diff --git a/src/bmm/workflows/4-implementation/dev-story/workflow.md b/src/bmm/workflows/4-implementation/dev-story/workflow.md
index 1d338fbe8..0a1a2f210 100644
--- a/src/bmm/workflows/4-implementation/dev-story/workflow.md
+++ b/src/bmm/workflows/4-implementation/dev-story/workflow.md
@@ -2,7 +2,7 @@
 name: dev-story
 description: "Execute a story by implementing tasks/subtasks, writing tests, validating, and updating the story file per acceptance criteria"
 projectRoot: '{project-root}'
-main_config: '{projectRoot}/_bmad/bmm/config.yaml'
+main_config: '{project-root}/_bmad/bmm/config.yaml'
 web_bundle: false
 ---
 
diff --git a/src/bmm/workflows/document-project/instructions.md b/src/bmm/workflows/document-project/instructions.md
index 44caa6e45..8b2269913 100644
--- a/src/bmm/workflows/document-project/instructions.md
+++ b/src/bmm/workflows/document-project/instructions.md
@@ -163,6 +163,11 @@ Your choice [1/2/3]:
     <action>Exit workflow</action>
   </check>
 
+  <check if="user input is not 1, 2, or 3">
+    <output>Invalid selection. Expected 1, 2, or 3. Exiting workflow without changes.</output>
+    <action>Exit workflow</action>
+  </check>
+
 </check>
 </check>
 
@@ -220,6 +225,11 @@ Your choice [1/2/3]:
     <action>Display message: "Keeping existing documentation. Exiting workflow."</action>
     <action>Exit workflow</action>
   </check>
+
+  <check if="user input is not 1, 2, or 3">
+    <output>Invalid selection. Expected 1, 2, or 3. Exiting workflow without changes.</output>
+    <action>Exit workflow</action>
+  </check>
 </check>
 
 <check if="index.md does not exist">
diff --git a/tools/cli/installers/lib/modules/manager.js b/tools/cli/installers/lib/modules/manager.js
index 508cdcf98..05109dbca 100644
--- a/tools/cli/installers/lib/modules/manager.js
+++ b/tools/cli/installers/lib/modules/manager.js
@@ -810,6 +810,8 @@ class ModuleManager {
       return content;
     }
 
+    const newline = frontmatterMatch[0].includes('\r\n') ? '\r\n' : '\n';
+
     try {
       const yaml = require('yaml');
       const parsed = yaml.parse(frontmatterMatch[1]);
@@ -827,7 +829,8 @@ class ModuleManager {
         })
         .trimEnd();
 
-      return content.replace(frontmatterMatch[0], `---\n${serialized}\n---`);
+      const normalized = newline === '\r\n' ? serialized.replaceAll('\n', '\r\n') : serialized;
+      return content.replace(frontmatterMatch[0], `---${newline}${normalized}${newline}---`);
     } catch (error) {
       console.warn(`Warning: Failed to parse workflow frontmatter for web_bundle removal: ${error.message}`);
       return content;