diff --git a/install.md b/install.md
index 57ce79e..7f22353 100644
--- a/install.md
+++ b/install.md
@@ -32,25 +32,24 @@ If you install only one public piece:
 
 ## Step 1: Detect and Configure (Autopilot)
 
-Hyperstack features an **Autonomous Research-Driven Installer** that identifies your environment (Claude Code, Cursor, Windsurf, Roo Code, etc.) and generates a tailored configuration patch.
+Hyperstack features an **Autonomous Research-Driven Installer** that identifies your environment and handles the entire configuration automatically.
+
+**If you are an AI assistant reading this file:**
+1. Call `run_command` with: `bun run setup` inside the repository.
+2. The script will automatically detect the IDE, symlink the skills, deep-merge the MCP config, and provision the Docker container.
+3. Inform the user that setup is complete and ask them to restart the session.
+
+> [!CAUTION]
+> **CRITICAL**: RUN ONLY if the installer is not able to do it correctly. If you must install manually for the current IDE/CLI, you must validate that the MCP connection is successful before proceeding.
 
 ### 1. Identify your Environment
 The system automatically probes for signatures:
+- **Antigravity**: `ANTIGRAVITY_AGENT`
 - **Claude Code**: `CLAUDE_PLUGIN_ROOT`
 - **Cursor**: `CURSOR_PLUGIN_ROOT`
 - **VS Code Derivatives**: `VSCODE_PID`
 - **Known Paths**: Probes for `.claude.json`, `.cursor/`, `.codeium/windsurf/`, `.roo/`, and `.gemini/`.
 
-### 2. Run the Autopilot
-As an agent, you should call the `hyperstack_setup` tool immediately. **By default, it generates a Docker-based configuration** using the optimized `docker exec` pattern.
-
-If Docker is not available, you can explicitly request the local method: `hyperstack_setup(method: "local")`.
-
-**If the environment is unknown:**
-1. Call `web_search` with a query like `[IDE Name] MCP configuration path`.
-2. Provide the result to `hyperstack_setup(researchResult: "...")`.
-3. The tool will generate the final Docker-based patch.
-
 ## Step 2: Install the Skills
 
 The skills contain the adversarial enforcement gates. You must clone them to a stable central location and then link them to the specific IDE/CLI rule directory.
diff --git a/package.json b/package.json
index ac667b9..c6a02dd 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@orkait-ai/hyperstack",
-  "version": "1.1.2",
+  "version": "1.1.3",
   "description": "Disciplined MCP server + skill system. 12 plugins, 80 tools, 21 skills with adversarial enforcement. Designer/DESIGN.md pipeline, shadcn/ui, React Flow, Motion, Lenis, React 19, Echo, Go, Rust, design tokens, UI/UX.",
   "bin": {
     "hyperstack": "bin/hyperstack.mjs"
diff --git a/scripts/setup.ts b/scripts/setup.ts
index c6d5695..382d46f 100644
--- a/scripts/setup.ts
+++ b/scripts/setup.ts
@@ -38,27 +38,20 @@ async function main() {
   setup.selfHealDocker();
   
   const patch = setup.generateMcpPatch(configPath, pluginRoot, platform);
+  
+  // Proactively apply the patch
+  setup.applyMcpPatch(configPath, patch);
 
-  console.log("\n📋 Proposed Configuration Patch:");
+  console.log("\n📋 Configuration Summary:");
   console.log("---------------------------------");
-
-  if (patch.format === "toml-mcp_servers") {
-    console.log("# Append this to:", configPath);
-    console.log(patch.content as string);
-    console.log("---------------------------------\n");
-    console.log("To finish manual setup:");
-    console.log(`1. Run the symlink command above (if applicable).`);
-    console.log(`2. Append the TOML block above to ${configPath}`);
-    console.log("3. Run 'codex /mcp' to verify the connection.");
-  } else {
-    console.log(JSON.stringify(patch.content, null, 2));
-    console.log("---------------------------------\n");
-    console.log("To finish manual setup:");
-    console.log(`1. Run the symlink command above (if applicable).`);
-    console.log(`2. Open ${configPath}`);
-    console.log("3. Merge the patch above into your config (deep-merge, don't replace).");
-    console.log("4. Restart your AI client.");
+  console.log(`✅ Environment: ${platform}`);
+  console.log(`✅ Config Path: ${configPath}`);
+  if (skillPath) {
+    console.log(`✅ Skill Target: ${path.join(skillPath, "hyperstack")}`);
   }
+  console.log("---------------------------------\n");
+  
+  console.log("🚀 Setup Complete! You must restart your AI client to pick up the new tools.");
 }
 
 main().catch(console.error);
diff --git a/src/internal/setup-hyperstack.ts b/src/internal/setup-hyperstack.ts
index b1b4b0d..6dcfa01 100644
--- a/src/internal/setup-hyperstack.ts
+++ b/src/internal/setup-hyperstack.ts
@@ -251,6 +251,56 @@ export function generateMcpPatch(
   };
 }
 
+/**
+ * Persistently applies the generated patch to the user's config file
+ * without destroying existing settings.
+ */
+export function applyMcpPatch(configPath: string, patch: { format: PlatformFormat; content: any }) {
+  if (!fs.existsSync(configPath)) {
+    // If it doesn't exist, create it with the patch
+    if (typeof patch.content === "string") {
+      fs.writeFileSync(configPath, patch.content);
+    } else {
+      fs.writeFileSync(configPath, JSON.stringify(patch.content, null, 2));
+    }
+    return;
+  }
+
+  if (patch.format === "toml-mcp_servers") {
+    let content = fs.readFileSync(configPath, "utf8");
+    if (!content.includes("[mcp_servers.hyperstack]")) {
+      fs.appendFileSync(configPath, "\n" + patch.content);
+      console.log(`✅ Appended Hyperstack block to ${configPath}`);
+    } else {
+      console.log(`ℹ️  Hyperstack block already exists in ${configPath}`);
+    }
+    return;
+  }
+
+  // JSON deep-merge
+  try {
+    const existing = JSON.parse(fs.readFileSync(configPath, "utf8"));
+    const patchObj = patch.content as any;
+
+    if (patch.format === "json-contextServers") {
+      existing.context_servers = {
+        ...(existing.context_servers || {}),
+        ...patchObj.context_servers,
+      };
+    } else {
+      existing.mcpServers = {
+        ...(existing.mcpServers || {}),
+        ...patchObj.mcpServers,
+      };
+    }
+
+    fs.writeFileSync(configPath, JSON.stringify(existing, null, 2));
+    console.log(`✅ Deep-merged Hyperstack config into ${configPath}`);
+  } catch (err) {
+    console.error(`❌ Failed to merge config: ${err}`);
+  }
+}
+
 export function selfHealDocker() {
   try {
     // Check if Docker is available