diff --git a/docs/native-skills-lean-shard-doc-prototype/phase-1-analysis.md b/docs/native-skills-lean-shard-doc-prototype/phase-1-analysis.md
new file mode 100644
index 000000000..0427e945d
--- /dev/null
+++ b/docs/native-skills-lean-shard-doc-prototype/phase-1-analysis.md
@@ -0,0 +1,44 @@
+# Phase 1 Analysis: Native Skills Lean PoC
+
+Date: 2026-03-07  
+Branch: `feature/native-skills-lean-shard-doc-prototype`  
+North-star reference: `docs/native-skills-transition-north-star-thread-2026-03-07.md`
+
+## Problem Statement
+
+The prior native-skills transition effort overshot scope. This recovery PoC must prove a single end-to-end duplicate native-skill path while preserving all current legacy task/help behavior.
+
+## Scope
+
+In scope:
+
+1. One duplicated native-skill prototype only: `bmad-shard-doc-skill-prototype`
+2. Source capability remains `src/core/tasks/shard-doc.xml`
+3. Installer behavior only for supported native-skill tools:
+   - discover prototype metadata
+   - register/copy to skill output surface
+4. Minimal tests proving prototype duplication for skill tools and no regression for non-skill tools
+
+Out of scope:
+
+1. Multi-capability conversion
+2. Broad authority/metadata redesign
+3. Command/help surface changes
+4. Repository-wide migration framework
+
+## Constraints
+
+1. Keep `module-help.csv` behavior unchanged
+2. Keep legacy `bmad-shard-doc` capability intact
+3. Keep PR lean and reviewable
+4. Avoid touching unrelated installer paths
+
+## Risks and Mitigations
+
+1. Risk: duplicate visible command surfaces  
+   Mitigation: apply prototype duplication only on `skill_format` installers
+2. Risk: behavior drift for legacy task/help paths  
+   Mitigation: no edits to legacy task file, task/help catalogs, or command generation rules
+3. Risk: hidden regressions across tool outputs  
+   Mitigation: add targeted install-component tests for one skill-format and one non-skill tool
+
diff --git a/docs/native-skills-lean-shard-doc-prototype/phase-2-prd.md b/docs/native-skills-lean-shard-doc-prototype/phase-2-prd.md
new file mode 100644
index 000000000..19d966963
--- /dev/null
+++ b/docs/native-skills-lean-shard-doc-prototype/phase-2-prd.md
@@ -0,0 +1,33 @@
+# Phase 2 PRD: Native Skills Lean PoC
+
+Date: 2026-03-07  
+Branch: `feature/native-skills-lean-shard-doc-prototype`
+
+## Goal
+
+Ship a narrow, testable PoC that installs a duplicated native skill for shard-doc as `bmad-shard-doc-skill-prototype` while preserving existing shard-doc command/help behavior.
+
+## Functional Requirements
+
+1. The core task skill metadata supports a prototype duplicate ID for `shard-doc.xml`.
+2. Installer discovery reads the prototype duplicate ID from source metadata.
+3. For `skill_format` tools, installer writes both:
+   - canonical skill: `bmad-shard-doc/SKILL.md`
+   - prototype skill: `bmad-shard-doc-skill-prototype/SKILL.md`
+4. For non-`skill_format` tools, installer output remains unchanged (no prototype duplicate command file).
+5. Existing shard-doc legacy artifact remains available via current task/help flows.
+
+## Non-Functional Requirements
+
+1. PR stays lean (minimal files and logic changes).
+2. No behavior change for existing command/help interfaces.
+3. Tests are deterministic and run in current installation component suite.
+
+## Acceptance Criteria
+
+1. `src/core/tasks/shard-doc.xml` remains unchanged as the legacy capability artifact.
+2. Installing for Codex creates `bmad-shard-doc-skill-prototype/SKILL.md` in `.agents/skills`.
+3. Installing for Codex still creates the existing `bmad-shard-doc/SKILL.md`.
+4. Installing for Gemini does not create `bmad-shard-doc-skill-prototype` command output.
+5. Existing install-component suite continues to pass with added assertions.
+
diff --git a/docs/native-skills-lean-shard-doc-prototype/phase-3-architecture.md b/docs/native-skills-lean-shard-doc-prototype/phase-3-architecture.md
new file mode 100644
index 000000000..e9441b133
--- /dev/null
+++ b/docs/native-skills-lean-shard-doc-prototype/phase-3-architecture.md
@@ -0,0 +1,47 @@
+# Phase 3 Architecture: Native Skills Lean PoC
+
+Date: 2026-03-07  
+Branch: `feature/native-skills-lean-shard-doc-prototype`
+
+## Existing Baseline
+
+1. Installer already uses `bmad-skill-manifest.yaml` for canonical skill IDs.
+2. `skill_format` platforms write directory-based skills (`<skill-name>/SKILL.md`).
+3. Task/help command surfaces are driven by existing manifests/catalogs.
+
+## Proposed Minimal Design
+
+### 1) Metadata Extension
+
+Extend per-file skill metadata to optionally include duplicate prototype IDs:
+
+```yaml
+shard-doc.xml:
+  canonicalId: bmad-shard-doc
+  prototypeIds:
+    - bmad-shard-doc-skill-prototype
+```
+
+### 2) Installer Duplication Rule
+
+In config-driven IDE setup, when `skill_format` is enabled:
+
+1. Write canonical skill output as today.
+2. Resolve prototype IDs for the same source artifact from sidecar metadata.
+3. Write additional `SKILL.md` outputs under each prototype ID directory.
+
+No duplication is applied for non-`skill_format` outputs.
+
+### 3) Invariants
+
+1. Legacy source artifact remains `src/core/tasks/shard-doc.xml`.
+2. Existing help/command catalogs remain unchanged.
+3. No new artifact category or broad migration framework introduced.
+
+## Touched Components
+
+1. `src/core/tasks/bmad-skill-manifest.yaml` (prototype metadata for shard-doc)
+2. `tools/cli/installers/lib/ide/shared/skill-manifest.js` (read prototype IDs)
+3. `tools/cli/installers/lib/ide/_config-driven.js` (duplicate skill write for skill-format installers)
+4. `test/test-installation-components.js` (targeted Codex/Gemini assertions)
+
diff --git a/docs/native-skills-lean-shard-doc-prototype/phase-4-implementation.md b/docs/native-skills-lean-shard-doc-prototype/phase-4-implementation.md
new file mode 100644
index 000000000..f91116b7b
--- /dev/null
+++ b/docs/native-skills-lean-shard-doc-prototype/phase-4-implementation.md
@@ -0,0 +1,32 @@
+# Phase 4 Implementation: Native Skills Lean PoC
+
+Date: 2026-03-07  
+Branch: `feature/native-skills-lean-shard-doc-prototype`
+
+## Story
+
+As BMAD installer maintainers, we need one duplicated native-skill prototype for shard-doc so we can validate intermediary migration behavior without changing existing task/help surfaces.
+
+## Tasks
+
+1. Add prototype ID metadata for `shard-doc.xml`.
+2. Extend skill-manifest helper to expose prototype IDs.
+3. Update config-driven installer to emit duplicate skill directories for `skill_format` targets only.
+4. Add install-component tests:
+   - Codex (skill-format) writes canonical + prototype shard-doc skills
+   - Gemini (non-skill) does not write prototype duplicate output
+5. Run installer component tests.
+
+## Verification Plan
+
+1. `node test/test-installation-components.js`
+2. Confirm no edits to legacy `shard-doc.xml` behavior content.
+3. Confirm no edits to `src/core/module-help.csv` command/help entries.
+
+## Done Criteria
+
+1. Four-phase artifacts exist in docs.
+2. Prototype skill duplication works on supported skill-format install path.
+3. Legacy shard-doc command/help behavior remains unchanged.
+4. Test suite passes with new assertions.
+
diff --git a/src/core/tasks/bmad-skill-manifest.yaml b/src/core/tasks/bmad-skill-manifest.yaml
index 4f7e6b40e..9c227aabc 100644
--- a/src/core/tasks/bmad-skill-manifest.yaml
+++ b/src/core/tasks/bmad-skill-manifest.yaml
@@ -30,6 +30,8 @@ review-edge-case-hunter.xml:
 
 shard-doc.xml:
   canonicalId: bmad-shard-doc
+  prototypeIds:
+    - bmad-shard-doc-skill-prototype
   type: task
   description: "Splits large markdown documents into smaller, organized files based on sections"
 
diff --git a/test/test-installation-components.js b/test/test-installation-components.js
index 63f2567f5..07faab05d 100644
--- a/test/test-installation-components.js
+++ b/test/test-installation-components.js
@@ -81,6 +81,41 @@ async function createTestBmadFixture() {
   return fixtureDir;
 }
 
+async function createShardDocPrototypeFixture() {
+  const fixtureDir = await createTestBmadFixture();
+
+  await fs.ensureDir(path.join(fixtureDir, 'core', 'tasks'));
+  await fs.writeFile(
+    path.join(fixtureDir, 'core', 'tasks', 'shard-doc.xml'),
+    '<task id="_bmad/core/tasks/shard-doc" name="Shard Document" description="Test shard-doc task"><objective>Test objective</objective></task>\n',
+  );
+
+  await fs.writeFile(
+    path.join(fixtureDir, 'core', 'tasks', 'bmad-skill-manifest.yaml'),
+    [
+      'shard-doc.xml:',
+      '  canonicalId: bmad-shard-doc',
+      '  prototypeIds:',
+      '    - bmad-shard-doc-skill-prototype',
+      '',
+    ].join('\n'),
+  );
+
+  await fs.writeFile(
+    path.join(fixtureDir, '_config', 'task-manifest.csv'),
+    [
+      'name,displayName,description,module,path,standalone,canonicalId',
+      'shard-doc,Shard Document,Test shard-doc task,core,_bmad/core/tasks/shard-doc.xml,true,bmad-shard-doc',
+      '',
+    ].join('\n'),
+  );
+
+  // Ensure tool manifest exists to avoid parser edge-cases in some environments.
+  await fs.writeFile(path.join(fixtureDir, '_config', 'tool-manifest.csv'), '');
+
+  return fixtureDir;
+}
+
 /**
  * Test Suite
  */
@@ -524,6 +559,65 @@ async function runTests() {
 
   console.log('');
 
+  // ============================================================
+  // Test 11: Shard-doc Prototype Duplication (Skill-Format Only)
+  // ============================================================
+  console.log(`${colors.yellow}Test Suite 11: Shard-doc Prototype Duplication${colors.reset}\n`);
+
+  try {
+    clearCache();
+    const platformCodes = await loadPlatformCodes();
+    const codexInstaller = platformCodes.platforms.codex?.installer;
+    const geminiInstaller = platformCodes.platforms.gemini?.installer;
+
+    assert(codexInstaller?.skill_format === true, 'Codex installer uses skill_format output');
+    assert(geminiInstaller?.skill_format !== true, 'Gemini installer remains non-skill_format');
+
+    const tempCodexProjectDir = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-codex-prototype-test-'));
+    const tempGeminiProjectDir = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-gemini-prototype-test-'));
+    const installedBmadDir = await createShardDocPrototypeFixture();
+
+    const ideManager = new IdeManager();
+    await ideManager.ensureInitialized();
+
+    const codexResult = await ideManager.setup('codex', tempCodexProjectDir, installedBmadDir, {
+      silent: true,
+      selectedModules: ['bmm'],
+    });
+
+    assert(codexResult.success === true, 'Codex setup succeeds for shard-doc prototype fixture');
+
+    const codexCanonicalSkill = path.join(tempCodexProjectDir, '.agents', 'skills', 'bmad-shard-doc', 'SKILL.md');
+    const codexPrototypeSkill = path.join(tempCodexProjectDir, '.agents', 'skills', 'bmad-shard-doc-skill-prototype', 'SKILL.md');
+    assert(await fs.pathExists(codexCanonicalSkill), 'Codex install writes canonical shard-doc skill');
+    assert(await fs.pathExists(codexPrototypeSkill), 'Codex install writes duplicated shard-doc prototype skill');
+
+    const codexCanonicalContent = await fs.readFile(codexCanonicalSkill, 'utf8');
+    const codexPrototypeContent = await fs.readFile(codexPrototypeSkill, 'utf8');
+    assert(codexCanonicalContent.includes('name: bmad-shard-doc'), 'Canonical shard-doc skill keeps canonical frontmatter name');
+    assert(codexPrototypeContent.includes('name: bmad-shard-doc-skill-prototype'), 'Prototype shard-doc skill uses prototype frontmatter name');
+
+    const geminiResult = await ideManager.setup('gemini', tempGeminiProjectDir, installedBmadDir, {
+      silent: true,
+      selectedModules: ['bmm'],
+    });
+
+    assert(geminiResult.success === true, 'Gemini setup succeeds for shard-doc prototype fixture');
+
+    const geminiCanonicalTask = path.join(tempGeminiProjectDir, '.gemini', 'commands', 'bmad-shard-doc.toml');
+    const geminiPrototypeTask = path.join(tempGeminiProjectDir, '.gemini', 'commands', 'bmad-shard-doc-skill-prototype.toml');
+    assert(await fs.pathExists(geminiCanonicalTask), 'Gemini install writes canonical shard-doc command artifact');
+    assert(!(await fs.pathExists(geminiPrototypeTask)), 'Gemini install does not write duplicated shard-doc prototype artifact');
+
+    await fs.remove(tempCodexProjectDir);
+    await fs.remove(tempGeminiProjectDir);
+    await fs.remove(installedBmadDir);
+  } catch (error) {
+    assert(false, 'Shard-doc prototype duplication test succeeds', error.message);
+  }
+
+  console.log('');
+
   // ============================================================
   // Summary
   // ============================================================
diff --git a/tools/cli/installers/lib/ide/_config-driven.js b/tools/cli/installers/lib/ide/_config-driven.js
index d23d8d6d0..30f2c4ae3 100644
--- a/tools/cli/installers/lib/ide/_config-driven.js
+++ b/tools/cli/installers/lib/ide/_config-driven.js
@@ -7,6 +7,7 @@ const prompts = require('../../../lib/prompts');
 const { AgentCommandGenerator } = require('./shared/agent-command-generator');
 const { WorkflowCommandGenerator } = require('./shared/workflow-command-generator');
 const { TaskToolCommandGenerator } = require('./shared/task-tool-command-generator');
+const { loadSkillManifest, getPrototypeIds } = require('./shared/skill-manifest');
 
 /**
  * Config-driven IDE setup handler
@@ -132,21 +133,21 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
     if (!artifact_types || artifact_types.includes('agents')) {
       const agentGen = new AgentCommandGenerator(this.bmadFolderName);
       const { artifacts } = await agentGen.collectAgentArtifacts(bmadDir, selectedModules);
-      results.agents = await this.writeAgentArtifacts(targetPath, artifacts, template_type, config);
+      results.agents = await this.writeAgentArtifacts(targetPath, artifacts, template_type, config, bmadDir);
     }
 
     // Install workflows
     if (!artifact_types || artifact_types.includes('workflows')) {
       const workflowGen = new WorkflowCommandGenerator(this.bmadFolderName);
       const { artifacts } = await workflowGen.collectWorkflowArtifacts(bmadDir);
-      results.workflows = await this.writeWorkflowArtifacts(targetPath, artifacts, template_type, config);
+      results.workflows = await this.writeWorkflowArtifacts(targetPath, artifacts, template_type, config, bmadDir);
     }
 
     // Install tasks and tools using template system (supports TOML for Gemini, MD for others)
     if (!artifact_types || artifact_types.includes('tasks') || artifact_types.includes('tools')) {
       const taskToolGen = new TaskToolCommandGenerator(this.bmadFolderName);
       const { artifacts } = await taskToolGen.collectTaskToolArtifacts(bmadDir);
-      const taskToolResult = await this.writeTaskToolArtifacts(targetPath, artifacts, template_type, config);
+      const taskToolResult = await this.writeTaskToolArtifacts(targetPath, artifacts, template_type, config, bmadDir);
       results.tasks = taskToolResult.tasks || 0;
       results.tools = taskToolResult.tools || 0;
     }
@@ -187,7 +188,7 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
    * @param {Object} config - Installation configuration
    * @returns {Promise<number>} Count of artifacts written
    */
-  async writeAgentArtifacts(targetPath, artifacts, templateType, config = {}) {
+  async writeAgentArtifacts(targetPath, artifacts, templateType, config = {}, bmadDir = null) {
     // Try to load platform-specific template, fall back to default-agent
     const { content: template, extension } = await this.loadTemplate(templateType, 'agent', config, 'default-agent');
     let count = 0;
@@ -197,7 +198,7 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
       const filename = this.generateFilename(artifact, 'agent', extension);
 
       if (config.skill_format) {
-        await this.writeSkillFile(targetPath, artifact, content);
+        await this.writeSkillFile(targetPath, artifact, content, bmadDir);
       } else {
         const filePath = path.join(targetPath, filename);
         await this.writeFile(filePath, content);
@@ -216,7 +217,7 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
    * @param {Object} config - Installation configuration
    * @returns {Promise<number>} Count of artifacts written
    */
-  async writeWorkflowArtifacts(targetPath, artifacts, templateType, config = {}) {
+  async writeWorkflowArtifacts(targetPath, artifacts, templateType, config = {}, bmadDir = null) {
     let count = 0;
 
     for (const artifact of artifacts) {
@@ -235,7 +236,7 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
         const filename = this.generateFilename(artifact, 'workflow', extension);
 
         if (config.skill_format) {
-          await this.writeSkillFile(targetPath, artifact, content);
+          await this.writeSkillFile(targetPath, artifact, content, bmadDir);
         } else {
           const filePath = path.join(targetPath, filename);
           await this.writeFile(filePath, content);
@@ -255,7 +256,7 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
    * @param {Object} config - Installation configuration
    * @returns {Promise<Object>} Counts of tasks and tools written
    */
-  async writeTaskToolArtifacts(targetPath, artifacts, templateType, config = {}) {
+  async writeTaskToolArtifacts(targetPath, artifacts, templateType, config = {}, bmadDir = null) {
     let taskCount = 0;
     let toolCount = 0;
 
@@ -283,7 +284,7 @@ class ConfigDrivenIdeSetup extends BaseIdeSetup {
       const filename = this.generateFilename(artifact, artifact.type, extension);
 
       if (config.skill_format) {
-        await this.writeSkillFile(targetPath, artifact, content);
+        await this.writeSkillFile(targetPath, artifact, content, bmadDir);
       } else {
         const filePath = path.join(targetPath, filename);
         await this.writeFile(filePath, content);
@@ -478,7 +479,7 @@ LOAD and execute from: {project-root}/{{bmadFolderName}}/{{path}}
    * @param {Object} artifact - Artifact data
    * @param {string} content - Rendered template content
    */
-  async writeSkillFile(targetPath, artifact, content) {
+  async writeSkillFile(targetPath, artifact, content, bmadDir = null) {
     const { resolveSkillName } = require('./shared/path-utils');
 
     // Get the skill name (prefers canonicalId, falls back to path-derived) and remove .md
@@ -497,6 +498,76 @@ LOAD and execute from: {project-root}/{{bmadFolderName}}/{{path}}
     const skillContent = this.transformToSkillFormat(content, skillName);
 
     await this.writeFile(path.join(skillDir, 'SKILL.md'), skillContent);
+
+    if (!bmadDir) return;
+
+    const duplicatePrototypeIds = await this.getPrototypeSkillIdsForArtifact(artifact, bmadDir);
+    for (const prototypeId of duplicatePrototypeIds) {
+      if (prototypeId === skillName) continue;
+      const prototypeDir = path.join(targetPath, prototypeId);
+      await this.ensureDir(prototypeDir);
+      const prototypeContent = this.transformToSkillFormat(content, prototypeId);
+      await this.writeFile(path.join(prototypeDir, 'SKILL.md'), prototypeContent);
+    }
+  }
+
+  /**
+   * Resolve duplicate prototype IDs for an artifact from the installed bmad source tree.
+   * @param {Object} artifact - Artifact metadata
+   * @param {string} bmadDir - Installed bmad directory
+   * @returns {Promise<string[]>} Prototype skill IDs
+   */
+  async getPrototypeSkillIdsForArtifact(artifact, bmadDir) {
+    const sourceRef = this.resolveArtifactSourceRef(artifact, bmadDir);
+    if (!sourceRef) return [];
+
+    const manifest = await loadSkillManifest(sourceRef.dirPath);
+    return getPrototypeIds(manifest, sourceRef.filename);
+  }
+
+  /**
+   * Resolve the artifact source directory + filename within installed bmad tree.
+   * @param {Object} artifact - Artifact metadata
+   * @param {string} bmadDir - Installed bmad directory
+   * @returns {{dirPath: string, filename: string}|null}
+   */
+  resolveArtifactSourceRef(artifact, bmadDir) {
+    let sourcePath = '';
+
+    if ((artifact.type === 'task' || artifact.type === 'tool') && artifact.path) {
+      sourcePath = artifact.path;
+    } else if (artifact.type === 'workflow-command' && artifact.workflowPath) {
+      sourcePath = artifact.workflowPath;
+    } else if (artifact.type === 'agent-launcher' && artifact.agentPath) {
+      sourcePath = artifact.agentPath;
+    } else if (typeof artifact.sourcePath === 'string') {
+      sourcePath = artifact.sourcePath;
+    }
+
+    if (!sourcePath) return null;
+
+    let normalized = sourcePath.replaceAll('\\', '/');
+    if (path.isAbsolute(normalized)) {
+      normalized = path.relative(bmadDir, normalized).replaceAll('\\', '/');
+    }
+
+    for (const prefix of [`${this.bmadFolderName}/`, '_bmad/', 'bmad/']) {
+      if (normalized.startsWith(prefix)) {
+        normalized = normalized.slice(prefix.length);
+        break;
+      }
+    }
+
+    // eslint-disable-next-line unicorn/prefer-string-replace-all -- regex replacement is intentional
+    normalized = normalized.replace(/^\/+/, '');
+    if (!normalized || normalized.startsWith('..')) return null;
+
+    const filename = path.basename(normalized);
+    if (!filename || filename === '.' || filename === '..') return null;
+
+    const relativeDir = path.dirname(normalized);
+    const dirPath = relativeDir === '.' ? bmadDir : path.join(bmadDir, relativeDir);
+    return { dirPath, filename };
   }
 
   /**
diff --git a/tools/cli/installers/lib/ide/shared/skill-manifest.js b/tools/cli/installers/lib/ide/shared/skill-manifest.js
index ff940242f..71a380cf0 100644
--- a/tools/cli/installers/lib/ide/shared/skill-manifest.js
+++ b/tools/cli/installers/lib/ide/shared/skill-manifest.js
@@ -31,18 +31,65 @@ async function loadSkillManifest(dirPath) {
  * @returns {string} canonicalId or empty string
  */
 function getCanonicalId(manifest, filename) {
-  if (!manifest) return '';
+  const manifestEntry = resolveManifestEntry(manifest, filename);
+  return manifestEntry?.canonicalId || '';
+}
+
+/**
+ * Get duplicate prototype skill IDs for a specific file from a loaded skill manifest.
+ * Prototype IDs are optional and only used by skill-format installers.
+ * @param {Object|null} manifest - Loaded manifest (from loadSkillManifest)
+ * @param {string} filename - Source filename to look up
+ * @returns {string[]} Duplicate prototype IDs
+ */
+function getPrototypeIds(manifest, filename) {
+  const manifestEntry = resolveManifestEntry(manifest, filename);
+  if (!manifestEntry) return [];
+
+  // Support one canonical field name plus temporary/fallback aliases during transition.
+  const rawIds = manifestEntry.prototypeIds ?? manifestEntry.skillPrototypeIds ?? manifestEntry.duplicateSkillIds ?? [];
+  return normalizeIdList(rawIds);
+}
+
+/**
+ * Resolve a manifest entry for a source filename.
+ * Handles single-entry manifests and extension fallbacks.
+ * @param {Object|null} manifest - Loaded manifest
+ * @param {string} filename - Source filename
+ * @returns {Object|null} Manifest entry object
+ */
+function resolveManifestEntry(manifest, filename) {
+  if (!manifest) return null;
   // Single-entry manifest applies to all files in the directory
-  if (manifest.__single) return manifest.__single.canonicalId || '';
+  if (manifest.__single) return manifest.__single;
   // Multi-entry: look up by filename directly
-  if (manifest[filename]) return manifest[filename].canonicalId || '';
+  if (manifest[filename]) return manifest[filename];
   // Fallback: try alternate extensions for compiled files
   const baseName = filename.replace(/\.(md|xml)$/i, '');
   const agentKey = `${baseName}.agent.yaml`;
-  if (manifest[agentKey]) return manifest[agentKey].canonicalId || '';
+  if (manifest[agentKey]) return manifest[agentKey];
   const xmlKey = `${baseName}.xml`;
-  if (manifest[xmlKey]) return manifest[xmlKey].canonicalId || '';
-  return '';
+  if (manifest[xmlKey]) return manifest[xmlKey];
+  return null;
 }
 
-module.exports = { loadSkillManifest, getCanonicalId };
+/**
+ * Normalize possible scalar/array ID list formats to a unique string array.
+ * @param {string|string[]|unknown} ids - Candidate IDs
+ * @returns {string[]} Normalized IDs
+ */
+function normalizeIdList(ids) {
+  const asArray = Array.isArray(ids) ? ids : typeof ids === 'string' ? [ids] : [];
+  const unique = new Set();
+
+  for (const id of asArray) {
+    if (typeof id !== 'string') continue;
+    const trimmed = id.trim();
+    if (!trimmed) continue;
+    unique.add(trimmed);
+  }
+
+  return [...unique];
+}
+
+module.exports = { loadSkillManifest, getCanonicalId, getPrototypeIds };