diff --git a/packages/cli/src/ui/components/messages/ToolConfirmationMessage.tsx b/packages/cli/src/ui/components/messages/ToolConfirmationMessage.tsx
index 9f65f1b9..19ccb466 100644
--- a/packages/cli/src/ui/components/messages/ToolConfirmationMessage.tsx
+++ b/packages/cli/src/ui/components/messages/ToolConfirmationMessage.tsx
@@ -60,11 +60,11 @@ export const ToolConfirmationMessage: React.FC<
     question = `Apply this change?`;
     options.push(
       {
-        label: 'Yes',
+        label: 'Yes, allow once',
         value: ToolConfirmationOutcome.ProceedOnce,
       },
       {
-        label: 'Yes (always allow)',
+        label: 'Yes, allow always', // TODO: this is extreme w/o being qualified by file or directory
         value: ToolConfirmationOutcome.ProceedAlways,
       },
       { label: 'No (esc)', value: ToolConfirmationOutcome.Cancel },
@@ -73,29 +73,22 @@ export const ToolConfirmationMessage: React.FC<
     const executionProps =
       confirmationDetails as ToolExecuteConfirmationDetails;
 
-    // For execution, we still need context display and description
-    const commandDisplay = (
-      <Text color={Colors.AccentCyan}>{executionProps.command}</Text>
-    );
-
-    // Combine command and description into bodyContent for layout consistency
     bodyContent = (
       <Box flexDirection="column">
         <Box paddingX={1} marginLeft={1}>
-          {commandDisplay}
+          <Text color={Colors.AccentCyan}>{executionProps.command}</Text>
         </Box>
       </Box>
     );
 
     question = `Allow execution?`;
-    const alwaysLabel = `Yes (always allow '${executionProps.rootCommand}' commands)`;
     options.push(
       {
-        label: 'Yes',
+        label: 'Yes, allow once',
         value: ToolConfirmationOutcome.ProceedOnce,
       },
       {
-        label: alwaysLabel,
+        label: `Yes, allow always for ${executionProps.rootCommand} ...`,
         value: ToolConfirmationOutcome.ProceedAlways,
       },
       { label: 'No (esc)', value: ToolConfirmationOutcome.Cancel },
diff --git a/packages/server/src/config/config.ts b/packages/server/src/config/config.ts
index 8a49380c..498c7257 100644
--- a/packages/server/src/config/config.ts
+++ b/packages/server/src/config/config.ts
@@ -147,7 +147,7 @@ function createToolRegistry(config: Config): ToolRegistry {
 
   // use ShellTool (next-gen TerminalTool) if environment variable is set
   if (process.env.SHELL_TOOL) {
-    tools.push(new ShellTool(targetDir, config));
+    tools.push(new ShellTool(config));
   } else {
     tools.push(new TerminalTool(targetDir, config));
   }
diff --git a/packages/server/src/tools/shell.ts b/packages/server/src/tools/shell.ts
index 7af6e703..bf4cf810 100644
--- a/packages/server/src/tools/shell.ts
+++ b/packages/server/src/tools/shell.ts
@@ -4,10 +4,15 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import path from 'path';
 import fs from 'fs';
 import { Config } from '../config/config.js';
-import { BaseTool, ToolResult } from './tools.js';
+import {
+  BaseTool,
+  ToolResult,
+  ToolCallConfirmationDetails,
+  ToolExecuteConfirmationDetails,
+  ToolConfirmationOutcome,
+} from './tools.js';
 import toolParameterSchema from './shell.json' with { type: 'json' };
 
 export interface ShellToolParams {
@@ -17,10 +22,11 @@ export interface ShellToolParams {
 
 export class ShellTool extends BaseTool<ShellToolParams, ToolResult> {
   static Name: string = 'execute_bash_command';
-  private readonly rootDirectory: string;
   private readonly config: Config;
+  private cwd: string;
+  private whitelist: Set<string> = new Set();
 
-  constructor(rootDirectory: string, config: Config) {
+  constructor(config: Config) {
     const toolDisplayName = 'Shell';
     const descriptionUrl = new URL('shell.md', import.meta.url);
     const toolDescription = fs.readFileSync(descriptionUrl, 'utf-8');
@@ -31,7 +37,41 @@ export class ShellTool extends BaseTool<ShellToolParams, ToolResult> {
       toolParameterSchema,
     );
     this.config = config;
-    this.rootDirectory = path.resolve(rootDirectory);
+    this.cwd = config.getTargetDir();
+  }
+
+  getDescription(params: ShellToolParams): string {
+    return params.description || `Execute \`${params.command}\` in ${this.cwd}`;
+  }
+
+  validateToolParams(_params: ShellToolParams): string | null {
+    // TODO: validate the command here
+    return null;
+  }
+
+  async shouldConfirmExecute(
+    params: ShellToolParams,
+  ): Promise<ToolCallConfirmationDetails | false> {
+    const rootCommand =
+      params.command
+        .trim()
+        .split(/[\s;&&|]+/)[0]
+        ?.split(/[/\\]/)
+        .pop() || 'unknown';
+    if (this.whitelist.has(rootCommand)) {
+      return false;
+    }
+    const confirmationDetails: ToolExecuteConfirmationDetails = {
+      title: 'Confirm Shell Command',
+      command: params.command,
+      rootCommand,
+      onConfirm: async (outcome: ToolConfirmationOutcome) => {
+        if (outcome === ToolConfirmationOutcome.ProceedAlways) {
+          this.whitelist.add(rootCommand);
+        }
+      },
+    };
+    return confirmationDetails;
   }
 
   async execute(_params: ShellToolParams): Promise<ToolResult> {
diff --git a/packages/server/src/tools/terminal.ts b/packages/server/src/tools/terminal.ts
index 0d5c3d96..64b8e652 100644
--- a/packages/server/src/tools/terminal.ts
+++ b/packages/server/src/tools/terminal.ts
@@ -253,12 +253,10 @@ Use this tool for running build steps (\`npm install\`, \`make\`), linters (\`es
     if (this.shouldAlwaysExecuteCommands.get(rootCommand)) {
       return false;
     }
-    const description = this.getDescription(params);
     const confirmationDetails: ToolExecuteConfirmationDetails = {
       title: 'Confirm Shell Command',
       command: params.command,
       rootCommand,
-      description: `Execute in '${this.currentCwd}':\n${description}`,
       onConfirm: async (outcome: ToolConfirmationOutcome) => {
         if (outcome === ToolConfirmationOutcome.ProceedAlways) {
           this.shouldAlwaysExecuteCommands.set(rootCommand, true);
diff --git a/packages/server/src/tools/tools.ts b/packages/server/src/tools/tools.ts
index ed7c017a..448ea206 100644
--- a/packages/server/src/tools/tools.ts
+++ b/packages/server/src/tools/tools.ts
@@ -181,7 +181,6 @@ export interface ToolExecuteConfirmationDetails
   extends ToolCallConfirmationDetails {
   command: string;
   rootCommand: string;
-  description: string;
 }
 
 export enum ToolConfirmationOutcome {