diff --git a/packages/cli/src/config/config.ts b/packages/cli/src/config/config.ts
index 571d81285..dbc4cd48b 100755
--- a/packages/cli/src/config/config.ts
+++ b/packages/cli/src/config/config.ts
@@ -729,14 +729,7 @@ export async function loadCliConfig(
 
   const includeDirectories = (settings.context?.includeDirectories || [])
     .map(resolvePath)
-    .concat((argv.includeDirectories || []).map(resolvePath))
-    .concat(
-      (
-        ((settings.permissions as Record<string, unknown> | undefined)?.[
-          'additionalDirectories'
-        ] as string[] | undefined) ?? []
-      ).map(resolvePath),
-    );
+    .concat((argv.includeDirectories || []).map(resolvePath));
 
   // LSP configuration: enabled only via --experimental-lsp flag
   const lspEnabled = argv.experimentalLsp === true;
diff --git a/packages/cli/src/config/settingsSchema.ts b/packages/cli/src/config/settingsSchema.ts
index 3bb327424..cfbed07f8 100644
--- a/packages/cli/src/config/settingsSchema.ts
+++ b/packages/cli/src/config/settingsSchema.ts
@@ -835,18 +835,6 @@ const SETTINGS_SCHEMA = {
         showInDialog: false,
         mergeStrategy: MergeStrategy.UNION,
       },
-      additionalDirectories: {
-        type: 'array',
-        label: 'Additional Directories',
-        category: 'Tools',
-        requiresRestart: false,
-        default: [] as string[],
-        description:
-          'Additional directories to include in the workspace context. ' +
-          'Alias for context.includeDirectories. Files in these directories are treated as workspace files.',
-        showInDialog: false,
-        mergeStrategy: MergeStrategy.CONCAT,
-      },
     },
   },
 
diff --git a/packages/core/src/tools/shell.test.ts b/packages/core/src/tools/shell.test.ts
index 552195f9d..1f6af0dec 100644
--- a/packages/core/src/tools/shell.test.ts
+++ b/packages/core/src/tools/shell.test.ts
@@ -957,6 +957,34 @@ describe('ShellTool', () => {
       expect(details.type).toBe('exec');
     });
 
+    it('should exclude read-only sub-commands from confirmation details in compound commands', async () => {
+      // "cd" is read-only, "npm run build" is not
+      const params = {
+        command: 'cd packages/core && npm run build',
+        is_background: false,
+      };
+      const invocation = shellTool.build(params);
+
+      const permission = await invocation.getDefaultPermission();
+      expect(permission).toBe('ask');
+
+      const details = (await invocation.getConfirmationDetails(
+        new AbortController().signal,
+      )) as { rootCommand: string; permissionRules: string[] };
+
+      // rootCommand should only include 'npm', not 'cd'
+      expect(details.rootCommand).not.toContain('cd');
+      expect(details.rootCommand).toContain('npm');
+
+      // permissionRules should not include Bash(cd *)
+      expect(details.permissionRules).not.toContainEqual(
+        expect.stringContaining('cd'),
+      );
+      expect(details.permissionRules).toContainEqual(
+        expect.stringContaining('npm'),
+      );
+    });
+
     it('should throw an error if validation fails', () => {
       expect(() =>
         shellTool.build({ command: '', is_background: false }),
diff --git a/packages/core/src/tools/shell.ts b/packages/core/src/tools/shell.ts
index 117f0b51a..af82103db 100644
--- a/packages/core/src/tools/shell.ts
+++ b/packages/core/src/tools/shell.ts
@@ -33,7 +33,9 @@ import { formatMemoryUsage } from '../utils/formatters.js';
 import type { AnsiOutput } from '../utils/terminalSerializer.js';
 import { isSubpath } from '../utils/paths.js';
 import {
+  getCommandRoot,
   getCommandRoots,
+  splitCommands,
   stripShellWrapper,
   detectCommandSubstitution,
 } from '../utils/shell-utils.js';
@@ -117,20 +119,52 @@ export class ShellToolInvocation extends BaseToolInvocation<
 
   /**
    * Constructs confirmation dialog details for a shell command that needs
-   * user approval.
+   * user approval.  For compound commands (e.g. `cd foo && npm run build`),
+   * sub-commands that are already allowed (read-only) are excluded from both
+   * the displayed root-command list and the suggested permission rules.
    */
   override async getConfirmationDetails(
     _abortSignal: AbortSignal,
   ): Promise<ToolCallConfirmationDetails> {
     const command = stripShellWrapper(this.params.command);
-    const rootCommands = [...new Set(getCommandRoots(command))];
 
-    // Extract minimum-scope permission rules for this command.
+    // Split compound command and filter out already-allowed (read-only) sub-commands
+    const subCommands = splitCommands(command);
+    const nonReadOnlySubCommands: string[] = [];
+    for (const sub of subCommands) {
+      try {
+        const isReadOnly = await isShellCommandReadOnlyAST(sub);
+        if (!isReadOnly) {
+          nonReadOnlySubCommands.push(sub);
+        }
+      } catch {
+        nonReadOnlySubCommands.push(sub); // conservative: include if check fails
+      }
+    }
+
+    // Fallback to all sub-commands if everything was filtered out (shouldn't
+    // normally happen since getDefaultPermission already returned 'ask').
+    const effectiveSubCommands =
+      nonReadOnlySubCommands.length > 0 ? nonReadOnlySubCommands : subCommands;
+
+    const rootCommands = [
+      ...new Set(
+        effectiveSubCommands
+          .map((c) => getCommandRoot(c))
+          .filter((c): c is string => !!c),
+      ),
+    ];
+
+    // Extract minimum-scope permission rules only for sub-commands that
+    // actually need confirmation.
     let permissionRules: string[] = [];
     try {
-      permissionRules = (await extractCommandRules(command)).map(
-        (rule) => `Bash(${rule})`,
-      );
+      const allRules: string[] = [];
+      for (const sub of effectiveSubCommands) {
+        const rules = await extractCommandRules(sub);
+        allRules.push(...rules);
+      }
+      permissionRules = [...new Set(allRules)].map((rule) => `Bash(${rule})`);
     } catch (e) {
       debugLogger.warn('Failed to extract command rules:', e);
     }
diff --git a/packages/vscode-ide-companion/schemas/settings.schema.json b/packages/vscode-ide-companion/schemas/settings.schema.json
index fdf83d3ba..94d1e9fd2 100644
--- a/packages/vscode-ide-companion/schemas/settings.schema.json
+++ b/packages/vscode-ide-companion/schemas/settings.schema.json
@@ -390,13 +390,6 @@
           "items": {
             "type": "string"
           }
-        },
-        "additionalDirectories": {
-          "description": "Additional directories to include in the workspace context. Alias for context.includeDirectories. Files in these directories are treated as workspace files.",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
         }
       }
     },