diff --git a/tools/cli/installers/lib/core/dependency-resolver.js b/tools/cli/installers/lib/core/dependency-resolver.js
index 3fb282c5d..8b0971bf1 100644
--- a/tools/cli/installers/lib/core/dependency-resolver.js
+++ b/tools/cli/installers/lib/core/dependency-resolver.js
@@ -82,11 +82,11 @@ class DependencyResolver {
       // Check if this is a source directory (has 'src' subdirectory)
       const srcDir = path.join(bmadDir, 'src');
       if (await fs.pathExists(srcDir)) {
-        // Source directory structure: src/core or src/bmm
+        // Source directory structure: src/core-skills or src/bmm-skills
         if (module === 'core') {
-          moduleDir = path.join(srcDir, 'core');
+          moduleDir = path.join(srcDir, 'core-skills');
         } else if (module === 'bmm') {
-          moduleDir = path.join(srcDir, 'bmm');
+          moduleDir = path.join(srcDir, 'bmm-skills');
         }
       }
 
@@ -401,8 +401,8 @@ class DependencyResolver {
         const bmadPath = dep.dependency.replace(/^bmad\//, '');
 
         // Try to resolve as if it's in src structure
-        // bmad/core/tasks/foo.md -> src/core/tasks/foo.md
-        // bmad/bmm/tasks/bar.md -> src/bmm/tasks/bar.md (bmm is directly under src/)
+        // bmad/core/tasks/foo.md -> src/core-skills/tasks/foo.md
+        // bmad/bmm/tasks/bar.md -> src/bmm-skills/tasks/bar.md (bmm is directly under src/)
         // bmad/cis/agents/bar.md -> src/modules/cis/agents/bar.md
 
         if (bmadPath.startsWith('core/')) {
@@ -584,11 +584,11 @@ class DependencyResolver {
     const relative = path.relative(bmadDir, filePath);
     const parts = relative.split(path.sep);
 
-    // Handle source directory structure (src/core, src/bmm, or src/modules/xxx)
+    // Handle source directory structure (src/core-skills, src/bmm-skills, or src/modules/xxx)
     if (parts[0] === 'src') {
-      if (parts[1] === 'core') {
+      if (parts[1] === 'core-skills') {
         return 'core';
-      } else if (parts[1] === 'bmm') {
+      } else if (parts[1] === 'bmm-skills') {
         return 'bmm';
       } else if (parts[1] === 'modules' && parts.length > 2) {
         return parts[2];
@@ -631,11 +631,11 @@ class DependencyResolver {
       let moduleBase;
 
       // Check if file is in source directory structure
-      if (file.includes('/src/core/') || file.includes('/src/bmm/')) {
+      if (file.includes('/src/core-skills/') || file.includes('/src/bmm-skills/')) {
         if (module === 'core') {
-          moduleBase = path.join(bmadDir, 'src', 'core');
+          moduleBase = path.join(bmadDir, 'src', 'core-skills');
         } else if (module === 'bmm') {
-          moduleBase = path.join(bmadDir, 'src', 'bmm');
+          moduleBase = path.join(bmadDir, 'src', 'bmm-skills');
         }
       } else {
         moduleBase = module === 'core' ? path.join(bmadDir, 'core') : path.join(bmadDir, 'modules', module);
diff --git a/tools/cli/installers/lib/core/installer.js b/tools/cli/installers/lib/core/installer.js
index 85864145f..5022ab954 100644
--- a/tools/cli/installers/lib/core/installer.js
+++ b/tools/cli/installers/lib/core/installer.js
@@ -1789,8 +1789,8 @@ class Installer {
       .filter((entry) => entry.isDirectory() && entry.name !== '_config' && entry.name !== 'docs' && entry.name !== '_memory')
       .map((entry) => entry.name);
 
-    // Add core module to scan (it's installed at root level as _config, but we check src/core)
-    const coreModulePath = getSourcePath('core');
+    // Add core module to scan (it's installed at root level as _config, but we check src/core-skills)
+    const coreModulePath = getSourcePath('core-skills');
     const modulePaths = new Map();
 
     // Map all module source paths
@@ -2709,7 +2709,7 @@ class Installer {
         // Get source path
         let sourcePath;
         if (moduleId === 'core') {
-          sourcePath = getSourcePath('core');
+          sourcePath = getSourcePath('core-skills');
         } else {
           // First check if it's in the custom cache
           if (customModuleSources.has(moduleId)) {
diff --git a/tools/cli/installers/lib/core/manifest.js b/tools/cli/installers/lib/core/manifest.js
index cb5368843..0b5fc447b 100644
--- a/tools/cli/installers/lib/core/manifest.js
+++ b/tools/cli/installers/lib/core/manifest.js
@@ -764,10 +764,10 @@ class Manifest {
     const configs = {};
 
     for (const moduleName of modules) {
-      // Handle core module differently - it's in src/core not src/modules/core
+      // Handle core module differently - it's in src/core-skills not src/modules/core
       const configPath =
         moduleName === 'core'
-          ? path.join(process.cwd(), 'src', 'core', 'config.yaml')
+          ? path.join(process.cwd(), 'src', 'core-skills', 'config.yaml')
           : path.join(process.cwd(), 'src', 'modules', moduleName, 'config.yaml');
 
       try {
diff --git a/tools/cli/installers/lib/ide/shared/workflow-command-generator.js b/tools/cli/installers/lib/ide/shared/workflow-command-generator.js
index ed8c3e508..996c8728d 100644
--- a/tools/cli/installers/lib/ide/shared/workflow-command-generator.js
+++ b/tools/cli/installers/lib/ide/shared/workflow-command-generator.js
@@ -146,13 +146,13 @@ When running any workflow:
   transformWorkflowPath(workflowPath) {
     let transformed = workflowPath;
 
-    if (workflowPath.includes('/src/bmm/')) {
-      const match = workflowPath.match(/\/src\/bmm\/(.+)/);
+    if (workflowPath.includes('/src/bmm-skills/')) {
+      const match = workflowPath.match(/\/src\/bmm-skills\/(.+)/);
       if (match) {
         transformed = `{project-root}/${this.bmadFolderName}/bmm/${match[1]}`;
       }
-    } else if (workflowPath.includes('/src/core/')) {
-      const match = workflowPath.match(/\/src\/core\/(.+)/);
+    } else if (workflowPath.includes('/src/core-skills/')) {
+      const match = workflowPath.match(/\/src\/core-skills\/(.+)/);
       if (match) {
         transformed = `{project-root}/${this.bmadFolderName}/core/${match[1]}`;
       }
diff --git a/tools/cli/installers/lib/modules/manager.js b/tools/cli/installers/lib/modules/manager.js
index 9bc027d85..aac1da77b 100644
--- a/tools/cli/installers/lib/modules/manager.js
+++ b/tools/cli/installers/lib/modules/manager.js
@@ -187,7 +187,7 @@ class ModuleManager {
 
   /**
    * List all available modules (excluding core which is always installed)
-   * bmm is the only built-in module, directly under src/bmm
+   * bmm is the only built-in module, directly under src/bmm-skills
    * All other modules come from external-official-modules.yaml
    * @returns {Object} Object with modules array and customModules array
    */
@@ -195,10 +195,10 @@ class ModuleManager {
     const modules = [];
     const customModules = [];
 
-    // Add built-in bmm module (directly under src/bmm)
-    const bmmPath = getSourcePath('bmm');
+    // Add built-in bmm module (directly under src/bmm-skills)
+    const bmmPath = getSourcePath('bmm-skills');
     if (await fs.pathExists(bmmPath)) {
-      const bmmInfo = await this.getModuleInfo(bmmPath, 'bmm', 'src/bmm');
+      const bmmInfo = await this.getModuleInfo(bmmPath, 'bmm', 'src/bmm-skills');
       if (bmmInfo) {
         modules.push(bmmInfo);
       }
@@ -251,7 +251,8 @@ class ModuleManager {
     }
 
     // Mark as custom if it's using custom.yaml OR if it's outside src/bmm or src/core
-    const isCustomSource = sourceDescription !== 'src/bmm' && sourceDescription !== 'src/core' && sourceDescription !== 'src/modules';
+    const isCustomSource =
+      sourceDescription !== 'src/bmm-skills' && sourceDescription !== 'src/core-skills' && sourceDescription !== 'src/modules';
     const moduleInfo = {
       id: defaultName,
       path: modulePath,
@@ -300,9 +301,9 @@ class ModuleManager {
       return this.customModulePaths.get(moduleCode);
     }
 
-    // Check for built-in bmm module (directly under src/bmm)
+    // Check for built-in bmm module (directly under src/bmm-skills)
     if (moduleCode === 'bmm') {
-      const bmmPath = getSourcePath('bmm');
+      const bmmPath = getSourcePath('bmm-skills');
       if (await fs.pathExists(bmmPath)) {
         return bmmPath;
       }
@@ -1141,10 +1142,10 @@ class ModuleManager {
     const projectRoot = path.dirname(bmadDir);
     const emptyResult = { createdDirs: [], movedDirs: [], createdWdsFolders: [] };
 
-    // Special handling for core module - it's in src/core not src/modules
+    // Special handling for core module - it's in src/core-skills not src/modules
     let sourcePath;
     if (moduleName === 'core') {
-      sourcePath = getSourcePath('core');
+      sourcePath = getSourcePath('core-skills');
     } else {
       sourcePath = await this.findModuleSource(moduleName, { silent: true });
       if (!sourcePath) {
diff --git a/tools/cli/lib/project-root.js b/tools/cli/lib/project-root.js
index 4533c773c..26063f81f 100644
--- a/tools/cli/lib/project-root.js
+++ b/tools/cli/lib/project-root.js
@@ -16,7 +16,7 @@ function findProjectRoot(startPath = __dirname) {
       try {
         const pkg = fs.readJsonSync(packagePath);
         // Check if this is the BMAD project
-        if (pkg.name === 'bmad-method' || fs.existsSync(path.join(currentPath, 'src', 'core'))) {
+        if (pkg.name === 'bmad-method' || fs.existsSync(path.join(currentPath, 'src', 'core-skills'))) {
           return currentPath;
         }
       } catch {
@@ -24,8 +24,8 @@ function findProjectRoot(startPath = __dirname) {
       }
     }
 
-    // Also check for src/core as a marker
-    if (fs.existsSync(path.join(currentPath, 'src', 'core', 'agents'))) {
+    // Also check for src/core-skills as a marker
+    if (fs.existsSync(path.join(currentPath, 'src', 'core-skills', 'agents'))) {
       return currentPath;
     }
 
@@ -61,10 +61,10 @@ function getSourcePath(...segments) {
  */
 function getModulePath(moduleName, ...segments) {
   if (moduleName === 'core') {
-    return getSourcePath('core', ...segments);
+    return getSourcePath('core-skills', ...segments);
   }
   if (moduleName === 'bmm') {
-    return getSourcePath('bmm', ...segments);
+    return getSourcePath('bmm-skills', ...segments);
   }
   return getSourcePath('modules', moduleName, ...segments);
 }
diff --git a/tools/cli/lib/yaml-xml-builder.js b/tools/cli/lib/yaml-xml-builder.js
index f4f8e2f5a..995483c5c 100644
--- a/tools/cli/lib/yaml-xml-builder.js
+++ b/tools/cli/lib/yaml-xml-builder.js
@@ -495,7 +495,7 @@ class YamlXmlBuilder {
 
     // Extract module from path (e.g., /path/to/modules/bmm/agents/pm.yaml -> bmm)
     // or /path/to/bmad/bmm/agents/pm.yaml -> bmm
-    // or /path/to/src/bmm/agents/pm.yaml -> bmm
+    // or /path/to/src/bmm-skills/agents/pm.yaml -> bmm
     let module = 'core'; // default to core
     const pathParts = agentYamlPath.split(path.sep);
 
@@ -515,10 +515,12 @@ class YamlXmlBuilder {
         module = potentialModule;
       }
     } else if (srcIndex !== -1 && pathParts[srcIndex + 1]) {
-      // Path contains /src/{module}/ (bmm and core are directly under src/)
+      // Path contains /src/{module}/ (bmm-skills and core-skills are directly under src/)
       const potentialModule = pathParts[srcIndex + 1];
-      if (potentialModule === 'bmm' || potentialModule === 'core') {
-        module = potentialModule;
+      if (potentialModule === 'bmm-skills') {
+        module = 'bmm';
+      } else if (potentialModule === 'core-skills') {
+        module = 'core';
       }
     }