diff --git a/cli/bin/commands/skills.mjs b/cli/bin/commands/skills.mjs
index 63e4efc32..a314e239a 100644
--- a/cli/bin/commands/skills.mjs
+++ b/cli/bin/commands/skills.mjs
@@ -1288,15 +1288,18 @@ function providerAgentsUpToDate(bundleDir, root, provider, scope) {
   const srcDir = join(bundleDir, provider, 'agents');
   if (!existsSync(srcDir)) return true;
 
-  const destDir = scope === 'user'
-    ? artifact.userDir(root)
-    : join(root, provider, 'agents');
+  const projectDir = join(root, provider, 'agents');
+  const destDirs = scope === 'user'
+    ? [artifact.userDir(root)]
+    : scope === 'project' || !isHomeDir(root)
+      ? [projectDir]
+      : [...new Set([artifact.userDir(root), projectDir])];
   const agentFiles = readdirSync(srcDir).filter(name => name.endsWith(artifact.ext));
-  return agentFiles.every(name => {
+  return agentFiles.every(name => destDirs.some(destDir => {
     const localPath = join(destDir, name);
     return existsSync(localPath)
       && hashSkillFile(join(srcDir, name)) === hashSkillFile(localPath);
-  });
+  }));
 }
 
 function copyProviderAgents(bundleDir, root, providers, { scope, home = homedir() } = {}) {
diff --git a/tests/skills-cli.test.js b/tests/skills-cli.test.js
index bda4e03b2..fde99abac 100644
--- a/tests/skills-cli.test.js
+++ b/tests/skills-cli.test.js
@@ -308,6 +308,23 @@ describe('copyProviderAgents: Claude, Copilot, and Cursor subagents', () => {
     rmSync(home, { recursive: true, force: true });
   });
 
+  test('skills check accepts current Copilot user agents in a home-rooted checkout', () => {
+    const home = mkdtempSync(join(tmpdir(), 'imp-agents-check-home-'));
+    execSync('git init', { cwd: home });
+    const bundleRoot = createFakeUniversalBundle(home, ['.github']);
+    const env = { ...process.env, HOME: home, IMPECCABLE_BUNDLE_PATH: bundleRoot };
+
+    run('skills install -y --scope=global --no-hooks --providers=github', { cwd: home, env });
+    expect(existsSync(join(home, '.copilot', 'agents', 'impeccable-finish-reviewer.agent.md'))).toBe(true);
+    expect(existsSync(join(home, '.github', 'agents'))).toBe(false);
+
+    const output = run('skills check', { cwd: home, env });
+    expect(output).toContain('Skills are up to date');
+    expect(output).not.toContain('Updates available');
+
+    rmSync(home, { recursive: true, force: true });
+  }, 15000);
+
   test('project scope reports user-level Copilot agents that shadow the installed ones; Cursor never does (project wins there)', () => {
     const tmp = mkdtempSync(join(tmpdir(), 'imp-agents-shadow-'));
     const home = mkdtempSync(join(tmpdir(), 'imp-agents-shadow-home-'));