diff --git a/packages/cli/src/config/config.ts b/packages/cli/src/config/config.ts
index 6d8c10f6..81117dab 100644
--- a/packages/cli/src/config/config.ts
+++ b/packages/cli/src/config/config.ts
@@ -72,6 +72,7 @@ export function loadCliConfig(): Config {
     argv.model || DEFAULT_GEMINI_MODEL,
     argv.target_dir || process.cwd(),
     argv.debug_mode || false,
+    // TODO: load passthroughCommands from .env file
   );
 }
 
diff --git a/packages/cli/src/ui/App.tsx b/packages/cli/src/ui/App.tsx
index cfbc024e..daf7845c 100644
--- a/packages/cli/src/ui/App.tsx
+++ b/packages/cli/src/ui/App.tsx
@@ -32,7 +32,7 @@ export const App = ({ config }: AppProps) => {
   const [history, setHistory] = useState<HistoryItem[]>([]);
   const [startupWarnings, setStartupWarnings] = useState<string[]>([]);
   const { streamingState, submitQuery, initError, debugMessage } =
-    useGeminiStream(setHistory, config.getApiKey(), config.getModel());
+    useGeminiStream(setHistory, config);
   const { elapsedTime, currentLoadingPhrase } =
     useLoadingIndicator(streamingState);
 
diff --git a/packages/cli/src/ui/hooks/useGeminiStream.ts b/packages/cli/src/ui/hooks/useGeminiStream.ts
index 1d839998..1cd9f5d6 100644
--- a/packages/cli/src/ui/hooks/useGeminiStream.ts
+++ b/packages/cli/src/ui/hooks/useGeminiStream.ts
@@ -14,6 +14,7 @@ import {
   getErrorMessage,
   isNodeError,
   ToolResult,
+  Config,
 } from '@gemini-code/server';
 import type { Chat, PartListUnion, FunctionDeclaration } from '@google/genai';
 // Import CLI types
@@ -27,8 +28,6 @@ import { StreamingState } from '../../core/gemini-stream.js';
 // Import CLI tool registry
 import { toolRegistry } from '../../tools/tool-registry.js';
 
-const _allowlistedCommands = ['ls']; // Prefix with underscore since it's unused
-
 const addHistoryItem = (
   setHistory: React.Dispatch<React.SetStateAction<HistoryItem[]>>,
   itemData: Omit<HistoryItem, 'id'>,
@@ -43,8 +42,7 @@ const addHistoryItem = (
 // Hook now accepts apiKey and model
 export const useGeminiStream = (
   setHistory: React.Dispatch<React.SetStateAction<HistoryItem[]>>,
-  apiKey: string,
-  model: string,
+  config: Config,
 ) => {
   const [streamingState, setStreamingState] = useState<StreamingState>(
     StreamingState.Idle,
@@ -62,15 +60,17 @@ export const useGeminiStream = (
     setInitError(null);
     if (!geminiClientRef.current) {
       try {
-        geminiClientRef.current = new GeminiClient(apiKey, model);
+        geminiClientRef.current = new GeminiClient(
+          config.getApiKey(),
+          config.getModel(),
+        );
       } catch (error: unknown) {
         setInitError(
           `Failed to initialize client: ${getErrorMessage(error) || 'Unknown error'}`,
         );
       }
     }
-    // Dependency array includes apiKey and model now
-  }, [apiKey, model]);
+  }, [config.getApiKey(), config.getModel()]);
 
   // Input Handling Effect (remains the same)
   useInput((input, key) => {
@@ -107,6 +107,39 @@ export const useGeminiStream = (
 
       if (typeof query === 'string') {
         setDebugMessage(`User query: ${query}`);
+        const maybeCommand = query.split(/\s+/)[0];
+        if (config.getPassthroughCommands().includes(maybeCommand)) {
+          // Execute and capture output
+          setDebugMessage(`Executing shell command directly: ${query}`);
+          _exec(query, (error, stdout, stderr) => {
+            const timestamp = getNextMessageId(Date.now());
+            if (error) {
+              addHistoryItem(
+                setHistory,
+                { type: 'error', text: error.message },
+                timestamp,
+              );
+            } else if (stderr) {
+              addHistoryItem(
+                setHistory,
+                { type: 'error', text: stderr },
+                timestamp,
+              );
+            } else {
+              // Add stdout as an info message
+              addHistoryItem(
+                setHistory,
+                { type: 'info', text: stdout || '' },
+                timestamp,
+              );
+            }
+            // Set state back to Idle *after* command finishes and output is added
+            setStreamingState(StreamingState.Idle);
+          });
+          // Set state to Responding while the command runs
+          setStreamingState(StreamingState.Responding);
+          return; // Prevent Gemini call
+        }
       }
 
       const userMessageTimestamp = Date.now();
@@ -391,7 +424,8 @@ export const useGeminiStream = (
         }
       } finally {
         abortControllerRef.current = null;
-        // Only set to Idle if not waiting for confirmation
+        // Only set to Idle if not waiting for confirmation.
+        // Passthrough commands handle their own Idle transition.
         if (streamingState !== StreamingState.WaitingForConfirmation) {
           setStreamingState(StreamingState.Idle);
         }
@@ -401,8 +435,8 @@ export const useGeminiStream = (
     [
       streamingState,
       setHistory,
-      apiKey,
-      model,
+      config.getApiKey(),
+      config.getModel(),
       getNextMessageId,
       updateGeminiMessage,
     ],
diff --git a/packages/server/src/config/config.ts b/packages/server/src/config/config.ts
index bd698cf6..fad219b5 100644
--- a/packages/server/src/config/config.ts
+++ b/packages/server/src/config/config.ts
@@ -9,22 +9,28 @@ import * as fs from 'node:fs';
 import * as path from 'node:path';
 import process from 'node:process';
 
+const DEFAULT_PASSTHROUGH_COMMANDS = ['ls', 'git', 'npm'];
+
 export class Config {
   private apiKey: string;
   private model: string;
   private targetDir: string;
   private debugMode: boolean;
+  private passthroughCommands: string[];
 
   constructor(
     apiKey: string,
     model: string,
     targetDir: string,
     debugMode: boolean,
+    passthroughCommands?: string[],
   ) {
     this.apiKey = apiKey;
     this.model = model;
     this.targetDir = targetDir;
     this.debugMode = debugMode;
+    this.passthroughCommands =
+      passthroughCommands || DEFAULT_PASSTHROUGH_COMMANDS;
   }
 
   getApiKey(): string {
@@ -42,6 +48,10 @@ export class Config {
   getDebugMode(): boolean {
     return this.debugMode;
   }
+
+  getPassthroughCommands(): string[] {
+    return this.passthroughCommands;
+  }
 }
 
 function findEnvFile(startDir: string): string | null {
@@ -72,6 +82,13 @@ export function createServerConfig(
   model: string,
   targetDir: string,
   debugMode: boolean,
+  passthroughCommands?: string[],
 ): Config {
-  return new Config(apiKey, model, path.resolve(targetDir), debugMode);
+  return new Config(
+    apiKey,
+    model,
+    path.resolve(targetDir),
+    debugMode,
+    passthroughCommands,
+  );
 }