fix(core): align logging and error handling with strict development rules

Addressed reviewer feedback by replacing process.stderr.write with debugLogger.error in config.ts and using isNodeError in storage.ts to adhere to codebase standards.

packages/core/src/config/config.test.ts

@@ -3423,8 +3423,8 @@ describe('Plans Directory Initialization', () => {
 
   it('should log a warning if the plan directory path is blocked by an existing file (EEXIST) in PLAN mode', async () => {
     const writeSpy = vi
-      .spyOn(process.stderr, 'write')
-      .mockImplementation(() => true);
+      .spyOn(debugLogger, 'error')
+      .mockImplementation(() => {});
     vi.spyOn(fs, 'mkdirSync').mockImplementation(() => {
       const err = new Error('File exists') as NodeJS.ErrnoException;
       err.code = 'EEXIST';
@@ -3449,8 +3449,8 @@ describe('Plans Directory Initialization', () => {
 
   it('should log a warning if mkdirSync fails during getPlansDir (e.g. EACCES) in PLAN mode', async () => {
     const writeSpy = vi
-      .spyOn(process.stderr, 'write')
-      .mockImplementation(() => true);
+      .spyOn(debugLogger, 'error')
+      .mockImplementation(() => {});
     vi.spyOn(fs, 'mkdirSync').mockImplementation(() => {
       const err = new Error('Permission denied') as NodeJS.ErrnoException;
       err.code = 'EACCES';

packages/core/src/config/config.ts

@@ -2275,20 +2275,17 @@ export class Config implements McpContext, AgentLoopContext {
 
         let realPlansDir = plansDir;
         try {
-          const resolved = resolveToRealPath(plansDir);
-          if (resolved) {
-            realPlansDir = resolved;
-          }
+          realPlansDir = resolveToRealPath(plansDir);
         } catch {
           // Ignore failures in mock environments
         }
         this.workspaceContext.addDirectory(realPlansDir);
-        this.initializedPlanDirs.add(plansDir);
       } catch (e: unknown) {
-        const errorMessage = e instanceof Error ? e.message : String(e);
-        process.stderr.write(
-          `Failed to initialize active plan directory at '${plansDir}': ${errorMessage}\n`,
+        debugLogger.error(
+          `Failed to initialize active plan directory at '${plansDir}': ${getErrorMessage(e)}`,
         );
+      } finally {
+        this.initializedPlanDirs.add(plansDir);
       }
     } else if (!this.planEnabled) {
       this.initializedPlanDirs.add(plansDir);

packages/core/src/config/storage.ts

@@ -18,6 +18,7 @@ import {
 } from '../utils/paths.js';
 import { ProjectRegistry } from './projectRegistry.js';
 import { StorageMigration } from './storageMigration.js';
+import { isNodeError } from '../utils/errors.js';
 
 export const OAUTH_FILE = 'oauth_creds.json';
 const TMP_DIR_NAME = 'tmp';
@@ -330,14 +331,7 @@ export class Storage {
       try {
         realResolvedPath = resolveToRealPath(resolvedPath);
       } catch (e: unknown) {
-        if (
-          !(
-            e &&
-            typeof e === 'object' &&
-            'code' in e &&
-            (e.code === 'ENOENT' || e.code === 'EISDIR')
-          )
-        ) {
+        if (!(isNodeError(e) && (e.code === 'ENOENT' || e.code === 'EISDIR'))) {
           throw e;
         }
         // Construct the fallback path safely against the real project root