fix(doctor): derive host skill manifests (SUP-3488) (#2961)

src/commands/doctor.ts

@@ -4345,7 +4345,7 @@ export async function buildChecks(
 
   // 2. Skill conformance (SKILL group — gated)
   if (scope === 'all' && skillsDir) {
-    const conformanceResult = checkSkillConformance(skillsDir);
+    const conformanceResult = skillConformanceCheck(skillsDir);
     checks.push(conformanceResult);
   }
 
@@ -7432,15 +7432,13 @@ function printAutoFixReport(report: AutoFixReport, dryRun: boolean, jsonOutput:
 
 
 /** Quick skill conformance check — frontmatter + required sections */
-function checkSkillConformance(skillsDir: string): Check {
-  const manifestPath = join(skillsDir, 'manifest.json');
-  if (!existsSync(manifestPath)) {
-    return { name: 'skill_conformance', status: 'warn', message: 'manifest.json not found' };
-  }
-
+export function skillConformanceCheck(skillsDir: string): Check {
   try {
-    const manifest = JSON.parse(readFileSync(manifestPath, 'utf-8'));
-    const skills = manifest.skills || [];
+    // Host workspaces are allowed to omit a gbrain-specific manifest. Keep
+    // conformance aligned with resolver_health and skill_brain_first by using
+    // the canonical fallback that derives entries from direct SKILL.md files.
+    const manifest = loadOrDeriveManifest(skillsDir);
+    const skills = manifest.skills;
     let passing = 0;
     const failing: string[] = [];
 
@@ -7460,7 +7458,8 @@ function checkSkillConformance(skillsDir: string): Check {
     }
 
     if (failing.length === 0) {
-      return { name: 'skill_conformance', status: 'ok', message: `${passing}/${skills.length} skills pass` };
+      const derivedNote = manifest.derived ? ' (derived from SKILL.md files)' : '';
+      return { name: 'skill_conformance', status: 'ok', message: `${passing}/${skills.length} skills pass${derivedNote}` };
     }
     return {
       name: 'skill_conformance',
@@ -7468,7 +7467,7 @@ function checkSkillConformance(skillsDir: string): Check {
       message: `${passing}/${skills.length} pass. Failing: ${failing.join(', ')}`,
     };
   } catch {
-    return { name: 'skill_conformance', status: 'warn', message: 'Could not parse manifest.json' };
+    return { name: 'skill_conformance', status: 'warn', message: 'Could not load or derive skills manifest' };
   }
 }
 

test/doctor.test.ts

@@ -1,4 +1,7 @@
 import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:test';
+import { mkdirSync, rmSync, writeFileSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
 
 describe('doctor command', () => {
   test('doctor module exports runDoctor', async () => {
@@ -120,6 +123,24 @@ describe('doctor command', () => {
     }
   });
 
+  test('skill conformance derives a valid host manifest when manifest.json is absent', async () => {
+    const { skillConformanceCheck } = await import('../src/commands/doctor.ts');
+    const skillsDir = join(tmpdir(), `gbrain-doctor-skills-${crypto.randomUUID()}`);
+    mkdirSync(join(skillsDir, 'host-only'), { recursive: true });
+    writeFileSync(
+      join(skillsDir, 'host-only', 'SKILL.md'),
+      '---\nname: host-only\ndescription: host-owned skill\n---\n\n# Host-only\n',
+    );
+    try {
+      const check = skillConformanceCheck(skillsDir);
+      expect(check).toMatchObject({ name: 'skill_conformance', status: 'ok' });
+      expect(check.message).toContain('1/1 skills pass');
+      expect(check.message).toContain('derived from SKILL.md files');
+    } finally {
+      rmSync(skillsDir, { recursive: true, force: true });
+    }
+  });
+
   // v0.31.2 — facts_extraction_health check added in PR1 commit 12.
   // Reads ingest_log rows with source_type='facts:absorb' (written by
   // writeFactsAbsorbLog from src/core/facts/absorb-log.ts), groups by