diff --git a/test/gen-skill-docs.test.ts b/test/gen-skill-docs.test.ts
index 6419b6de..b0a7538f 100644
--- a/test/gen-skill-docs.test.ts
+++ b/test/gen-skill-docs.test.ts
@@ -1979,6 +1979,35 @@ describe('setup script validation', () => {
     expect(fnBody).toContain('ln -snf "$gstack_dir/$dir_name/SKILL.md" "$target/SKILL.md"');
   });
 
+  // REGRESSION: cleanup functions must handle both old symlinks AND new real-directory pattern
+  test('cleanup functions handle real directories with symlinked SKILL.md', () => {
+    // cleanup_old_claude_symlinks must detect and remove real dirs with SKILL.md symlinks
+    const cleanupOldStart = setupContent.indexOf('cleanup_old_claude_symlinks()');
+    const cleanupOldEnd = setupContent.indexOf('}', setupContent.indexOf('cleaned up old', cleanupOldStart));
+    const cleanupOldBody = setupContent.slice(cleanupOldStart, cleanupOldEnd);
+    expect(cleanupOldBody).toContain('-d "$old_target"');
+    expect(cleanupOldBody).toContain('-L "$old_target/SKILL.md"');
+    expect(cleanupOldBody).toContain('rm -rf "$old_target"');
+
+    // cleanup_prefixed_claude_symlinks must also handle the new pattern
+    const cleanupPrefixedStart = setupContent.indexOf('cleanup_prefixed_claude_symlinks()');
+    const cleanupPrefixedEnd = setupContent.indexOf('}', setupContent.indexOf('cleaned up prefixed', cleanupPrefixedStart));
+    const cleanupPrefixedBody = setupContent.slice(cleanupPrefixedStart, cleanupPrefixedEnd);
+    expect(cleanupPrefixedBody).toContain('-d "$prefixed_target"');
+    expect(cleanupPrefixedBody).toContain('-L "$prefixed_target/SKILL.md"');
+    expect(cleanupPrefixedBody).toContain('rm -rf "$prefixed_target"');
+  });
+
+  // REGRESSION: link function must upgrade old directory symlinks
+  test('link_claude_skill_dirs removes old directory symlinks before creating real dirs', () => {
+    const fnStart = setupContent.indexOf('link_claude_skill_dirs()');
+    const fnEnd = setupContent.indexOf('}', setupContent.indexOf('linked[@]}', fnStart));
+    const fnBody = setupContent.slice(fnStart, fnEnd);
+    // Must check for and remove old symlinks before mkdir
+    expect(fnBody).toContain('if [ -L "$target" ]');
+    expect(fnBody).toContain('rm -f "$target"');
+  });
+
   test('setup supports --host auto|claude|codex|kiro', () => {
     expect(setupContent).toContain('--host');
     expect(setupContent).toContain('claude|codex|kiro|factory|auto');
diff --git a/test/relink.test.ts b/test/relink.test.ts
index b368d2bf..9e560b71 100644
--- a/test/relink.test.ts
+++ b/test/relink.test.ts
@@ -97,6 +97,71 @@ describe('gstack-relink (#578)', () => {
     expect(output).toContain('flat');
   });
 
+  // REGRESSION: unprefixed skills must be real directories, not symlinks (#761)
+  // Claude Code auto-prefixes skills nested under a parent dir symlink.
+  // e.g., `qa -> gstack/qa` gets discovered as "gstack-qa", not "qa".
+  // The fix: create real directories with SKILL.md symlinks inside.
+  test('unprefixed skills are real directories with SKILL.md symlinks, not dir symlinks', () => {
+    setupMockInstall(['qa', 'ship', 'review', 'plan-ceo-review']);
+    run(`${path.join(installDir, 'bin', 'gstack-config')} set skill_prefix false`);
+    run(`${path.join(installDir, 'bin', 'gstack-relink')}`, {
+      GSTACK_INSTALL_DIR: installDir,
+      GSTACK_SKILLS_DIR: skillsDir,
+    });
+    for (const skill of ['qa', 'ship', 'review', 'plan-ceo-review']) {
+      const skillPath = path.join(skillsDir, skill);
+      const skillMdPath = path.join(skillPath, 'SKILL.md');
+      // Must be a real directory, NOT a symlink
+      expect(fs.lstatSync(skillPath).isDirectory()).toBe(true);
+      expect(fs.lstatSync(skillPath).isSymbolicLink()).toBe(false);
+      // Must contain a SKILL.md that IS a symlink
+      expect(fs.existsSync(skillMdPath)).toBe(true);
+      expect(fs.lstatSync(skillMdPath).isSymbolicLink()).toBe(true);
+      // The SKILL.md symlink must point to the source skill's SKILL.md
+      const target = fs.readlinkSync(skillMdPath);
+      expect(target).toContain(skill);
+      expect(target).toEndWith('/SKILL.md');
+    }
+  });
+
+  // Same invariant for prefixed mode
+  test('prefixed skills are real directories with SKILL.md symlinks, not dir symlinks', () => {
+    setupMockInstall(['qa', 'ship']);
+    run(`${path.join(installDir, 'bin', 'gstack-config')} set skill_prefix true`);
+    run(`${path.join(installDir, 'bin', 'gstack-relink')}`, {
+      GSTACK_INSTALL_DIR: installDir,
+      GSTACK_SKILLS_DIR: skillsDir,
+    });
+    for (const skill of ['gstack-qa', 'gstack-ship']) {
+      const skillPath = path.join(skillsDir, skill);
+      const skillMdPath = path.join(skillPath, 'SKILL.md');
+      expect(fs.lstatSync(skillPath).isDirectory()).toBe(true);
+      expect(fs.lstatSync(skillPath).isSymbolicLink()).toBe(false);
+      expect(fs.lstatSync(skillMdPath).isSymbolicLink()).toBe(true);
+    }
+  });
+
+  // Upgrade: old directory symlinks get replaced with real directories
+  test('upgrades old directory symlinks to real directories', () => {
+    setupMockInstall(['qa', 'ship']);
+    // Simulate old behavior: create directory symlinks (the old pattern)
+    fs.symlinkSync(path.join(installDir, 'qa'), path.join(skillsDir, 'qa'));
+    fs.symlinkSync(path.join(installDir, 'ship'), path.join(skillsDir, 'ship'));
+    // Verify they start as symlinks
+    expect(fs.lstatSync(path.join(skillsDir, 'qa')).isSymbolicLink()).toBe(true);
+
+    run(`${path.join(installDir, 'bin', 'gstack-config')} set skill_prefix false`);
+    run(`${path.join(installDir, 'bin', 'gstack-relink')}`, {
+      GSTACK_INSTALL_DIR: installDir,
+      GSTACK_SKILLS_DIR: skillsDir,
+    });
+
+    // After relink: must be real directories, not symlinks
+    expect(fs.lstatSync(path.join(skillsDir, 'qa')).isSymbolicLink()).toBe(false);
+    expect(fs.lstatSync(path.join(skillsDir, 'qa')).isDirectory()).toBe(true);
+    expect(fs.lstatSync(path.join(skillsDir, 'qa', 'SKILL.md')).isSymbolicLink()).toBe(true);
+  });
+
   // Test 13: cleans stale symlinks from opposite mode
   test('cleans up stale symlinks from opposite mode', () => {
     setupMockInstall(['qa', 'ship']);