fix: Global skill installs work without manual folder moves

Packages/src/Cli~/src/__tests__/cli-e2e.test.ts

@@ -669,6 +669,7 @@ describe('CLI E2E Tests (requires running Unity)', () => {
     });
 
     it('should install skills for claude target', () => {
+      // Verifies default installs land where Claude Code can discover skills.
       // First uninstall to ensure clean state
       runCli('skills uninstall --claude');
 
@@ -677,7 +678,6 @@ describe('CLI E2E Tests (requires running Unity)', () => {
         UNITY_PROJECT_ROOT,
         '.claude',
         'skills',
-        'unity-cli-loop',
         'uloop-compile',
         'SKILL.md',
       );
@@ -687,7 +687,8 @@ describe('CLI E2E Tests (requires running Unity)', () => {
       expect(existsSync(installedSkillPath)).toBe(true);
     });
 
-    it('should install skills directly under skills when grouping is disabled', () => {
+    it('should install skills directly under skills when flat flag is provided', () => {
+      // Verifies the explicit flat flag remains accepted for discoverable installs.
       runCli('skills uninstall --claude');
 
       const { stdout, exitCode } = runCli('skills install --claude --flat');

Packages/src/Cli~/src/__tests__/skills-command.test.ts

@@ -0,0 +1,79 @@
+interface MockInstallResult {
+  installed: number;
+  updated: number;
+  skipped: number;
+  bundledCount: number;
+  projectCount: number;
+  deprecatedRemoved: number;
+}
+
+interface MockUninstallResult {
+  removed: number;
+  notFound: number;
+}
+
+const mockGetAllSkillStatuses = jest.fn<unknown[], [unknown, boolean, boolean]>();
+const mockInstallAllSkills = jest.fn<MockInstallResult, [unknown, boolean, boolean]>();
+const mockUninstallAllSkills = jest.fn<MockUninstallResult, [unknown, boolean, boolean]>();
+const mockGetInstallDir = jest.fn<string, [unknown, boolean, boolean]>();
+const mockGetTotalSkillCount = jest.fn<number, []>();
+
+jest.mock('../skills/skills-manager.js', () => ({
+  DEFAULT_GROUP_MANAGED_SKILLS: false,
+  getAllSkillStatuses: (target: unknown, global: boolean, groupManagedSkills: boolean): unknown[] =>
+    mockGetAllSkillStatuses(target, global, groupManagedSkills),
+  installAllSkills: (
+    target: unknown,
+    global: boolean,
+    groupManagedSkills: boolean,
+  ): MockInstallResult => mockInstallAllSkills(target, global, groupManagedSkills),
+  uninstallAllSkills: (
+    target: unknown,
+    global: boolean,
+    groupManagedSkills: boolean,
+  ): MockUninstallResult => mockUninstallAllSkills(target, global, groupManagedSkills),
+  getInstallDir: (target: unknown, global: boolean, groupManagedSkills: boolean): string =>
+    mockGetInstallDir(target, global, groupManagedSkills),
+  getTotalSkillCount: (): number => mockGetTotalSkillCount(),
+}));
+
+import { Command } from 'commander';
+import { registerSkillsCommand } from '../skills/skills-command.js';
+
+describe('skills command', () => {
+  let consoleLogSpy: jest.SpyInstance;
+
+  beforeEach(() => {
+    jest.clearAllMocks();
+    consoleLogSpy = jest.spyOn(console, 'log').mockImplementation(() => undefined);
+    mockInstallAllSkills.mockReturnValue({
+      installed: 1,
+      updated: 0,
+      skipped: 0,
+      bundledCount: 1,
+      projectCount: 0,
+      deprecatedRemoved: 0,
+    });
+    mockUninstallAllSkills.mockReturnValue({ removed: 1, notFound: 0 });
+    mockGetInstallDir.mockReturnValue('/home/user/.claude/skills');
+    mockGetTotalSkillCount.mockReturnValue(1);
+  });
+
+  afterEach(() => {
+    consoleLogSpy.mockRestore();
+  });
+
+  it('installs Claude Code skills into the discoverable flat layout by default', async () => {
+    // Verifies the default CLI path matches Claude Code skill discovery.
+    const program = new Command();
+    registerSkillsCommand(program);
+
+    await program.parseAsync(['node', 'uloop', 'skills', 'install', '--claude', '--global']);
+
+    expect(mockInstallAllSkills).toHaveBeenCalledWith(
+      expect.objectContaining({ id: 'claude' }),
+      true,
+      false,
+    );
+  });
+});

Packages/src/Cli~/src/__tests__/skills-manager.test.ts

@@ -19,6 +19,7 @@ import {
   parseFrontmatter,
   removeDeprecatedSkillDirs,
   syncInstalledSkillDirectory,
+  uninstallAllSkills,
 } from '../skills/skills-manager.js';
 import { getTargetConfig } from '../skills/target-config.js';
 
@@ -225,6 +226,13 @@ describe('skill install layout', () => {
     );
   });
 
+  it('should resolve the flat install directory by default', () => {
+    // Verifies default installs land where Claude Code can discover skills.
+    expect(getInstallDir(getTargetConfig('claude'), true)).toBe(
+      join(homedir(), '.claude', 'skills'),
+    );
+  });
+
   it('should resolve the selected skill directory for uninstall operations', () => {
     const skillsRoot = createSkillsRoot();
 
@@ -376,7 +384,7 @@ describe('skill install layout', () => {
 
     process.chdir(projectRoot);
 
-    const skillsRoot = getInstallDir(getTargetConfig('claude'), false);
+    const skillsRoot = getInstallDir(getTargetConfig('claude'), false, true);
     syncInstalledSkillDirectory(
       join(skillsRoot, 'uloop-capture-tool'),
       'SKILL.md',
@@ -437,6 +445,28 @@ describe('skill install layout', () => {
     expect(existsSync(join(managedSkillsRoot, 'uloop-unity-search'))).toBe(false);
   });
 
+  it('should remove an installed skill from both layouts by default', () => {
+    // Verifies default uninstall cleans up the previous grouped CLI layout.
+    const projectRoot = createUnityProjectRoot();
+    const skillsRoot = join(projectRoot, '.claude', 'skills');
+    const projectSkillDir = join(projectRoot, 'Assets', 'Test', 'Editor', 'CleanupTool', 'Skill');
+    const skillName = 'uloop-cleanup-test';
+
+    writeSkill(
+      projectSkillDir,
+      ['---', `name: ${skillName}`, '---', '', '# Cleanup Test', ''].join('\n'),
+    );
+    writeSkill(join(skillsRoot, skillName));
+    writeSkill(join(skillsRoot, 'unity-cli-loop', skillName));
+    process.chdir(projectRoot);
+
+    const result = uninstallAllSkills(getTargetConfig('claude'), false);
+
+    expect(result.removed).toBe(1);
+    expect(existsSync(join(skillsRoot, skillName))).toBe(false);
+    expect(existsSync(join(skillsRoot, 'unity-cli-loop', skillName))).toBe(false);
+  });
+
   it('should remove stale files when syncing an installed skill directory', () => {
     const skillsRoot = createSkillsRoot();
     const skillDir = join(skillsRoot, 'unity-cli-loop', 'uloop-execute-dynamic-code');

Packages/src/Cli~/src/skills/skills-command.ts

@@ -12,6 +12,7 @@ import {
   uninstallAllSkills,
   getInstallDir,
   getTotalSkillCount,
+  DEFAULT_GROUP_MANAGED_SKILLS,
 } from './skills-manager.js';
 import { TargetConfig, ALL_TARGET_IDS, getTargetConfig } from './target-config.js';
 
@@ -36,7 +37,7 @@ export function registerSkillsCommand(program: Command): void {
     .command('list')
     .description('List all uloop skills and their installation status')
     .option('-g, --global', 'Check global installation')
-    .option('--flat', 'Install directly under skills/ instead of skills/unity-cli-loop/')
+    .option('--flat', 'Use skills/ directly (default)')
     .option('--claude', 'Check Claude Code installation')
     .option('--codex', 'Check Codex CLI installation')
     .option('--cursor', 'Check Cursor installation')
@@ -47,14 +48,14 @@ export function registerSkillsCommand(program: Command): void {
     .action((options: SkillsOptions) => {
       const targets = resolveTargets(options);
       const global = options.global ?? false;
-      listSkills(targets, global, !(options.flat ?? false));
+      listSkills(targets, global, DEFAULT_GROUP_MANAGED_SKILLS);
     });
 
   skillsCmd
     .command('install')
     .description('Install all uloop skills')
     .option('-g, --global', 'Install to global location')
-    .option('--flat', 'Install directly under skills/ instead of skills/unity-cli-loop/')
+    .option('--flat', 'Install directly under skills/ (default)')
     .option('--claude', 'Install to Claude Code')
     .option('--codex', 'Install to Codex CLI')
     .option('--cursor', 'Install to Cursor')
@@ -68,14 +69,14 @@ export function registerSkillsCommand(program: Command): void {
         showTargetGuidance('install');
         return;
       }
-      installSkills(targets, options.global ?? false, !(options.flat ?? false));
+      installSkills(targets, options.global ?? false, DEFAULT_GROUP_MANAGED_SKILLS);
     });
 
   skillsCmd
     .command('uninstall')
     .description('Uninstall all uloop skills')
     .option('-g, --global', 'Uninstall from global location')
-    .option('--flat', 'Uninstall skills installed directly under skills/')
+    .option('--flat', 'Uninstall skills installed directly under skills/ (default)')
     .option('--claude', 'Uninstall from Claude Code')
     .option('--codex', 'Uninstall from Codex CLI')
     .option('--cursor', 'Uninstall from Cursor')
@@ -89,7 +90,7 @@ export function registerSkillsCommand(program: Command): void {
         showTargetGuidance('uninstall');
         return;
       }
-      uninstallSkills(targets, options.global ?? false, !(options.flat ?? false));
+      uninstallSkills(targets, options.global ?? false, DEFAULT_GROUP_MANAGED_SKILLS);
     });
 }
 
@@ -123,17 +124,17 @@ function showTargetGuidance(command: string): void {
   console.log(`\nPlease specify at least one target for '${command}':`);
   console.log('');
   console.log('Available targets:');
-  console.log('  --claude        Claude Code (.claude/skills/unity-cli-loop/)');
-  console.log('  --codex         Codex CLI (.codex/skills/unity-cli-loop/)');
-  console.log('  --cursor        Cursor (.cursor/skills/unity-cli-loop/)');
-  console.log('  --gemini        Gemini CLI (.gemini/skills/unity-cli-loop/)');
-  console.log('  --agents        Other (.agents) (.agents/skills/unity-cli-loop/)');
-  console.log('  --windsurf      Windsurf (.agents/skills/unity-cli-loop/)');
-  console.log('  --antigravity   Antigravity (.agent/skills/unity-cli-loop/)');
+  console.log('  --claude        Claude Code (.claude/skills/)');
+  console.log('  --codex         Codex CLI (.codex/skills/)');
+  console.log('  --cursor        Cursor (.cursor/skills/)');
+  console.log('  --gemini        Gemini CLI (.gemini/skills/)');
+  console.log('  --agents        Other (.agents) (.agents/skills/)');
+  console.log('  --windsurf      Windsurf (.agents/skills/)');
+  console.log('  --antigravity   Antigravity (.agent/skills/)');
   console.log('');
   console.log('Options:');
   console.log('  -g, --global   Use global location');
-  console.log('  --flat         Use skills/ directly instead of skills/unity-cli-loop/');
+  console.log('  --flat         Use skills/ directly (default)');
   console.log('');
   console.log('Examples:');
   console.log(`  uloop skills ${command} --claude`);

Packages/src/Cli~/src/skills/skills-manager.ts

@@ -56,6 +56,7 @@ const EXCLUDED_DIRS = new Set([
   'Skill',
 ]);
 const EXCLUDED_FILES = new Set(['.meta', '.DS_Store', '.gitkeep']);
+export const DEFAULT_GROUP_MANAGED_SKILLS = false;
 class SkillsPathConstants {
   public static readonly PACKAGES_DIR = 'Packages';
   public static readonly SRC_DIR = 'src';
@@ -268,7 +269,7 @@ function getSkillStatus(
   return 'installed';
 }
 
-/** @internal Move managed skills from the legacy flat layout into the namespaced install root. */
+/** @internal Move top-level managed skills into the namespaced install root when grouping is requested. */
 export function migrateLegacyManagedSkills(
   baseDir: string,
   managedSkillDirNames: readonly string[],
@@ -625,7 +626,7 @@ function resolveSkillSearchRootCandidate(candidate: string): string {
 export function getAllSkillStatuses(
   target: TargetConfig,
   global: boolean,
-  groupManagedSkills: boolean = true,
+  groupManagedSkills: boolean = DEFAULT_GROUP_MANAGED_SKILLS,
 ): SkillInfo[] {
   const allSkills = collectAllSkills();
   return allSkills.map((skill) => ({
@@ -755,7 +756,7 @@ interface InstallResult {
 export function installAllSkills(
   target: TargetConfig,
   global: boolean,
-  groupManagedSkills: boolean = true,
+  groupManagedSkills: boolean = DEFAULT_GROUP_MANAGED_SKILLS,
 ): InstallResult {
   const result: InstallResult = {
     installed: 0,
@@ -826,7 +827,7 @@ interface UninstallResult {
 export function uninstallAllSkills(
   target: TargetConfig,
   global: boolean,
-  groupManagedSkills: boolean = true,
+  groupManagedSkills: boolean = DEFAULT_GROUP_MANAGED_SKILLS,
 ): UninstallResult {
   const result: UninstallResult = { removed: 0, notFound: 0 };
 
@@ -835,7 +836,11 @@ export function uninstallAllSkills(
 
   const allSkills = collectAllSkills();
   for (const skill of allSkills) {
-    if (uninstallSkill(skill, target, global, groupManagedSkills)) {
+    const removed = groupManagedSkills
+      ? uninstallSkill(skill, target, global, groupManagedSkills)
+      : uninstallSkillFromAllLayouts(skill, target, global);
+
+    if (removed) {
       result.removed++;
     } else {
       result.notFound++;
@@ -848,7 +853,7 @@ export function uninstallAllSkills(
 export function getInstallDir(
   target: TargetConfig,
   global: boolean,
-  groupManagedSkills: boolean = true,
+  groupManagedSkills: boolean = DEFAULT_GROUP_MANAGED_SKILLS,
 ): string {
   const baseDir = getSkillsBaseDir(target, global);
   return groupManagedSkills ? getManagedSkillsDir(baseDir) : baseDir;