diff --git a/src-tauri/Cargo.lock b/src-tauri/Cargo.lock
index fd68779..9e26d9b 100644
--- a/src-tauri/Cargo.lock
+++ b/src-tauri/Cargo.lock
@@ -1636,7 +1636,7 @@ checksum = "7f24254aa9a54b5c858eaee2f5bccdb46aaf0e486a595ed5fd8f86ba55232a70"
 
 [[package]]
 name = "hikari-desktop"
-version = "1.2.0"
+version = "1.3.0"
 dependencies = [
  "chrono",
  "dirs 5.0.1",
diff --git a/src/lib/commands/slashCommands.ts b/src/lib/commands/slashCommands.ts
index 90271a0..86b31f8 100644
--- a/src/lib/commands/slashCommands.ts
+++ b/src/lib/commands/slashCommands.ts
@@ -37,6 +37,12 @@ async function changeDirectory(path: string): Promise<void> {
     // Capture conversation history before disconnecting
     const conversationHistory = claudeStore.getConversationHistory();
 
+    // Get currently granted tools and config auto-granted tools
+    const activeConversation = get(conversationsStore.activeConversation);
+    const grantedTools = activeConversation ? Array.from(activeConversation.grantedTools) : [];
+    const config = configStore.getConfig();
+    const allAllowedTools = [...new Set([...grantedTools, ...config.auto_granted_tools])];
+
     await invoke("stop_claude", { conversationId });
 
     // Wait for clean shutdown
@@ -50,12 +56,11 @@ async function changeDirectory(path: string): Promise<void> {
       conversationId,
       options: {
         working_dir: validatedPath,
+        allowed_tools: allAllowedTools,
       },
     });
 
     // Update Discord RPC when reconnecting after directory change
-    const config = configStore.getConfig();
-    const activeConversation = get(conversationsStore.activeConversation);
     if (activeConversation) {
       await updateDiscordRpc(
         activeConversation.name,
diff --git a/src/lib/components/PermissionModal.svelte b/src/lib/components/PermissionModal.svelte
index e96afd5..13f3e45 100644
--- a/src/lib/components/PermissionModal.svelte
+++ b/src/lib/components/PermissionModal.svelte
@@ -1,22 +1,17 @@
 <script lang="ts">
   import { invoke } from "@tauri-apps/api/core";
   import { get } from "svelte/store";
-  import { claudeStore, hasPermissionPending } from "$lib/stores/claude";
+  import { claudeStore } from "$lib/stores/claude";
   import { characterState } from "$lib/stores/character";
   import type { PermissionRequest } from "$lib/types/messages";
   import { updateDiscordRpc } from "$lib/tauri";
   import { conversationsStore } from "$lib/stores/conversations";
   import { configStore } from "$lib/stores/config";
 
-  let isVisible = $state(false);
   let permission: PermissionRequest | null = $state(null);
   let grantedToolsList: string[] = $state([]);
   let workingDirectory = $state("");
 
-  hasPermissionPending.subscribe((pending) => {
-    isVisible = pending;
-  });
-
   claudeStore.pendingPermission.subscribe((perm) => {
     permission = perm;
     if (perm) {
@@ -125,7 +120,7 @@ Please continue where we left off and retry that action now that you have permis
   }
 
   function handleKeydown(event: KeyboardEvent) {
-    if (!isVisible || !permission) return;
+    if (!permission) return;
 
     if (event.key === "Enter") {
       event.preventDefault();
@@ -139,7 +134,7 @@ Please continue where we left off and retry that action now that you have permis
 
 <svelte:window onkeydown={handleKeydown} />
 
-{#if isVisible && permission}
+{#if permission}
   <div
     class="permission-overlay fixed inset-0 bg-black/70 flex items-center justify-center z-50 backdrop-blur-sm"
   >
diff --git a/src/lib/components/StatusBar.svelte b/src/lib/components/StatusBar.svelte
index 1e95ee1..ecf2b36 100644
--- a/src/lib/components/StatusBar.svelte
+++ b/src/lib/components/StatusBar.svelte
@@ -190,6 +190,9 @@
         throw new Error("No active conversation");
       }
       await invoke("stop_claude", { conversationId });
+
+      // Clear granted permissions when user explicitly disconnects
+      claudeStore.revokeAllTools();
     } catch (error) {
       console.error("Failed to stop Claude:", error);
     }