext {
     return this.shellExecutionConfig;
   }
 
-  setShellExecutionConfig(config: ShellExecutionConfig): void {
+  setShellExecutionConfig(config: Partial<ShellExecutionConfig>): void {
     this.shellExecutionConfig = {
       ...this.shellExecutionConfig,
-      terminalWidth:
-        config.terminalWidth ?? this.shellExecutionConfig.terminalWidth,
-      terminalHeight:
-        config.terminalHeight ?? this.shellExecutionConfig.terminalHeight,
-      showColor: config.showColor ?? this.shellExecutionConfig.showColor,
-      pager: config.pager ?? this.shellExecutionConfig.pager,
-      sanitizationConfig:
-        config.sanitizationConfig ??
-        this.shellExecutionConfig.sanitizationConfig,
-      sandboxManager:
-        config.sandboxManager ?? this.shellExecutionConfig.sandboxManager,
+      ...config,
     };
   }
   getScreenReader(): boolean {
diff --git a/packages/core/src/config/projectRegistry.test.ts b/packages/core/src/config/projectRegistry.test.ts
index a441de8b3e..4777bcb203 100644
--- a/packages/core/src/config/projectRegistry.test.ts
+++ b/packages/core/src/config/projectRegistry.test.ts
@@ -300,4 +300,36 @@ describe('ProjectRegistry', () => {
       'ProjectRegistry must be initialized before use',
     );
   });
+
+  it('retries on EBUSY during save', async () => {
+    const registry = new ProjectRegistry(registryPath);
+    await registry.initialize();
+
+    const renameSpy = vi.spyOn(fs.promises, 'rename');
+    let ebusyCount = 0;
+
+    renameSpy.mockImplementation(async (oldPath, newPath) => {
+      // Only throw for the specific temporary file generated by save()
+      if (oldPath.toString().includes('.tmp') && ebusyCount < 2) {
+        ebusyCount++;
+        const err = new Error('Resource busy or locked');
+        (err as { code?: string }).code = 'EBUSY';
+        throw err;
+      }
+      return fs.promises
+        .copyFile(oldPath, newPath)
+        .then(() => fs.promises.unlink(oldPath));
+    });
+
+    const projectPath = path.join(tempDir, 'ebusy-project');
+    const shortId = await registry.getShortId(projectPath);
+    expect(shortId).toBe('ebusy-project');
+    expect(ebusyCount).toBe(2);
+
+    // Verify it actually saved properly after retries
+    const data = JSON.parse(fs.readFileSync(registryPath, 'utf8'));
+    expect(data.projects[normalizePath(projectPath)]).toBe('ebusy-project');
+
+    renameSpy.mockRestore();
+  });
 });
diff --git a/packages/core/src/config/projectRegistry.ts b/packages/core/src/config/projectRegistry.ts
index c58fb55ce8..ec9bb92d05 100644
--- a/packages/core/src/config/projectRegistry.ts
+++ b/packages/core/src/config/projectRegistry.ts
@@ -10,6 +10,7 @@ import * as path from 'node:path';
 import * as os from 'node:os';
 import { lock } from 'proper-lockfile';
 import { debugLogger } from '../utils/debugLogger.js';
+import { isNodeError } from '../utils/errors.js';
 
 export interface RegistryData {
   projects: Record<string, string>;
@@ -83,17 +84,48 @@ export class ProjectRegistry {
       await fs.promises.mkdir(dir, { recursive: true });
     }
 
+    const tmpPath = this.registryPath + '.' + randomUUID() + '.tmp';
     try {
       const content = JSON.stringify(data, null, 2);
-      // Use a randomized tmp path to avoid ENOENT crashes when save() is called concurrently
-      const tmpPath = this.registryPath + '.' + randomUUID() + '.tmp';
       await fs.promises.writeFile(tmpPath, content, 'utf8');
-      await fs.promises.rename(tmpPath, this.registryPath);
+
+      // Exponential backoff for OS-level file locks (EBUSY/EPERM) during rename
+      const maxRetries = 5;
+      for (let attempt = 0; attempt < maxRetries; attempt++) {
+        try {
+          await fs.promises.rename(tmpPath, this.registryPath);
+          break; // Success
+        } catch (error: unknown) {
+          const code = isNodeError(error) ? error.code : '';
+
+          if (
+            (code === 'EBUSY' || code === 'EPERM') &&
+            attempt < maxRetries - 1
+          ) {
+            const delayMs = Math.pow(2, attempt) * 50;
+            debugLogger.debug(
+              `Rename failed with ${code}, retrying in ${delayMs}ms (attempt ${attempt + 1}/${maxRetries})...`,
+            );
+            await new Promise((resolve) => setTimeout(resolve, delayMs));
+            continue;
+          }
+          throw error;
+        }
+      }
     } catch (error) {
       debugLogger.error(
         `Failed to save project registry to ${this.registryPath}:`,
         error,
       );
+    } finally {
+      // Clean up the temporary file if it was left behind
+      try {
+        if (fs.existsSync(tmpPath)) {
+          await fs.promises.unlink(tmpPath);
+        }
+      } catch {
+        // Ignore errors during cleanup
+      }
     }
   }