diff --git a/server/src/io/fs.rs b/server/src/io/fs.rs
index e1961f9..5580820 100644
--- a/server/src/io/fs.rs
+++ b/server/src/io/fs.rs
@@ -230,7 +230,8 @@ This folder contains the "Living Specification" for the project. It serves as th
 3.  If a Story changes behavior, update the spec *first*, get approval, then write code.
 "#;
 
-const STORY_KIT_CONTEXT: &str = r#"# Project Context
+const STORY_KIT_CONTEXT: &str = r#"<!-- story-kit:scaffold-template -->
+# Project Context
 
 ## High-Level Goal
 To build a standalone **Agentic AI Code Assistant** application as a single Rust binary that serves a Vite/React web UI and exposes a WebSocket API. The assistant will facilitate a "Story-Driven Spec Workflow" (SDSW) for software development. Unlike a passive chat interface, this assistant acts as an **Agent**, capable of using tools to read the filesystem, execute shell commands, manage git repositories, and modify code directly to implement features.
@@ -265,7 +266,8 @@ To build a standalone **Agentic AI Code Assistant** application as a single Rust
 *   **Tool Call:** A structured request from the LLM to execute a specific native function.
 "#;
 
-const STORY_KIT_STACK: &str = r#"# Tech Stack & Constraints
+const STORY_KIT_STACK: &str = r#"<!-- story-kit:scaffold-template -->
+# Tech Stack & Constraints
 
 ## Overview
 This project is a standalone Rust **web server binary** that serves a Vite/React frontend and exposes a **WebSocket API**. The built frontend assets are packaged with the binary (in a `frontend` directory) and served as static files. It functions as an **Agentic Code Assistant** capable of safely executing tools on the host system.
diff --git a/server/src/io/onboarding.rs b/server/src/io/onboarding.rs
index 8e4dc1e..f2e0622 100644
--- a/server/src/io/onboarding.rs
+++ b/server/src/io/onboarding.rs
@@ -1,12 +1,10 @@
 use std::path::Path;
 
-/// Unique marker found in the scaffold template for `00_CONTEXT.md`.
-/// If the project's context file contains this phrase, it is still the
-/// default scaffold content and needs to be replaced.
-const TEMPLATE_MARKER_CONTEXT: &str = "Agentic AI Code Assistant";
-
-/// Unique marker found in the scaffold template for `STACK.md`.
-const TEMPLATE_MARKER_STACK: &str = "Agentic Code Assistant";
+/// Sentinel comment injected as the first line of scaffold templates.
+/// Only untouched templates contain this marker — real project content
+/// will never include it, so it avoids false positives when the project
+/// itself is an "Agentic AI Code Assistant".
+const TEMPLATE_SENTINEL: &str = "<!-- story-kit:scaffold-template -->";
 
 /// Marker found in the default `script/test` scaffold output.
 const TEMPLATE_MARKER_SCRIPT: &str = "No tests configured";
@@ -40,11 +38,11 @@ pub fn check_onboarding_status(project_root: &Path) -> OnboardingStatus {
     OnboardingStatus {
         needs_context: is_template_or_missing(
             &story_kit.join("specs").join("00_CONTEXT.md"),
-            TEMPLATE_MARKER_CONTEXT,
+            TEMPLATE_SENTINEL,
         ),
         needs_stack: is_template_or_missing(
             &story_kit.join("specs").join("tech").join("STACK.md"),
-            TEMPLATE_MARKER_STACK,
+            TEMPLATE_SENTINEL,
         ),
         needs_test_script: is_template_or_missing(
             &project_root.join("script").join("test"),
@@ -102,19 +100,19 @@ mod tests {
     }
 
     #[test]
-    fn needs_onboarding_true_when_specs_contain_scaffold_markers() {
+    fn needs_onboarding_true_when_specs_contain_scaffold_sentinel() {
         let dir = TempDir::new().unwrap();
         let root = setup_project(&dir);
 
-        // Write scaffold template content
+        // Write content that includes the scaffold sentinel
         fs::write(
             root.join(".story_kit/specs/00_CONTEXT.md"),
-            "# Project Context\nTo build a standalone Agentic AI Code Assistant...",
+            "<!-- story-kit:scaffold-template -->\n# Project Context\nPlaceholder...",
         )
         .unwrap();
         fs::write(
             root.join(".story_kit/specs/tech/STACK.md"),
-            "# Tech Stack\nThis is an Agentic Code Assistant binary...",
+            "<!-- story-kit:scaffold-template -->\n# Tech Stack\nPlaceholder...",
         )
         .unwrap();
 
@@ -124,6 +122,30 @@ mod tests {
         assert!(status.needs_onboarding());
     }
 
+    #[test]
+    fn needs_onboarding_false_when_content_mentions_agentic_but_no_sentinel() {
+        let dir = TempDir::new().unwrap();
+        let root = setup_project(&dir);
+
+        // Real project content that happens to mention "Agentic AI Code Assistant"
+        // but does NOT contain the scaffold sentinel — should NOT trigger onboarding.
+        fs::write(
+            root.join(".story_kit/specs/00_CONTEXT.md"),
+            "# Project Context\nTo build a standalone Agentic AI Code Assistant application.",
+        )
+        .unwrap();
+        fs::write(
+            root.join(".story_kit/specs/tech/STACK.md"),
+            "# Tech Stack\nThis is an Agentic Code Assistant binary.",
+        )
+        .unwrap();
+
+        let status = check_onboarding_status(&root);
+        assert!(!status.needs_context);
+        assert!(!status.needs_stack);
+        assert!(!status.needs_onboarding());
+    }
+
     #[test]
     fn needs_onboarding_false_when_specs_have_custom_content() {
         let dir = TempDir::new().unwrap();
@@ -239,13 +261,13 @@ mod tests {
         let dir = TempDir::new().unwrap();
         let root = setup_project(&dir);
 
-        // Context is still template
+        // Context still has sentinel
         fs::write(
             root.join(".story_kit/specs/00_CONTEXT.md"),
-            "Agentic AI Code Assistant placeholder",
+            "<!-- story-kit:scaffold-template -->\n# Project Context\nPlaceholder...",
         )
         .unwrap();
-        // Stack is customised
+        // Stack is customised (no sentinel)
         fs::write(
             root.join(".story_kit/specs/tech/STACK.md"),
             "# My Stack\nRuby on Rails + PostgreSQL",