diff --git a/apps/desktop/src/main/lib/agent-setup.ts b/apps/desktop/src/main/lib/agent-setup.ts
deleted file mode 100644
index 2e22ec83e40..00000000000
--- a/apps/desktop/src/main/lib/agent-setup.ts
+++ /dev/null
@@ -1,250 +0,0 @@
-import { execSync } from "node:child_process";
-import fs from "node:fs";
-import os from "node:os";
-import path from "node:path";
-import { PORTS, SUPERSET_DIR_NAME, SUPERSET_DIR_NAMES } from "shared/constants";
-import { SUPERSET_HOME_DIR } from "./app-environment";
-
-const BIN_DIR = path.join(SUPERSET_HOME_DIR, "bin");
-const HOOKS_DIR = path.join(SUPERSET_HOME_DIR, "hooks");
-const ZSH_DIR = path.join(SUPERSET_HOME_DIR, "zsh");
-const BASH_DIR = path.join(SUPERSET_HOME_DIR, "bash");
-
-/**
- * Finds the real path of a binary, skipping our wrapper scripts.
- * Filters out both dev and prod superset bin directories
- * to avoid wrapper scripts calling each other.
- */
-function findRealBinary(name: string): string | null {
-	try {
-		// Get all paths, filter out both dev and prod superset bin dirs
-		const result = execSync(`which -a ${name} 2>/dev/null || true`, {
-			encoding: "utf-8",
-		});
-		const homedir = os.homedir();
-		const supersetBinDirs = [
-			path.join(homedir, SUPERSET_DIR_NAMES.PROD, "bin"),
-			path.join(homedir, SUPERSET_DIR_NAMES.DEV, "bin"),
-		];
-		const paths = result
-			.trim()
-			.split("\n")
-			.filter((p) => p && !supersetBinDirs.some((dir) => p.startsWith(dir)));
-		return paths[0] || null;
-	} catch {
-		return null;
-	}
-}
-
-/**
- * Creates the notify.sh script
- */
-function createNotifyScript(): void {
-	const notifyPath = path.join(HOOKS_DIR, "notify.sh");
-	const script = `#!/bin/bash
-# Superset agent notification hook
-# Called by CLI agents (Claude Code, Codex, etc.) when they complete or need input
-
-# Only run if inside a Superset terminal
-[ -z "$SUPERSET_TAB_ID" ] && exit 0
-
-# Get JSON input - Codex passes as argument, Claude pipes to stdin
-if [ -n "$1" ]; then
-  INPUT="$1"
-else
-  INPUT=$(cat)
-fi
-
-# Extract event type - Claude uses "hook_event_name", Codex uses "type"
-EVENT_TYPE=$(echo "$INPUT" | grep -o '"hook_event_name":"[^"]*"' | cut -d'"' -f4)
-if [ -z "$EVENT_TYPE" ]; then
-  # Check for Codex "type" field (e.g., "agent-turn-complete")
-  CODEX_TYPE=$(echo "$INPUT" | grep -o '"type":"[^"]*"' | cut -d'"' -f4)
-  if [ "$CODEX_TYPE" = "agent-turn-complete" ]; then
-    EVENT_TYPE="Stop"
-  fi
-fi
-
-# Default to "Stop" if not found
-[ -z "$EVENT_TYPE" ] && EVENT_TYPE="Stop"
-
-curl -sG "http://127.0.0.1:\${SUPERSET_PORT:-${PORTS.NOTIFICATIONS}}/hook/complete" \\
-  --data-urlencode "paneId=$SUPERSET_PANE_ID" \\
-  --data-urlencode "tabId=$SUPERSET_TAB_ID" \\
-  --data-urlencode "workspaceId=$SUPERSET_WORKSPACE_ID" \\
-  --data-urlencode "eventType=$EVENT_TYPE" \\
-  > /dev/null 2>&1
-`;
-	fs.writeFileSync(notifyPath, script, { mode: 0o755 });
-}
-
-/**
- * Creates wrapper script for Claude Code
- */
-function createClaudeWrapper(): void {
-	const wrapperPath = path.join(BIN_DIR, "claude");
-	const realClaude = findRealBinary("claude");
-
-	if (!realClaude) {
-		console.log("[agent-setup] Claude not found, skipping wrapper");
-		return;
-	}
-
-	// Use $HOME instead of ~ because tilde doesn't expand inside JSON strings.
-	// Using ~ causes Claude Code's file watcher to malfunction and watch TMPDIR.
-	const script = `#!/bin/bash
-# Superset wrapper for Claude Code
-# Injects notification hook settings
-
-NOTIFY_SCRIPT="$HOME/${SUPERSET_DIR_NAME}/hooks/notify.sh"
-SUPERSET_CLAUDE_SETTINGS="{\\"hooks\\":{\\"Stop\\":[{\\"hooks\\":[{\\"type\\":\\"command\\",\\"command\\":\\"$NOTIFY_SCRIPT\\"}]}],\\"PermissionRequest\\":[{\\"matcher\\":\\"*\\",\\"hooks\\":[{\\"type\\":\\"command\\",\\"command\\":\\"$NOTIFY_SCRIPT\\"}]}]}}"
-
-exec "${realClaude}" --settings "$SUPERSET_CLAUDE_SETTINGS" "$@"
-`;
-	fs.writeFileSync(wrapperPath, script, { mode: 0o755 });
-	console.log(`[agent-setup] Created Claude wrapper -> ${realClaude}`);
-}
-
-/**
- * Creates wrapper script for Codex
- */
-function createCodexWrapper(): void {
-	const wrapperPath = path.join(BIN_DIR, "codex");
-	const realCodex = findRealBinary("codex");
-
-	if (!realCodex) {
-		console.log("[agent-setup] Codex not found, skipping wrapper");
-		return;
-	}
-
-	const notifyPath = path.join(HOOKS_DIR, "notify.sh");
-	const script = `#!/bin/bash
-# Superset wrapper for Codex
-# Injects notification hook settings
-
-exec "${realCodex}" -c 'notify=["bash","${notifyPath}"]' "$@"
-`;
-	fs.writeFileSync(wrapperPath, script, { mode: 0o755 });
-	console.log(`[agent-setup] Created Codex wrapper -> ${realCodex}`);
-}
-
-/**
- * Creates zsh initialization wrapper that intercepts shell startup
- * Sources user's real shell config files then prepends our bin to PATH
- */
-function createZshWrapper(): void {
-	// Create .zprofile to source user's .zprofile (runs for login shells before .zshrc)
-	// This is critical - without it, brew/nvm PATH setup in ~/.zprofile is skipped
-	// Don't change ZDOTDIR here - we need our .zshrc to run after this
-	const zprofilePath = path.join(ZSH_DIR, ".zprofile");
-	const zprofileScript = `# Superset zsh profile wrapper
-_superset_home="\${SUPERSET_ORIG_ZDOTDIR:-$HOME}"
-[[ -f "$_superset_home/.zprofile" ]] && source "$_superset_home/.zprofile"
-`;
-	fs.writeFileSync(zprofilePath, zprofileScript, { mode: 0o644 });
-
-	// Create .zshrc - reset ZDOTDIR before sourcing so Oh My Zsh works correctly
-	const zshrcPath = path.join(ZSH_DIR, ".zshrc");
-	const zshrcScript = `# Superset zsh rc wrapper
-_superset_home="\${SUPERSET_ORIG_ZDOTDIR:-$HOME}"
-export ZDOTDIR="$_superset_home"
-[[ -f "$_superset_home/.zshrc" ]] && source "$_superset_home/.zshrc"
-export PATH="$HOME/${SUPERSET_DIR_NAME}/bin:$PATH"
-`;
-	fs.writeFileSync(zshrcPath, zshrcScript, { mode: 0o644 });
-	console.log("[agent-setup] Created zsh wrapper");
-}
-
-/**
- * Creates bash initialization wrapper that intercepts shell startup
- * Sources user's real bashrc/profile then prepends our bin to PATH
- */
-function createBashWrapper(): void {
-	const rcfilePath = path.join(BASH_DIR, "rcfile");
-	const script = `# Superset bash rcfile wrapper
-
-# Source system profile
-[[ -f /etc/profile ]] && source /etc/profile
-
-# Source user's login profile
-if [[ -f "$HOME/.bash_profile" ]]; then
-  source "$HOME/.bash_profile"
-elif [[ -f "$HOME/.bash_login" ]]; then
-  source "$HOME/.bash_login"
-elif [[ -f "$HOME/.profile" ]]; then
-  source "$HOME/.profile"
-fi
-
-# Source bashrc if separate
-[[ -f "$HOME/.bashrc" ]] && source "$HOME/.bashrc"
-
-# Prepend superset bin to PATH
-export PATH="$HOME/${SUPERSET_DIR_NAME}/bin:$PATH"
-# Minimal prompt (path/env shown in toolbar) - emerald to match app theme
-export PS1=$'\\[\\e[1;38;2;52;211;153m\\]❯\\[\\e[0m\\] '
-`;
-	fs.writeFileSync(rcfilePath, script, { mode: 0o644 });
-	console.log("[agent-setup] Created bash wrapper");
-}
-
-/**
- * Sets up the ~/.superset directory structure and agent wrappers
- * Called on app startup
- */
-export function setupAgentHooks(): void {
-	console.log("[agent-setup] Initializing agent hooks...");
-
-	// Create directories
-	fs.mkdirSync(BIN_DIR, { recursive: true });
-	fs.mkdirSync(HOOKS_DIR, { recursive: true });
-	fs.mkdirSync(ZSH_DIR, { recursive: true });
-	fs.mkdirSync(BASH_DIR, { recursive: true });
-
-	// Create scripts
-	createNotifyScript();
-	createClaudeWrapper();
-	createCodexWrapper();
-
-	// Create shell initialization wrappers
-	createZshWrapper();
-	createBashWrapper();
-
-	console.log("[agent-setup] Agent hooks initialized");
-}
-
-/**
- * Returns shell-specific environment variables for intercepting shell initialization
- */
-export function getShellEnv(shell: string): Record<string, string> {
-	if (shell.includes("zsh")) {
-		return {
-			SUPERSET_ORIG_ZDOTDIR: process.env.ZDOTDIR || os.homedir(),
-			ZDOTDIR: ZSH_DIR,
-		};
-	}
-	// Bash doesn't need special env vars - we use --rcfile instead
-	return {};
-}
-
-/**
- * Returns shell-specific arguments for intercepting shell initialization
- */
-export function getShellArgs(shell: string): string[] {
-	if (shell.includes("zsh")) {
-		// Zsh uses ZDOTDIR env var, no special args needed
-		// -l for login shell behavior
-		return ["-l"];
-	}
-	if (shell.includes("bash")) {
-		// Use our custom rcfile that sources user's files then fixes PATH
-		return ["--rcfile", path.join(BASH_DIR, "rcfile")];
-	}
-	return [];
-}
-
-/**
- * Returns the bin directory path
- */
-export function getSupersetBinDir(): string {
-	return BIN_DIR;
-}
diff --git a/apps/desktop/src/main/lib/agent-setup/agent-wrappers.ts b/apps/desktop/src/main/lib/agent-setup/agent-wrappers.ts
new file mode 100644
index 00000000000..8f9155845b0
--- /dev/null
+++ b/apps/desktop/src/main/lib/agent-setup/agent-wrappers.ts
@@ -0,0 +1,71 @@
+import fs from "node:fs";
+import path from "node:path";
+import { BIN_DIR, HOOKS_DIR } from "./paths";
+import { findRealBinary } from "./utils";
+
+/**
+ * Creates the Claude Code settings JSON file with notification hooks
+ */
+function createClaudeSettings(): string {
+	const settingsPath = path.join(HOOKS_DIR, "claude-settings.json");
+	const notifyPath = path.join(HOOKS_DIR, "notify.sh");
+
+	const settings = {
+		hooks: {
+			Stop: [{ hooks: [{ type: "command", command: notifyPath }] }],
+			PermissionRequest: [
+				{ matcher: "*", hooks: [{ type: "command", command: notifyPath }] },
+			],
+		},
+	};
+
+	fs.writeFileSync(settingsPath, JSON.stringify(settings), { mode: 0o644 });
+	return settingsPath;
+}
+
+/**
+ * Creates wrapper script for Claude Code
+ */
+export function createClaudeWrapper(): void {
+	const wrapperPath = path.join(BIN_DIR, "claude");
+	const realClaude = findRealBinary("claude");
+
+	if (!realClaude) {
+		console.log("[agent-setup] Claude not found, skipping wrapper");
+		return;
+	}
+
+	const settingsPath = createClaudeSettings();
+
+	const script = `#!/bin/bash
+# Superset wrapper for Claude Code
+# Injects notification hook settings
+
+exec "${realClaude}" --settings "${settingsPath}" "$@"
+`;
+	fs.writeFileSync(wrapperPath, script, { mode: 0o755 });
+	console.log(`[agent-setup] Created Claude wrapper -> ${realClaude}`);
+}
+
+/**
+ * Creates wrapper script for Codex
+ */
+export function createCodexWrapper(): void {
+	const wrapperPath = path.join(BIN_DIR, "codex");
+	const realCodex = findRealBinary("codex");
+
+	if (!realCodex) {
+		console.log("[agent-setup] Codex not found, skipping wrapper");
+		return;
+	}
+
+	const notifyPath = path.join(HOOKS_DIR, "notify.sh");
+	const script = `#!/bin/bash
+# Superset wrapper for Codex
+# Injects notification hook settings
+
+exec "${realCodex}" -c 'notify=["bash","${notifyPath}"]' "$@"
+`;
+	fs.writeFileSync(wrapperPath, script, { mode: 0o755 });
+	console.log(`[agent-setup] Created Codex wrapper -> ${realCodex}`);
+}
diff --git a/apps/desktop/src/main/lib/agent-setup/index.ts b/apps/desktop/src/main/lib/agent-setup/index.ts
new file mode 100644
index 00000000000..8bab19b4045
--- /dev/null
+++ b/apps/desktop/src/main/lib/agent-setup/index.ts
@@ -0,0 +1,45 @@
+import fs from "node:fs";
+import { createClaudeWrapper, createCodexWrapper } from "./agent-wrappers";
+import { createNotifyScript } from "./notify-hook";
+import { BASH_DIR, BIN_DIR, HOOKS_DIR, ZSH_DIR } from "./paths";
+import {
+	createBashWrapper,
+	createZshWrapper,
+	getShellArgs,
+	getShellEnv,
+} from "./shell-wrappers";
+
+/**
+ * Sets up the ~/.superset directory structure and agent wrappers
+ * Called on app startup
+ */
+export function setupAgentHooks(): void {
+	console.log("[agent-setup] Initializing agent hooks...");
+
+	// Create directories
+	fs.mkdirSync(BIN_DIR, { recursive: true });
+	fs.mkdirSync(HOOKS_DIR, { recursive: true });
+	fs.mkdirSync(ZSH_DIR, { recursive: true });
+	fs.mkdirSync(BASH_DIR, { recursive: true });
+
+	// Create scripts
+	createNotifyScript();
+	createClaudeWrapper();
+	createCodexWrapper();
+
+	// Create shell initialization wrappers
+	createZshWrapper();
+	createBashWrapper();
+
+	console.log("[agent-setup] Agent hooks initialized");
+}
+
+/**
+ * Returns the bin directory path
+ */
+export function getSupersetBinDir(): string {
+	return BIN_DIR;
+}
+
+// Re-export shell utilities for terminal usage
+export { getShellArgs, getShellEnv };
diff --git a/apps/desktop/src/main/lib/agent-setup/notify-hook.ts b/apps/desktop/src/main/lib/agent-setup/notify-hook.ts
new file mode 100644
index 00000000000..98b1a37f928
--- /dev/null
+++ b/apps/desktop/src/main/lib/agent-setup/notify-hook.ts
@@ -0,0 +1,46 @@
+import fs from "node:fs";
+import path from "node:path";
+import { PORTS } from "shared/constants";
+import { HOOKS_DIR } from "./paths";
+
+/**
+ * Creates the notify.sh script
+ */
+export function createNotifyScript(): void {
+	const notifyPath = path.join(HOOKS_DIR, "notify.sh");
+	const script = `#!/bin/bash
+# Superset agent notification hook
+# Called by CLI agents (Claude Code, Codex, etc.) when they complete or need input
+
+# Only run if inside a Superset terminal
+[ -z "$SUPERSET_TAB_ID" ] && exit 0
+
+# Get JSON input - Codex passes as argument, Claude pipes to stdin
+if [ -n "$1" ]; then
+  INPUT="$1"
+else
+  INPUT=$(cat)
+fi
+
+# Extract event type - Claude uses "hook_event_name", Codex uses "type"
+EVENT_TYPE=$(echo "$INPUT" | grep -o '"hook_event_name":"[^"]*"' | cut -d'"' -f4)
+if [ -z "$EVENT_TYPE" ]; then
+  # Check for Codex "type" field (e.g., "agent-turn-complete")
+  CODEX_TYPE=$(echo "$INPUT" | grep -o '"type":"[^"]*"' | cut -d'"' -f4)
+  if [ "$CODEX_TYPE" = "agent-turn-complete" ]; then
+    EVENT_TYPE="Stop"
+  fi
+fi
+
+# Default to "Stop" if not found
+[ -z "$EVENT_TYPE" ] && EVENT_TYPE="Stop"
+
+curl -sG "http://127.0.0.1:\${SUPERSET_PORT:-${PORTS.NOTIFICATIONS}}/hook/complete" \\
+  --data-urlencode "paneId=$SUPERSET_PANE_ID" \\
+  --data-urlencode "tabId=$SUPERSET_TAB_ID" \\
+  --data-urlencode "workspaceId=$SUPERSET_WORKSPACE_ID" \\
+  --data-urlencode "eventType=$EVENT_TYPE" \\
+  > /dev/null 2>&1
+`;
+	fs.writeFileSync(notifyPath, script, { mode: 0o755 });
+}
diff --git a/apps/desktop/src/main/lib/agent-setup/paths.ts b/apps/desktop/src/main/lib/agent-setup/paths.ts
new file mode 100644
index 00000000000..0d8619a22fe
--- /dev/null
+++ b/apps/desktop/src/main/lib/agent-setup/paths.ts
@@ -0,0 +1,7 @@
+import path from "node:path";
+import { SUPERSET_HOME_DIR } from "../app-environment";
+
+export const BIN_DIR = path.join(SUPERSET_HOME_DIR, "bin");
+export const HOOKS_DIR = path.join(SUPERSET_HOME_DIR, "hooks");
+export const ZSH_DIR = path.join(SUPERSET_HOME_DIR, "zsh");
+export const BASH_DIR = path.join(SUPERSET_HOME_DIR, "bash");
diff --git a/apps/desktop/src/main/lib/agent-setup/shell-wrappers.ts b/apps/desktop/src/main/lib/agent-setup/shell-wrappers.ts
new file mode 100644
index 00000000000..f440e96e6e8
--- /dev/null
+++ b/apps/desktop/src/main/lib/agent-setup/shell-wrappers.ts
@@ -0,0 +1,94 @@
+import fs from "node:fs";
+import os from "node:os";
+import path from "node:path";
+import { SUPERSET_DIR_NAME } from "shared/constants";
+import { BASH_DIR, ZSH_DIR } from "./paths";
+
+/**
+ * Creates zsh initialization wrapper that intercepts shell startup
+ * Sources user's real shell config files then prepends our bin to PATH
+ */
+export function createZshWrapper(): void {
+	// Create .zprofile to source user's .zprofile (runs for login shells before .zshrc)
+	// This is critical - without it, brew/nvm PATH setup in ~/.zprofile is skipped
+	// Don't change ZDOTDIR here - we need our .zshrc to run after this
+	const zprofilePath = path.join(ZSH_DIR, ".zprofile");
+	const zprofileScript = `# Superset zsh profile wrapper
+_superset_home="\${SUPERSET_ORIG_ZDOTDIR:-$HOME}"
+[[ -f "$_superset_home/.zprofile" ]] && source "$_superset_home/.zprofile"
+`;
+	fs.writeFileSync(zprofilePath, zprofileScript, { mode: 0o644 });
+
+	// Create .zshrc - reset ZDOTDIR before sourcing so Oh My Zsh works correctly
+	const zshrcPath = path.join(ZSH_DIR, ".zshrc");
+	const zshrcScript = `# Superset zsh rc wrapper
+_superset_home="\${SUPERSET_ORIG_ZDOTDIR:-$HOME}"
+export ZDOTDIR="$_superset_home"
+[[ -f "$_superset_home/.zshrc" ]] && source "$_superset_home/.zshrc"
+export PATH="$HOME/${SUPERSET_DIR_NAME}/bin:$PATH"
+`;
+	fs.writeFileSync(zshrcPath, zshrcScript, { mode: 0o644 });
+	console.log("[agent-setup] Created zsh wrapper");
+}
+
+/**
+ * Creates bash initialization wrapper that intercepts shell startup
+ * Sources user's real bashrc/profile then prepends our bin to PATH
+ */
+export function createBashWrapper(): void {
+	const rcfilePath = path.join(BASH_DIR, "rcfile");
+	const script = `# Superset bash rcfile wrapper
+
+# Source system profile
+[[ -f /etc/profile ]] && source /etc/profile
+
+# Source user's login profile
+if [[ -f "$HOME/.bash_profile" ]]; then
+  source "$HOME/.bash_profile"
+elif [[ -f "$HOME/.bash_login" ]]; then
+  source "$HOME/.bash_login"
+elif [[ -f "$HOME/.profile" ]]; then
+  source "$HOME/.profile"
+fi
+
+# Source bashrc if separate
+[[ -f "$HOME/.bashrc" ]] && source "$HOME/.bashrc"
+
+# Prepend superset bin to PATH
+export PATH="$HOME/${SUPERSET_DIR_NAME}/bin:$PATH"
+# Minimal prompt (path/env shown in toolbar) - emerald to match app theme
+export PS1=$'\\[\\e[1;38;2;52;211;153m\\]❯\\[\\e[0m\\] '
+`;
+	fs.writeFileSync(rcfilePath, script, { mode: 0o644 });
+	console.log("[agent-setup] Created bash wrapper");
+}
+
+/**
+ * Returns shell-specific environment variables for intercepting shell initialization
+ */
+export function getShellEnv(shell: string): Record<string, string> {
+	if (shell.includes("zsh")) {
+		return {
+			SUPERSET_ORIG_ZDOTDIR: process.env.ZDOTDIR || os.homedir(),
+			ZDOTDIR: ZSH_DIR,
+		};
+	}
+	// Bash doesn't need special env vars - we use --rcfile instead
+	return {};
+}
+
+/**
+ * Returns shell-specific arguments for intercepting shell initialization
+ */
+export function getShellArgs(shell: string): string[] {
+	if (shell.includes("zsh")) {
+		// Zsh uses ZDOTDIR env var, no special args needed
+		// -l for login shell behavior
+		return ["-l"];
+	}
+	if (shell.includes("bash")) {
+		// Use our custom rcfile that sources user's files then fixes PATH
+		return ["--rcfile", path.join(BASH_DIR, "rcfile")];
+	}
+	return [];
+}
diff --git a/apps/desktop/src/main/lib/agent-setup/utils.ts b/apps/desktop/src/main/lib/agent-setup/utils.ts
new file mode 100644
index 00000000000..e30d94cb6db
--- /dev/null
+++ b/apps/desktop/src/main/lib/agent-setup/utils.ts
@@ -0,0 +1,30 @@
+import { execSync } from "node:child_process";
+import os from "node:os";
+import path from "node:path";
+import { SUPERSET_DIR_NAMES } from "shared/constants";
+
+/**
+ * Finds the real path of a binary, skipping our wrapper scripts.
+ * Filters out both dev and prod superset bin directories
+ * to avoid wrapper scripts calling each other.
+ */
+export function findRealBinary(name: string): string | null {
+	try {
+		// Get all paths, filter out both dev and prod superset bin dirs
+		const result = execSync(`which -a ${name} 2>/dev/null || true`, {
+			encoding: "utf-8",
+		});
+		const homedir = os.homedir();
+		const supersetBinDirs = [
+			path.join(homedir, SUPERSET_DIR_NAMES.PROD, "bin"),
+			path.join(homedir, SUPERSET_DIR_NAMES.DEV, "bin"),
+		];
+		const paths = result
+			.trim()
+			.split("\n")
+			.filter((p) => p && !supersetBinDirs.some((dir) => p.startsWith(dir)));
+		return paths[0] || null;
+	} catch {
+		return null;
+	}
+}