fix(config): Resolve duplicate config loading from home directory (#5090)

Co-authored-by: Allen Hutchison <adh@google.com>
Co-authored-by: Allen Hutchison <allen@hutchison.org>

packages/cli/src/config/config.ts

@@ -4,6 +4,9 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
+import * as fs from 'fs';
+import * as path from 'path';
+import { homedir } from 'node:os';
 import yargs from 'yargs/yargs';
 import { hideBin } from 'yargs/helpers';
 import process from 'node:process';
@@ -244,16 +247,24 @@ export async function loadHierarchicalGeminiMemory(
   memoryImportFormat: 'flat' | 'tree' = 'tree',
   fileFilteringOptions?: FileFilteringOptions,
 ): Promise<{ memoryContent: string; fileCount: number }> {
+  // FIX: Use real, canonical paths for a reliable comparison to handle symlinks.
+  const realCwd = fs.realpathSync(path.resolve(currentWorkingDirectory));
+  const realHome = fs.realpathSync(path.resolve(homedir()));
+  const isHomeDirectory = realCwd === realHome;
+
+  // If it is the home directory, pass an empty string to the core memory
+  // function to signal that it should skip the workspace search.
+  const effectiveCwd = isHomeDirectory ? '' : currentWorkingDirectory;
+
   if (debugMode) {
     logger.debug(
       `CLI: Delegating hierarchical memory load to server for CWD: ${currentWorkingDirectory} (memoryImportFormat: ${memoryImportFormat})`,
     );
   }
 
-  // Directly call the server function.
-  // The server function will use its own homedir() for the global path.
+  // Directly call the server function with the corrected path.
   return loadServerHierarchicalMemory(
-    currentWorkingDirectory,
+    effectiveCwd,
     debugMode,
     fileService,
     extensionContextFilePaths,