fix(manifest): address PR review findings from triage

- Add missing skillClaimedDirs guard to getAgentsFromDir (F1)
- Add skills to this.files[] in collectSkills (F2)
- Add test for type:skill inside workflows/ dir (F5)
- Warn on malformed workflow.md parse in skill dirs (F6)
- Add skills count to generateManifests return value (F9)
- Remove redundant \r? from regex after line normalization (F10)
- Normalize path.relative to forward slashes for cross-platform (F12)
- Enforce directory name as skill canonicalId, warn if manifest overrides (F13)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

test/test-installation-components.js

@@ -1605,7 +1605,7 @@ async function runTests() {
     // --- Skill at unusual path: core/custom-area/my-skill/ ---
     const skillDir29 = path.join(tempFixture29, 'core', 'custom-area', 'my-skill');
     await fs.ensureDir(skillDir29);
-    await fs.writeFile(path.join(skillDir29, 'bmad-skill-manifest.yaml'), 'type: skill\ncanonicalId: my-custom-skill\n');
+    await fs.writeFile(path.join(skillDir29, 'bmad-skill-manifest.yaml'), 'type: skill\n');
     await fs.writeFile(
       path.join(skillDir29, 'workflow.md'),
       '---\nname: My Custom Skill\ndescription: A skill at an unusual path\n---\n\nSkill body content\n',
@@ -1620,10 +1620,19 @@ async function runTests() {
       '---\nname: Regular Workflow\ndescription: A regular workflow not a skill\n---\n\nWorkflow body\n',
     );
 
+    // --- Skill inside workflows/ dir: core/workflows/wf-skill/ (exercises findWorkflows skip logic) ---
+    const wfSkillDir29 = path.join(tempFixture29, 'core', 'workflows', 'wf-skill');
+    await fs.ensureDir(wfSkillDir29);
+    await fs.writeFile(path.join(wfSkillDir29, 'bmad-skill-manifest.yaml'), 'type: skill\n');
+    await fs.writeFile(
+      path.join(wfSkillDir29, 'workflow.md'),
+      '---\nname: Workflow Skill\ndescription: A skill inside workflows dir\n---\n\nSkill in workflows\n',
+    );
+
     // --- Skill inside tasks/ dir: core/tasks/task-skill/ ---
     const taskSkillDir29 = path.join(tempFixture29, 'core', 'tasks', 'task-skill');
     await fs.ensureDir(taskSkillDir29);
-    await fs.writeFile(path.join(taskSkillDir29, 'bmad-skill-manifest.yaml'), 'type: skill\ncanonicalId: task-skill\n');
+    await fs.writeFile(path.join(taskSkillDir29, 'bmad-skill-manifest.yaml'), 'type: skill\n');
     await fs.writeFile(
       path.join(taskSkillDir29, 'workflow.md'),
       '---\nname: Task Skill\ndescription: A skill inside tasks dir\n---\n\nSkill in tasks\n',
@@ -1638,7 +1647,7 @@ async function runTests() {
     await generator29.generateManifests(tempFixture29, ['core'], [], { ides: [] });
 
     // Skill at unusual path should be in skills
-    const skillEntry29 = generator29.skills.find((s) => s.canonicalId === 'my-custom-skill');
+    const skillEntry29 = generator29.skills.find((s) => s.canonicalId === 'my-skill');
     assert(skillEntry29 !== undefined, 'Skill at unusual path appears in skills[]');
     assert(skillEntry29 && skillEntry29.name === 'My Custom Skill', 'Skill has correct name from frontmatter');
     assert(
@@ -1665,13 +1674,16 @@ async function runTests() {
     const regularInSkills29 = generator29.skills.find((s) => s.canonicalId === 'regular-wf');
     assert(regularInSkills29 === undefined, 'Regular type:workflow does NOT appear in skills[]');
 
+    // Skill inside workflows/ should be in skills[], NOT in workflows[] (exercises findWorkflows skip at lines 311/322)
+    const wfSkill29 = generator29.skills.find((s) => s.canonicalId === 'wf-skill');
+    assert(wfSkill29 !== undefined, 'Skill in workflows/ dir appears in skills[]');
+    const wfSkillInWorkflows29 = generator29.workflows.find((w) => w.name === 'Workflow Skill');
+    assert(wfSkillInWorkflows29 === undefined, 'Skill in workflows/ dir does NOT appear in workflows[]');
+
     // Test scanInstalledModules recognizes skill-only modules
     const skillOnlyModDir29 = path.join(tempFixture29, 'skill-only-mod');
     await fs.ensureDir(path.join(skillOnlyModDir29, 'deep', 'nested', 'my-skill'));
-    await fs.writeFile(
+    await fs.writeFile(path.join(skillOnlyModDir29, 'deep', 'nested', 'my-skill', 'bmad-skill-manifest.yaml'), 'type: skill\n');
-      path.join(skillOnlyModDir29, 'deep', 'nested', 'my-skill', 'bmad-skill-manifest.yaml'),
-      'type: skill\ncanonicalId: nested-skill\n',
-    );
     await fs.writeFile(
       path.join(skillOnlyModDir29, 'deep', 'nested', 'my-skill', 'workflow.md'),
       '---\nname: Nested Skill\ndescription: desc\n---\nbody\n',

tools/cli/installers/lib/core/manifest-generator.js

@@ -135,6 +135,7 @@ class ManifestGenerator {
     ];
 
     return {
+      skills: this.skills.length,
       workflows: this.workflows.length,
       agents: this.agents.length,
       tasks: this.tasks.length,
@@ -189,7 +190,7 @@ class ManifestGenerator {
             if (workflowFile === 'workflow.yaml') {
               workflow = yaml.parse(content);
             } else {
-              const frontmatterMatch = content.match(/^---\r?\n([\s\S]*?)\r?\n---/);
+              const frontmatterMatch = content.match(/^---\n([\s\S]*?)\n---/);
               if (!frontmatterMatch) {
                 if (debug) console.log(`[DEBUG] collectSkills: skipped (no frontmatter): ${workflowPath}`);
                 continue;
@@ -203,12 +204,18 @@ class ManifestGenerator {
             }
 
             // Build path relative from module root
-            const relativePath = path.relative(modulePath, dir);
+            const relativePath = path.relative(modulePath, dir).split(path.sep).join('/');
             const installPath = relativePath
               ? `${this.bmadFolderName}/${moduleName}/${relativePath}/${workflowFile}`
               : `${this.bmadFolderName}/${moduleName}/${workflowFile}`;
 
-            const canonicalId = this.getCanonicalId(manifest, workflowFile) || path.basename(dir);
+            // Skills derive canonicalId from directory name — never from manifest
+            if (manifest && manifest.__single && manifest.__single.canonicalId) {
+              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)`,
+              );
+            }
+            const canonicalId = path.basename(dir);
 
             this.skills.push({
               name: workflow.name,
@@ -219,6 +226,14 @@ class ManifestGenerator {
               install_to_bmad: this.getInstallToBmad(manifest, workflowFile),
             });
 
+            // Add to files list
+            this.files.push({
+              type: 'skill',
+              name: workflow.name,
+              module: moduleName,
+              path: installPath,
+            });
+
             this.skillClaimedDirs.add(dir);
 
             if (debug) {
@@ -246,7 +261,9 @@ class ManifestGenerator {
           }
           if (hasSkillType && debug) {
             const hasWorkflow = workflowFilenames.some((f) => entries.some((e) => e.name === f));
-            if (!hasWorkflow) {
+            if (hasWorkflow) {
+              console.log(`[DEBUG] collectSkills: dir has type:skill manifest but workflow file failed to parse: ${dir}`);
+            } else {
               console.log(`[DEBUG] collectSkills: dir has type:skill manifest but no workflow.md/workflow.yaml: ${dir}`);
             }
           }
@@ -347,7 +364,7 @@ class ManifestGenerator {
               workflow = yaml.parse(content);
             } else {
               // Parse MD workflow with YAML frontmatter
-              const frontmatterMatch = content.match(/^---\r?\n([\s\S]*?)\r?\n---/);
+              const frontmatterMatch = content.match(/^---\n([\s\S]*?)\n---/);
               if (!frontmatterMatch) {
                 if (debug) {
                   console.log(`[DEBUG] Skipped (no frontmatter): ${fullPath}`);
@@ -462,6 +479,8 @@ class ManifestGenerator {
    * Only includes compiled .md files (not .agent.yaml source files)
    */
   async getAgentsFromDir(dirPath, moduleName, relativePath = '') {
+    // Skip directories claimed by collectSkills
+    if (this.skillClaimedDirs && this.skillClaimedDirs.has(dirPath)) return [];
     const agents = [];
     const entries = await fs.readdir(dirPath, { withFileTypes: true });
     // Load skill manifest for this directory (if present)