fix(auth): preserve bare profile behavior across runtime and sync

src/auth/commands/create-command.ts

@@ -111,6 +111,9 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
   const previousUnifiedProfile = existsUnified
     ? ctx.registry.getAllAccountsUnified()[profileName]
     : undefined;
+  const previousBare =
+    previousLegacyProfile?.bare === true || previousUnifiedProfile?.bare === true;
+  const effectiveBare = bare === true || (profileExistedBeforeCreate && previousBare);
   const previousContextPolicy =
     profileExistedBeforeCreate && (previousUnifiedProfile || previousLegacyProfile)
       ? resolveAccountContextPolicy(previousUnifiedProfile || previousLegacyProfile)
@@ -169,7 +172,9 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
 
     if (previousContextPolicy) {
       try {
-        await ctx.instanceMgr.ensureInstance(profileName, previousContextPolicy);
+        await ctx.instanceMgr.ensureInstance(profileName, previousContextPolicy, {
+          bare: previousBare,
+        });
       } catch {
         // Best-effort rollback for context mode/group.
       }
@@ -180,7 +185,7 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
     // Create instance directory
     console.log(info(`Creating profile: ${profileName}`));
     const instancePath = await ctx.instanceMgr.ensureInstance(profileName, contextPolicy, {
-      bare: !!bare,
+      bare: effectiveBare,
     });
 
     // Create/update profile entry based on config mode
@@ -190,13 +195,13 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
         ctx.registry.updateAccountUnified(profileName, {
           context_mode: contextMetadata.context_mode,
           context_group: contextMetadata.context_group,
-          ...(bare ? { bare: true } : {}),
+          ...(effectiveBare ? { bare: true } : {}),
         });
         ctx.registry.touchAccountUnified(profileName);
       } else {
         ctx.registry.createAccountUnified(profileName, {
           ...contextMetadata,
-          ...(bare ? { bare: true } : {}),
+          ...(effectiveBare ? { bare: true } : {}),
         });
       }
     } else {
@@ -206,14 +211,14 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
           type: 'account',
           context_mode: contextMetadata.context_mode,
           context_group: contextMetadata.context_group,
-          ...(bare ? { bare: true } : {}),
+          ...(effectiveBare ? { bare: true } : {}),
         });
       } else {
         ctx.registry.createProfile(profileName, {
           type: 'account',
           context_mode: contextMetadata.context_mode,
           context_group: contextMetadata.context_group,
-          ...(bare ? { bare: true } : {}),
+          ...(effectiveBare ? { bare: true } : {}),
         });
       }
     }
@@ -271,7 +276,7 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
               `Instance: ${instancePath}\n` +
               `Type:     account\n` +
               `Context:  ${formatAccountContextPolicy(contextPolicy)}` +
-              (bare ? '\nMode:     bare (no shared symlinks)' : ''),
+              (effectiveBare ? '\nMode:     bare (no shared symlinks)' : ''),
             'Profile Created'
           )
         );

src/auth/profile-continuity-inheritance.ts

@@ -146,7 +146,9 @@ export async function resolveProfileContinuityInheritance(
       isAccountContextMetadata(mappedProfile) ? mappedProfile : undefined
     );
     const instanceMgr = new InstanceManager();
-    const instancePath = await instanceMgr.ensureInstance(sourceAccount, contextPolicy);
+    const instancePath = await instanceMgr.ensureInstance(sourceAccount, contextPolicy, {
+      bare: mappedProfile.bare === true,
+    });
 
     return {
       sourceAccount,

src/auth/profile-detector.ts

@@ -203,6 +203,7 @@ class ProfileDetector {
           context_mode: account.context_mode,
           context_group: account.context_group,
           continuity_mode: account.continuity_mode,
+          bare: account.bare,
         },
       };
     }

src/auth/profile-registry.ts

@@ -45,6 +45,7 @@ interface CreateMetadata {
   context_mode?: 'isolated' | 'shared';
   context_group?: string;
   continuity_mode?: 'standard' | 'deeper';
+  bare?: boolean;
 }
 
 export class ProfileRegistry {
@@ -173,6 +174,7 @@ export class ProfileRegistry {
       context_mode: metadata.context_mode,
       context_group: metadata.context_group,
       continuity_mode: metadata.continuity_mode,
+      bare: metadata.bare,
     });
 
     // Note: No longer auto-set as default
@@ -321,6 +323,7 @@ export class ProfileRegistry {
       context_mode: metadata.context_mode,
       context_group: metadata.context_group,
       continuity_mode: metadata.continuity_mode,
+      bare: metadata.bare,
     });
     saveUnifiedConfig(config);
   }
@@ -449,6 +452,7 @@ export class ProfileRegistry {
         context_mode: account.context_mode,
         context_group: account.context_group,
         continuity_mode: account.continuity_mode,
+        bare: account.bare,
       };
     }
 

src/ccs.ts

@@ -1132,10 +1132,16 @@ async function main(): Promise<void> {
       const accountMetadata = isAccountContextMetadata(profileInfo.profile)
         ? profileInfo.profile
         : undefined;
+      const isBareProfile =
+        typeof profileInfo.profile === 'object' &&
+        profileInfo.profile !== null &&
+        (profileInfo.profile as { bare?: unknown }).bare === true;
       const contextPolicy = resolveAccountContextPolicy(accountMetadata);
 
       // Ensure instance exists (lazy init if needed)
-      const instancePath = await instanceMgr.ensureInstance(profileInfo.name, contextPolicy);
+      const instancePath = await instanceMgr.ensureInstance(profileInfo.name, contextPolicy, {
+        bare: isBareProfile,
+      });
 
       // Update last_used timestamp (check unified config first, fallback to legacy)
       if (registry.hasAccountUnified(profileInfo.name)) {

src/commands/sync-command.ts

@@ -53,9 +53,13 @@ export async function handleSyncCommand(): Promise<void> {
     if (profile.bare) {
       continue; // Skip bare profiles
     }
+
+    if (!instanceMgr.hasInstance(name)) {
+      continue;
+    }
+
     const instancePath = instanceMgr.getInstancePath(name);
-    if (instancePath) {
+    if (instanceMgr.syncMcpServers(instancePath)) {
-      instanceMgr.syncMcpServers(instancePath);
       mcpSynced++;
     }
   }

src/management/instance-manager.ts

@@ -14,7 +14,7 @@ import { AccountContextPolicy, DEFAULT_ACCOUNT_CONTEXT_MODE } from '../auth/acco
 import { getCcsDir, getCcsHome } from '../utils/config-manager';
 
 /** Options for instance creation */
-interface InstanceOptions {
+export interface InstanceOptions {
   /** Skip shared symlinks (commands, skills, agents, settings.json) */
   bare?: boolean;
 }
@@ -108,9 +108,6 @@ class InstanceManager {
       if (!options.bare) {
         this.sharedManager.linkSharedDirectories(instancePath);
       }
-
-      // Copy global configs if exist (settings.json only)
-      this.copyGlobalConfigs(instancePath);
     } catch (error) {
       throw new Error(
         `Failed to initialize instance for ${profileName}: ${(error as Error).message}`
@@ -180,33 +177,31 @@ class InstanceManager {
     return fs.existsSync(instancePath);
   }
 
-  /**
-   * Copy global configs to instance (optional)
-   */
-  private copyGlobalConfigs(_instancePath: string): void {
-    // No longer needed - settings.json now symlinked via SharedManager
-  }
-
   /**
    * Sync MCP servers from global ~/.claude.json to instance .claude.json.
    * Selectively copies only mcpServers key (not OAuth sessions or caches).
    */
-  syncMcpServers(instancePath: string): void {
+  syncMcpServers(instancePath: string): boolean {
     const homeDir = getCcsHome();
     const globalClaudeJson = path.join(homeDir, '.claude.json');
 
     if (!fs.existsSync(globalClaudeJson)) {
-      return;
+      return false;
     }
 
     try {
       const globalContent = JSON.parse(fs.readFileSync(globalClaudeJson, 'utf8'));
-      const mcpServers = globalContent.mcpServers;
+      const rawMcpServers = globalContent.mcpServers;
-
+      if (
-      if (!mcpServers || Object.keys(mcpServers).length === 0) {
+        !rawMcpServers ||
-        return;
+        typeof rawMcpServers !== 'object' ||
+        Array.isArray(rawMcpServers) ||
+        Object.keys(rawMcpServers).length === 0
+      ) {
+        return false;
       }
 
+      const mcpServers = rawMcpServers as Record<string, unknown>;
       const instanceClaudeJson = path.join(instancePath, '.claude.json');
       let instanceContent: Record<string, unknown> = {};
 
@@ -220,12 +215,22 @@ class InstanceManager {
       }
 
       // Merge: global MCP servers as base, instance-specific overrides on top
-      const existingMcp = (instanceContent.mcpServers as Record<string, unknown> | undefined) || {};
+      const rawExistingMcp = instanceContent.mcpServers;
+      const existingMcp =
+        rawExistingMcp && typeof rawExistingMcp === 'object' && !Array.isArray(rawExistingMcp)
+          ? (rawExistingMcp as Record<string, unknown>)
+          : {};
       instanceContent.mcpServers = { ...mcpServers, ...existingMcp };
 
-      fs.writeFileSync(instanceClaudeJson, JSON.stringify(instanceContent, null, 2), 'utf8');
+      fs.writeFileSync(instanceClaudeJson, JSON.stringify(instanceContent, null, 2), {
-    } catch {
+        encoding: 'utf8',
+        mode: 0o600,
+      });
+      return true;
+    } catch (error) {
       // Best-effort: don't fail instance creation if MCP sync fails
+      console.warn(`[!] MCP sync skipped: ${(error as Error).message}`);
+      return false;
     }
   }
 

src/web-server/routes/account-routes.ts

@@ -268,6 +268,7 @@ router.put('/:name/context', async (req: Request, res: Response): Promise<void>
 
     const previousUnified = existsUnified ? registry.getAllAccountsUnified()[name] : undefined;
     const previousLegacy = existsLegacy ? registry.getProfile(name) : undefined;
+    const isBare = previousUnified?.bare === true || previousLegacy?.bare === true;
 
     try {
       if (existsUnified) {
@@ -277,7 +278,7 @@ router.put('/:name/context', async (req: Request, res: Response): Promise<void>
         registry.updateProfile(name, metadata);
       }
 
-      await instanceMgr.ensureInstance(name, policy);
+      await instanceMgr.ensureInstance(name, policy, { bare: isBare });
     } catch (error) {
       if (existsUnified && previousUnified) {
         registry.updateAccountUnified(name, previousUnified);

tests/unit/auth-command-args.test.ts

@@ -47,6 +47,22 @@ describe('auth command args parsing', () => {
     expect(parsed.deeperContinuity).toBe(true);
   });
 
+  it('parses bare flag for create command', () => {
+    const parsed = parseArgs(['work', '--bare']);
+
+    expect(parsed.profileName).toBe('work');
+    expect(parsed.bare).toBe(true);
+  });
+
+  it('parses bare flag with shared context flags', () => {
+    const parsed = parseArgs(['work', '--bare', '--share-context', '--context-group', 'sprint-a']);
+
+    expect(parsed.profileName).toBe('work');
+    expect(parsed.bare).toBe(true);
+    expect(parsed.shareContext).toBe(true);
+    expect(parsed.contextGroup).toBe('sprint-a');
+  });
+
   it('tracks unknown flags and keeps positional profile intact', () => {
     const parsed = parseArgs(['--foo', 'bar', 'work']);
 

tests/unit/auth/profile-continuity-inheritance.test.ts

@@ -61,7 +61,7 @@ describe('resolveProfileContinuityInheritance', () => {
       mode: 'shared',
       group: 'team-alpha',
       continuityMode: 'deeper',
-    });
+    }, { bare: false });
   });
 
   it('supports legacy continuity_inherit_from_account fallback', async () => {
@@ -255,7 +255,46 @@ describe('resolveProfileContinuityInheritance', () => {
     });
     expect(ensureInstanceSpy).toHaveBeenCalledWith('pro', {
       mode: 'isolated',
+    }, { bare: false });
+  });
+
+  it('propagates bare source-account mode when inheriting continuity', async () => {
+    spyOn(configLoader, 'loadOrCreateUnifiedConfig').mockReturnValue({
+      version: 8,
+      continuity: {
+        inherit_from_account: {
+          glm: 'pro',
+        },
+      },
+    } as ReturnType<typeof configLoader.loadOrCreateUnifiedConfig>);
+
+    const ensureInstanceSpy = spyOn(InstanceManager.prototype, 'ensureInstance').mockResolvedValue(
+      '/tmp/.ccs/instances/pro'
+    );
+    spyOn(ProfileRegistry.prototype, 'getAllProfilesMerged').mockReturnValue({
+      pro: {
+        type: 'account',
+        created: '2026-03-01T00:00:00.000Z',
+        last_used: null,
+        bare: true,
+      },
     });
+
+    const result = await resolveProfileContinuityInheritance({
+      profileName: 'glm',
+      profileType: 'settings',
+      target: 'claude',
+    });
+
+    expect(result).toEqual({
+      sourceAccount: 'pro',
+      claudeConfigDir: '/tmp/.ccs/instances/pro',
+    });
+    expect(ensureInstanceSpy).toHaveBeenCalledWith(
+      'pro',
+      { mode: 'isolated' },
+      { bare: true }
+    );
   });
 
   it('does not apply km settings alias mapping to kimi cliproxy profile', async () => {

tests/unit/auth/profile-detector.test.ts

@@ -161,7 +161,7 @@ describe('ProfileDetector', () => {
       const mockUnifiedConfig = {
         version: 2,
         accounts: {
-          work: { created: '2025-01-01', last_used: '2025-01-02' },
+          work: { created: '2025-01-01', last_used: '2025-01-02', bare: true },
         },
       };
 
@@ -176,6 +176,7 @@ describe('ProfileDetector', () => {
         expect(result.name).toBe('work');
         expect(result.profile).toBeDefined();
         expect((result.profile as any).type).toBe('account');
+        expect((result.profile as any).bare).toBe(true);
       } finally {
         isUnifiedModeSpy.mockRestore();
         loadUnifiedConfigSpy.mockRestore();

tests/unit/auth/profile-registry-context-normalization.test.ts

@@ -91,4 +91,43 @@ describe('profile-registry context normalization', () => {
     expect(accounts.work.context_group).toBeUndefined();
     expect(accounts.work.continuity_mode).toBe('standard');
   });
+
+  it('persists bare flag for legacy profiles', () => {
+    const registry = new ProfileRegistry();
+    registry.createProfile('work', { type: 'account', bare: true });
+
+    const profile = registry.getProfile('work');
+    expect(profile.bare).toBe(true);
+  });
+
+  it('persists bare flag for unified accounts and merged projection', () => {
+    process.env.CCS_UNIFIED_CONFIG = '1';
+    const ccsDir = path.join(tempHome, '.ccs');
+    fs.mkdirSync(ccsDir, { recursive: true });
+    fs.writeFileSync(
+      path.join(ccsDir, 'config.yaml'),
+      [
+        'version: 8',
+        'accounts:',
+        '  work:',
+        '    created: "2026-03-05T00:00:00.000Z"',
+        '    last_used: null',
+        '    bare: true',
+        'profiles: {}',
+        'cliproxy:',
+        '  oauth_accounts: {}',
+        '  providers: {}',
+        '  variants: {}',
+      ].join('\n'),
+      'utf8'
+    );
+
+    const registry = new ProfileRegistry();
+
+    const accounts = registry.getAllAccountsUnified();
+    expect(accounts.work.bare).toBe(true);
+
+    const merged = registry.getAllProfilesMerged();
+    expect(merged.work.bare).toBe(true);
+  });
 });

tests/unit/commands/sync-command.test.ts

@@ -0,0 +1,84 @@
+import { afterEach, beforeEach, describe, expect, it, mock, spyOn } from 'bun:test';
+import { handleSyncCommand } from '../../../src/commands/sync-command';
+import { ClaudeDirInstaller } from '../../../src/utils/claude-dir-installer';
+import { ClaudeSymlinkManager } from '../../../src/utils/claude-symlink-manager';
+import SharedManager from '../../../src/management/shared-manager';
+import { InstanceManager } from '../../../src/management/instance-manager';
+import ProfileRegistry from '../../../src/auth/profile-registry';
+import type { ProfileMetadata } from '../../../src/types';
+
+function profile(metadata: Partial<ProfileMetadata> = {}): ProfileMetadata {
+  return {
+    type: 'account',
+    created: '2026-03-05T00:00:00.000Z',
+    last_used: null,
+    ...metadata,
+  };
+}
+
+describe('sync command MCP sync behavior', () => {
+  let originalProcessExit: typeof process.exit;
+
+  beforeEach(() => {
+    originalProcessExit = process.exit;
+    process.exit = ((code?: number) => {
+      throw new Error(`process.exit(${code ?? 0})`);
+    }) as typeof process.exit;
+  });
+
+  afterEach(() => {
+    process.exit = originalProcessExit;
+    mock.restore();
+  });
+
+  it('syncs MCP servers only to non-bare profiles', async () => {
+    spyOn(ClaudeDirInstaller.prototype, 'install').mockReturnValue(true);
+    spyOn(ClaudeDirInstaller.prototype, 'cleanupDeprecated').mockReturnValue({
+      success: true,
+      cleanedFiles: [],
+    });
+    spyOn(ClaudeSymlinkManager.prototype, 'install').mockImplementation(() => {});
+    spyOn(SharedManager.prototype, 'ensureSharedDirectories').mockImplementation(() => {});
+    spyOn(ProfileRegistry.prototype, 'getAllProfilesMerged').mockReturnValue({
+      work: profile(),
+      sandbox: profile({ bare: true }),
+      personal: profile(),
+    });
+    spyOn(InstanceManager.prototype, 'hasInstance').mockReturnValue(true);
+
+    const getInstancePathSpy = spyOn(InstanceManager.prototype, 'getInstancePath').mockImplementation(
+      (name: string) => `/tmp/${name}`
+    );
+    const syncMcpSpy = spyOn(InstanceManager.prototype, 'syncMcpServers').mockImplementation(
+      () => true
+    );
+
+    await expect(handleSyncCommand()).rejects.toThrow('process.exit(0)');
+
+    expect(getInstancePathSpy.mock.calls.map((call) => call[0])).toEqual(['work', 'personal']);
+    expect(syncMcpSpy.mock.calls.map((call) => call[0])).toEqual(['/tmp/work', '/tmp/personal']);
+  });
+
+  it('skips MCP sync when all profiles are bare', async () => {
+    spyOn(ClaudeDirInstaller.prototype, 'install').mockReturnValue(true);
+    spyOn(ClaudeDirInstaller.prototype, 'cleanupDeprecated').mockReturnValue({
+      success: true,
+      cleanedFiles: [],
+    });
+    spyOn(ClaudeSymlinkManager.prototype, 'install').mockImplementation(() => {});
+    spyOn(SharedManager.prototype, 'ensureSharedDirectories').mockImplementation(() => {});
+    spyOn(ProfileRegistry.prototype, 'getAllProfilesMerged').mockReturnValue({
+      sandbox: profile({ bare: true }),
+      experiment: profile({ bare: true }),
+    });
+    spyOn(InstanceManager.prototype, 'hasInstance').mockReturnValue(true);
+
+    const syncMcpSpy = spyOn(InstanceManager.prototype, 'syncMcpServers').mockImplementation(
+      () => true
+    );
+
+    await expect(handleSyncCommand()).rejects.toThrow('process.exit(0)');
+
+    expect(syncMcpSpy).not.toHaveBeenCalled();
+  });
+});

tests/unit/instance-manager-mcp-sync.test.ts

@@ -0,0 +1,114 @@
+import { afterEach, beforeEach, describe, expect, it, mock, spyOn } from 'bun:test';
+import * as fs from 'fs';
+import * as os from 'os';
+import * as path from 'path';
+import { InstanceManager } from '../../src/management/instance-manager';
+import SharedManager from '../../src/management/shared-manager';
+
+describe('InstanceManager MCP sync', () => {
+  let tempRoot = '';
+  let originalCcsHome: string | undefined;
+  let originalCcsDir: string | undefined;
+
+  beforeEach(() => {
+    tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), 'ccs-instance-mcp-test-'));
+    originalCcsHome = process.env.CCS_HOME;
+    originalCcsDir = process.env.CCS_DIR;
+
+    process.env.CCS_HOME = tempRoot;
+    delete process.env.CCS_DIR;
+  });
+
+  afterEach(() => {
+    mock.restore();
+
+    if (originalCcsHome !== undefined) process.env.CCS_HOME = originalCcsHome;
+    else delete process.env.CCS_HOME;
+
+    if (originalCcsDir !== undefined) process.env.CCS_DIR = originalCcsDir;
+    else delete process.env.CCS_DIR;
+
+    if (tempRoot && fs.existsSync(tempRoot)) {
+      fs.rmSync(tempRoot, { recursive: true, force: true });
+    }
+  });
+
+  it('merges global MCP servers and preserves instance-specific overrides', () => {
+    fs.writeFileSync(
+      path.join(tempRoot, '.claude.json'),
+      JSON.stringify(
+        {
+          mcpServers: {
+            globalOnly: { command: 'global-cmd' },
+            shared: { command: 'global-shared' },
+          },
+        },
+        null,
+        2
+      ),
+      'utf8'
+    );
+
+    const manager = new InstanceManager();
+    const instancePath = manager.getInstancePath('work');
+    fs.mkdirSync(instancePath, { recursive: true });
+    fs.writeFileSync(
+      path.join(instancePath, '.claude.json'),
+      JSON.stringify(
+        {
+          mcpServers: {
+            shared: { command: 'instance-shared' },
+            instanceOnly: { command: 'instance-only' },
+          },
+          otherKey: 'keep-me',
+        },
+        null,
+        2
+      ),
+      'utf8'
+    );
+
+    const synced = manager.syncMcpServers(instancePath);
+    expect(synced).toBe(true);
+
+    const instanceContent = JSON.parse(fs.readFileSync(path.join(instancePath, '.claude.json'), 'utf8'));
+    expect(instanceContent.otherKey).toBe('keep-me');
+    expect(instanceContent.mcpServers).toEqual({
+      globalOnly: { command: 'global-cmd' },
+      shared: { command: 'instance-shared' },
+      instanceOnly: { command: 'instance-only' },
+    });
+  });
+
+  it('logs warning when global MCP sync fails', () => {
+    fs.writeFileSync(path.join(tempRoot, '.claude.json'), '{invalid-json', 'utf8');
+    const warnSpy = spyOn(console, 'warn').mockImplementation(() => {});
+
+    const manager = new InstanceManager();
+    const instancePath = manager.getInstancePath('work');
+    fs.mkdirSync(instancePath, { recursive: true });
+
+    const synced = manager.syncMcpServers(instancePath);
+
+    expect(synced).toBe(false);
+    expect(warnSpy).toHaveBeenCalledTimes(1);
+    expect(String(warnSpy.mock.calls[0]?.[0] || '')).toContain('MCP sync skipped');
+  });
+
+  it('skips shared symlinks and MCP sync for bare instance creation', async () => {
+    const linkSharedSpy = spyOn(SharedManager.prototype, 'linkSharedDirectories').mockImplementation(
+      () => {}
+    );
+    spyOn(SharedManager.prototype, 'syncProjectContext').mockResolvedValue(undefined);
+    spyOn(SharedManager.prototype, 'syncAdvancedContinuityArtifacts').mockResolvedValue(undefined);
+    const syncMcpSpy = spyOn(InstanceManager.prototype, 'syncMcpServers').mockImplementation(
+      () => false
+    );
+
+    const manager = new InstanceManager();
+    await manager.ensureInstance('sandbox', { mode: 'isolated' }, { bare: true });
+
+    expect(linkSharedSpy).not.toHaveBeenCalled();
+    expect(syncMcpSpy).not.toHaveBeenCalled();
+  });
+});