diff --git a/test/test-installation-components.js b/test/test-installation-components.js
index dda834079..fd3a854ba 100644
--- a/test/test-installation-components.js
+++ b/test/test-installation-components.js
@@ -1635,6 +1635,15 @@ async function runTests() {
     );
     await fs.writeFile(path.join(taskSkillDir29, 'workflow.md'), '# Task Skill\n\nSkill in tasks\n');
 
+    // --- Native agent entrypoint inside agents/: core/agents/bmad-tea/ ---
+    const nativeAgentDir29 = path.join(tempFixture29, 'core', 'agents', 'bmad-tea');
+    await fs.ensureDir(nativeAgentDir29);
+    await fs.writeFile(path.join(nativeAgentDir29, 'bmad-skill-manifest.yaml'), 'type: agent\ncanonicalId: bmad-tea\n');
+    await fs.writeFile(
+      path.join(nativeAgentDir29, 'SKILL.md'),
+      '---\nname: bmad-tea\ndescription: Native agent entrypoint\n---\n\nPresent a capability menu.\n',
+    );
+
     // Minimal agent so core module is detected
     await fs.ensureDir(path.join(tempFixture29, 'core', 'agents'));
     const minimalAgent29 = '<agent name="Test" title="T"><persona>p</persona></agent>';
@@ -1664,6 +1673,17 @@ async function runTests() {
     const inTasks29 = generator29.tasks.find((t) => t.name === 'task-skill');
     assert(inTasks29 === undefined, 'Skill in tasks/ dir does NOT appear in tasks[]');
 
+    // Native agent entrypoint should be installed as a verbatim skill and also
+    // remain visible to the agent manifest pipeline.
+    const nativeAgentEntry29 = generator29.skills.find((s) => s.canonicalId === 'bmad-tea');
+    assert(nativeAgentEntry29 !== undefined, 'Native type:agent SKILL.md dir appears in skills[]');
+    assert(
+      nativeAgentEntry29 && nativeAgentEntry29.path.includes('agents/bmad-tea/SKILL.md'),
+      'Native type:agent SKILL.md path points to the agent directory entrypoint',
+    );
+    const nativeAgentManifest29 = generator29.agents.find((a) => a.name === 'bmad-tea');
+    assert(nativeAgentManifest29 !== undefined, 'Native type:agent SKILL.md dir appears in agents[] for agent metadata');
+
     // Regular workflow should be in workflows, NOT in skills
     const regularWf29 = generator29.workflows.find((w) => w.name === 'Regular Workflow');
     assert(regularWf29 !== undefined, 'Regular type:workflow appears in workflows[]');
@@ -1689,6 +1709,22 @@ async function runTests() {
 
     const scannedModules29 = await generator29.scanInstalledModules(tempFixture29);
     assert(scannedModules29.includes('skill-only-mod'), 'scanInstalledModules recognizes skill-only module');
+
+    // Test scanInstalledModules recognizes native-agent-only modules too
+    const agentOnlyModDir29 = path.join(tempFixture29, 'agent-only-mod');
+    await fs.ensureDir(path.join(agentOnlyModDir29, 'deep', 'nested', 'bmad-tea'));
+    await fs.writeFile(path.join(agentOnlyModDir29, 'deep', 'nested', 'bmad-tea', 'bmad-skill-manifest.yaml'), 'type: agent\n');
+    await fs.writeFile(
+      path.join(agentOnlyModDir29, 'deep', 'nested', 'bmad-tea', 'SKILL.md'),
+      '---\nname: bmad-tea\ndescription: desc\n---\n\nAgent menu.\n',
+    );
+
+    const rescannedModules29 = await generator29.scanInstalledModules(tempFixture29);
+    assert(rescannedModules29.includes('agent-only-mod'), 'scanInstalledModules recognizes native-agent-only module');
+
+    // skill-manifest.csv should include the native agent entrypoint
+    const skillManifestCsv29 = await fs.readFile(path.join(tempFixture29, '_config', 'skill-manifest.csv'), 'utf8');
+    assert(skillManifestCsv29.includes('bmad-tea'), 'skill-manifest.csv includes native type:agent SKILL.md entrypoint');
   } catch (error) {
     assert(false, 'Unified skill scanner test succeeds', error.message);
   } finally {
diff --git a/tools/cli/installers/lib/core/manifest-generator.js b/tools/cli/installers/lib/core/manifest-generator.js
index 68d0c9eab..7932f1516 100644
--- a/tools/cli/installers/lib/core/manifest-generator.js
+++ b/tools/cli/installers/lib/core/manifest-generator.js
@@ -50,6 +50,16 @@ class ManifestGenerator {
     return getInstallToBmadShared(manifest, filename);
   }
 
+  /**
+   * Native SKILL.md entrypoints can be packaged as either skills or agents.
+   * Both need verbatim installation for skill-format IDEs.
+   * @param {string|null} artifactType - Manifest type resolved for SKILL.md
+   * @returns {boolean} True when the directory should be installed verbatim
+   */
+  isNativeSkillDirType(artifactType) {
+    return artifactType === 'skill' || artifactType === 'agent';
+  }
+
   /**
    * Clean text for CSV output by normalizing whitespace.
    * Note: Quote escaping is handled by escapeCsv() at write time.
@@ -146,9 +156,10 @@ class ManifestGenerator {
   }
 
   /**
-   * Recursively walk a module directory tree, collecting skill directories.
-   * A skill directory is one that contains both a bmad-skill-manifest.yaml with
-   * type: skill AND a SKILL.md file with name/description frontmatter.
+   * Recursively walk a module directory tree, collecting native SKILL.md entrypoints.
+   * A native entrypoint directory is one that contains both a
+   * bmad-skill-manifest.yaml with type: skill or type: agent AND a SKILL.md file
+   * with name/description frontmatter.
    * Populates this.skills[] and this.skillClaimedDirs (Set of absolute paths).
    */
   async collectSkills() {
@@ -172,11 +183,11 @@ class ManifestGenerator {
         // Check this directory for skill manifest
         const manifest = await this.loadSkillManifest(dir);
 
-        // Determine if this directory is a skill (type: skill in manifest)
+        // Determine if this directory is a native SKILL.md entrypoint
         const skillFile = 'SKILL.md';
         const artifactType = this.getArtifactType(manifest, skillFile);
 
-        if (artifactType === 'skill' || artifactType === 'agent') {
+        if (this.isNativeSkillDirType(artifactType)) {
           const skillMdPath = path.join(dir, 'SKILL.md');
           const dirName = path.basename(dir);
 
@@ -190,11 +201,12 @@ class ManifestGenerator {
               ? `${this.bmadFolderName}/${moduleName}/${relativePath}/${skillFile}`
               : `${this.bmadFolderName}/${moduleName}/${skillFile}`;
 
-            // Skills derive canonicalId from directory name — never from manifest
-            // (agent-type skills legitimately use canonicalId for agent-manifest mapping, so skip warning)
+            // Native SKILL.md entrypoints derive canonicalId from directory name.
+            // Agent entrypoints may keep canonicalId metadata for compatibility, so
+            // only warn for non-agent SKILL.md directories.
             if (manifest && manifest.__single && manifest.__single.canonicalId && artifactType !== 'agent') {
               console.warn(
-                `Warning: Skill manifest at ${dir}/bmad-skill-manifest.yaml contains canonicalId — this field is ignored for skills (directory name is the canonical ID)`,
+                `Warning: Native entrypoint manifest at ${dir}/bmad-skill-manifest.yaml contains canonicalId — this field is ignored for SKILL.md directories (directory name is the canonical ID)`,
               );
             }
             const canonicalId = dirName;
@@ -224,21 +236,21 @@ class ManifestGenerator {
           }
         }
 
-        // Warn if manifest says type:skill but directory was not claimed
+        // Warn if manifest says this is a native entrypoint but the directory was not claimed
         if (manifest && !this.skillClaimedDirs.has(dir)) {
-          let hasSkillType = false;
+          let hasNativeSkillType = false;
           if (manifest.__single) {
-            hasSkillType = manifest.__single.type === 'skill' || manifest.__single.type === 'agent';
+            hasNativeSkillType = this.isNativeSkillDirType(manifest.__single.type);
           } else {
             for (const key of Object.keys(manifest)) {
-              if (manifest[key]?.type === 'skill' || manifest[key]?.type === 'agent') {
-                hasSkillType = true;
+              if (this.isNativeSkillDirType(manifest[key]?.type)) {
+                hasNativeSkillType = true;
                 break;
               }
             }
           }
-          if (hasSkillType && debug) {
-            console.log(`[DEBUG] collectSkills: dir has type:skill manifest but failed validation: ${dir}`);
+          if (hasNativeSkillType && debug) {
+            console.log(`[DEBUG] collectSkills: dir has native SKILL.md manifest but failed validation: ${dir}`);
           }
         }
 
@@ -1359,7 +1371,8 @@ class ManifestGenerator {
         const hasTasks = await fs.pathExists(path.join(modulePath, 'tasks'));
         const hasTools = await fs.pathExists(path.join(modulePath, 'tools'));
 
-        // Check for skill-only modules: recursive scan for bmad-skill-manifest.yaml with type: skill
+        // Check for native-entrypoint-only modules: recursive scan for
+        // bmad-skill-manifest.yaml with type: skill or type: agent
         let hasSkills = false;
         if (!hasAgents && !hasWorkflows && !hasTasks && !hasTools) {
           hasSkills = await this._hasSkillManifestRecursive(modulePath);
@@ -1378,7 +1391,8 @@ class ManifestGenerator {
   }
 
   /**
-   * Recursively check if a directory tree contains a bmad-skill-manifest.yaml with type: skill.
+   * Recursively check if a directory tree contains a bmad-skill-manifest.yaml with
+   * type: skill or type: agent.
    * Skips directories starting with . or _.
    * @param {string} dir - Directory to search
    * @returns {boolean} True if a skill manifest is found
@@ -1395,7 +1409,7 @@ class ManifestGenerator {
     const manifest = await this.loadSkillManifest(dir);
     if (manifest) {
       const type = this.getArtifactType(manifest, 'workflow.md');
-      if (type === 'skill') return true;
+      if (this.isNativeSkillDirType(type)) return true;
     }
 
     // Recurse into subdirectories
diff --git a/tools/cli/installers/lib/ide/_config-driven.js b/tools/cli/installers/lib/ide/_config-driven.js
index a93fe0c87..e94cb9edb 100644
--- a/tools/cli/installers/lib/ide/_config-driven.js
+++ b/tools/cli/installers/lib/ide/_config-driven.js
@@ -630,7 +630,7 @@ LOAD and execute from: {project-root}/{{bmadFolderName}}/{{path}}
   }
 
   /**
-   * Install verbatim skill directories (type: skill entries from skill-manifest.csv).
+   * Install verbatim native SKILL.md directories from skill-manifest.csv.
    * Copies the entire source directory as-is into the IDE skill directory.
    * The source SKILL.md is used directly — no frontmatter transformation or file generation.
    * @param {string} projectDir - Project directory