feat(auth): add --bare flag and MCP server sync for profiles

- Add --bare flag to `ccs auth create` to skip shared symlinks
  (commands/, skills/, agents/, settings.json). Bare profiles are
  clean instances without ClaudeKit or other global extensions.
  `ccs sync` respects bare flag and skips re-linking.

- Add MCP server sync from global ~/.claude.json to instances.
  Claude Code stores MCP config in ~/.claude.json (not settings.json),
  which was invisible to CCS profiles using CLAUDE_CONFIG_DIR isolation.
  Selective copy of mcpServers key only (not OAuth sessions/caches).
  `ccs sync` refreshes MCP servers across all non-bare instances.

Closes #691
Closes #692

src/auth/auth-commands.ts

@@ -91,6 +91,9 @@ class AuthCommands {
       `  ${color('ccs auth create backup --context-group sprint-a --deeper-continuity', 'command')}`
     );
     console.log('');
+    console.log(`  ${dim('# Create clean profile without shared commands/skills/agents')}`);
+    console.log(`  ${color('ccs auth create sandbox --bare', 'command')}`);
+    console.log('');
     console.log(`  ${dim('# Set work as default')}`);
     console.log(`  ${color('ccs auth default work', 'command')}`);
     console.log('');
@@ -116,6 +119,9 @@ class AuthCommands {
     console.log(
       `  ${color('--deeper-continuity', 'command')}       Advanced shared mode: sync additional continuity artifacts`
     );
+    console.log(
+      `  ${color('--bare', 'command')}                    Create clean profile without shared symlinks (no CK/commands/skills)`
+    );
     console.log(
       `  ${color('--yes, -y', 'command')}                 Skip confirmation prompts (remove)`
     );

src/auth/commands/create-command.ts

@@ -31,7 +31,7 @@ function sanitizeProfileNameForInstance(name: string): string {
  */
 export async function handleCreate(ctx: CommandContext, args: string[]): Promise<void> {
   await initUI();
-  const { profileName, force, shareContext, contextGroup, deeperContinuity, unknownFlags } =
+  const { profileName, force, shareContext, contextGroup, deeperContinuity, bare, unknownFlags } =
     parseArgs(args);
 
   if (unknownFlags && unknownFlags.length > 0) {
@@ -39,7 +39,7 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
     console.log(fail(`Unknown option(s): ${unknownList}`));
     console.log('');
     console.log(
-      `Usage: ${color('ccs auth create <profile> [--force] [--share-context] [--context-group <name>] [--deeper-continuity]', 'command')}`
+      `Usage: ${color('ccs auth create <profile> [--force] [--bare] [--share-context] [--context-group <name>] [--deeper-continuity]', 'command')}`
     );
     console.log(`Help:  ${color('ccs auth --help', 'command')}`);
     console.log('');
@@ -50,7 +50,7 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
     console.log(fail('Profile name is required'));
     console.log('');
     console.log(
-      `Usage: ${color('ccs auth create <profile> [--force] [--share-context] [--context-group <name>] [--deeper-continuity]', 'command')}`
+      `Usage: ${color('ccs auth create <profile> [--force] [--bare] [--share-context] [--context-group <name>] [--deeper-continuity]', 'command')}`
     );
     console.log('');
     console.log('Example:');
@@ -179,7 +179,9 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
   try {
     // Create instance directory
     console.log(info(`Creating profile: ${profileName}`));
-    const instancePath = await ctx.instanceMgr.ensureInstance(profileName, contextPolicy);
+    const instancePath = await ctx.instanceMgr.ensureInstance(profileName, contextPolicy, {
+      bare: !!bare,
+    });
 
     // Create/update profile entry based on config mode
     if (useUnifiedConfig) {
@@ -188,10 +190,14 @@ 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 } : {}),
         });
         ctx.registry.touchAccountUnified(profileName);
       } else {
-        ctx.registry.createAccountUnified(profileName, contextMetadata);
+        ctx.registry.createAccountUnified(profileName, {
+          ...contextMetadata,
+          ...(bare ? { bare: true } : {}),
+        });
       }
     } else {
       // Use legacy profiles.json
@@ -200,12 +206,14 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
           type: 'account',
           context_mode: contextMetadata.context_mode,
           context_group: contextMetadata.context_group,
+          ...(bare ? { bare: true } : {}),
         });
       } else {
         ctx.registry.createProfile(profileName, {
           type: 'account',
           context_mode: contextMetadata.context_mode,
           context_group: contextMetadata.context_group,
+          ...(bare ? { bare: true } : {}),
         });
       }
     }
@@ -262,7 +270,8 @@ export async function handleCreate(ctx: CommandContext, args: string[]): Promise
             `Profile:  ${profileName}\n` +
               `Instance: ${instancePath}\n` +
               `Type:     account\n` +
-              `Context:  ${formatAccountContextPolicy(contextPolicy)}`,
+              `Context:  ${formatAccountContextPolicy(contextPolicy)}` +
+              (bare ? '\nMode:     bare (no shared symlinks)' : ''),
             'Profile Created'
           )
         );

src/auth/commands/show-command.ts

@@ -63,6 +63,7 @@ export async function handleShow(ctx: CommandContext, args: string[]): Promise<v
         continuity_mode: contextPolicy.mode === 'shared' ? contextPolicy.continuityMode : null,
         instance_path: instancePath,
         session_count: sessionCount,
+        ...(profile.bare ? { bare: true } : {}),
       };
       console.log(JSON.stringify(output, null, 2));
       return;
@@ -80,6 +81,7 @@ export async function handleShow(ctx: CommandContext, args: string[]): Promise<v
       ['Created', new Date(profile.created).toLocaleString()],
       ['Last Used', profile.last_used ? new Date(profile.last_used).toLocaleString() : 'Never'],
       ['Context', formatAccountContextPolicy(contextPolicy)],
+      ...(profile.bare ? [['Bare', 'yes (no shared symlinks)']] : []),
       ['Sessions', `${sessionCount}`],
     ];
 

src/auth/commands/types.ts

@@ -22,6 +22,7 @@ export interface AuthCommandArgs {
   shareContext?: boolean;
   contextGroup?: string;
   deeperContinuity?: boolean;
+  bare?: boolean;
   unknownFlags?: string[];
 }
 
@@ -39,6 +40,7 @@ export interface ProfileOutput {
   continuity_mode?: 'standard' | 'deeper' | null;
   instance_path?: string;
   session_count?: number;
+  bare?: boolean;
 }
 
 /**
@@ -73,6 +75,7 @@ export function parseArgs(args: string[]): AuthCommandArgs {
     '-y',
     '--share-context',
     '--deeper-continuity',
+    '--bare',
   ]);
   const knownValueFlags = new Set(['--context-group']);
 
@@ -125,6 +128,7 @@ export function parseArgs(args: string[]): AuthCommandArgs {
     yes: args.includes('--yes') || args.includes('-y'),
     shareContext: args.includes('--share-context'),
     deeperContinuity: args.includes('--deeper-continuity'),
+    bare: args.includes('--bare'),
     contextGroup,
     unknownFlags: [...unknownFlags],
   };

src/commands/help-command.ts

@@ -156,7 +156,7 @@ Run ${color('ccs config', 'command')} for web dashboard`.trim();
       ['ccs auth --help', 'Show account management commands'],
       [
         'ccs auth create <name>',
-        'Create account profile (supports shared groups + --deeper-continuity)',
+        'Create account profile (supports --bare, shared groups, --deeper-continuity)',
       ],
       ['ccs config', 'Dashboard: Accounts table can edit context mode/group/continuity depth'],
       [

src/commands/sync-command.ts

@@ -4,7 +4,7 @@
  * Handle sync command for CCS.
  */
 
-import { initUI, header, ok } from '../utils/ui';
+import { initUI, header, ok, info } from '../utils/ui';
 
 /**
  * Handle sync command
@@ -41,6 +41,31 @@ export async function handleSyncCommand(): Promise<void> {
   sharedManager.ensureSharedDirectories();
   console.log(ok('Shared symlinks verified'));
 
+  // Sync MCP servers from global ~/.claude.json to all non-bare instances
+  const { InstanceManager } = await import('../management/instance-manager');
+  const instanceMgr = new InstanceManager();
+  const ProfileRegistry = (await import('../auth/profile-registry')).default;
+  const registry = new ProfileRegistry();
+  const allProfiles = registry.getAllProfilesMerged();
+  let mcpSynced = 0;
+
+  for (const [name, profile] of Object.entries(allProfiles)) {
+    if (profile.bare) {
+      continue; // Skip bare profiles
+    }
+    const instancePath = instanceMgr.getInstancePath(name);
+    if (instancePath) {
+      instanceMgr.syncMcpServers(instancePath);
+      mcpSynced++;
+    }
+  }
+
+  if (mcpSynced > 0) {
+    console.log(ok(`MCP servers synced to ${mcpSynced} instance(s)`));
+  } else {
+    console.log(info('No instances to sync MCP servers'));
+  }
+
   console.log('');
   console.log(ok('Sync complete!'));
   console.log('');

src/config/unified-config-types.ts

@@ -46,6 +46,8 @@ export interface AccountConfig {
   context_group?: string;
   /** Shared continuity depth when context_mode='shared' */
   continuity_mode?: 'standard' | 'deeper';
+  /** Bare profile: no shared symlinks (commands, skills, agents, settings.json) */
+  bare?: boolean;
 }
 
 /**

src/management/instance-manager.ts

@@ -11,7 +11,13 @@ import * as path from 'path';
 import SharedManager from './shared-manager';
 import ProfileContextSyncLock from './profile-context-sync-lock';
 import { AccountContextPolicy, DEFAULT_ACCOUNT_CONTEXT_MODE } from '../auth/account-context';
-import { getCcsDir } from '../utils/config-manager';
+import { getCcsDir, getCcsHome } from '../utils/config-manager';
+
+/** Options for instance creation */
+interface InstanceOptions {
+  /** Skip shared symlinks (commands, skills, agents, settings.json) */
+  bare?: boolean;
+}
 
 /**
  * Instance Manager Class
@@ -32,7 +38,8 @@ class InstanceManager {
    */
   async ensureInstance(
     profileName: string,
-    contextPolicy: AccountContextPolicy = { mode: DEFAULT_ACCOUNT_CONTEXT_MODE }
+    contextPolicy: AccountContextPolicy = { mode: DEFAULT_ACCOUNT_CONTEXT_MODE },
+    options: InstanceOptions = {}
   ): Promise<string> {
     const instancePath = this.getInstancePath(profileName);
 
@@ -40,7 +47,7 @@ class InstanceManager {
     await this.contextSyncLock.withLock(profileName, async () => {
       // Lazy initialization
       if (!fs.existsSync(instancePath)) {
-        this.initializeInstance(profileName, instancePath);
+        this.initializeInstance(profileName, instancePath, options);
       }
 
       // Validate structure (auto-fix missing dirs)
@@ -51,6 +58,11 @@ class InstanceManager {
       await this.sharedManager.syncAdvancedContinuityArtifacts(instancePath, contextPolicy);
     });
 
+    // Sync MCP servers from global ~/.claude.json (unless bare)
+    if (!options.bare) {
+      this.syncMcpServers(instancePath);
+    }
+
     return instancePath;
   }
 
@@ -65,7 +77,11 @@ class InstanceManager {
   /**
    * Initialize new instance directory
    */
-  private initializeInstance(profileName: string, instancePath: string): void {
+  private initializeInstance(
+    profileName: string,
+    instancePath: string,
+    options: InstanceOptions = {}
+  ): void {
     try {
       // Create base directory
       fs.mkdirSync(instancePath, { recursive: true, mode: 0o700 });
@@ -88,8 +104,10 @@ class InstanceManager {
         }
       });
 
-      // Symlink shared directories (Phase 1: commands, skills)
-      this.sharedManager.linkSharedDirectories(instancePath);
+      // Bare profiles skip shared symlinks (commands, skills, agents, settings.json)
+      if (!options.bare) {
+        this.sharedManager.linkSharedDirectories(instancePath);
+      }
 
       // Copy global configs if exist (settings.json only)
       this.copyGlobalConfigs(instancePath);
@@ -167,33 +185,49 @@ class InstanceManager {
    */
   private copyGlobalConfigs(_instancePath: string): void {
     // No longer needed - settings.json now symlinked via SharedManager
-    // Keeping method for backward compatibility (empty implementation)
-    // Can be removed in future major version
   }
 
   /**
-   * Copy directory recursively - Currently unused
+   * Sync MCP servers from global ~/.claude.json to instance .claude.json.
+   * Selectively copies only mcpServers key (not OAuth sessions or caches).
    */
-  /*
-  private copyDirectory(src: string, dest: string): void {
-    if (!fs.existsSync(dest)) {
-      fs.mkdirSync(dest, { recursive: true, mode: 0o700 });
+  syncMcpServers(instancePath: string): void {
+    const homeDir = getCcsHome();
+    const globalClaudeJson = path.join(homeDir, '.claude.json');
+
+    if (!fs.existsSync(globalClaudeJson)) {
+      return;
     }
 
-    const entries = fs.readdirSync(src, { withFileTypes: true });
+    try {
+      const globalContent = JSON.parse(fs.readFileSync(globalClaudeJson, 'utf8'));
+      const mcpServers = globalContent.mcpServers;
 
-    for (const entry of entries) {
-      const srcPath = path.join(src, entry.name);
-      const destPath = path.join(dest, entry.name);
-
-      if (entry.isDirectory()) {
-        this.copyDirectory(srcPath, destPath);
-      } else {
-        fs.copyFileSync(srcPath, destPath);
+      if (!mcpServers || Object.keys(mcpServers).length === 0) {
+        return;
       }
+
+      const instanceClaudeJson = path.join(instancePath, '.claude.json');
+      let instanceContent: Record<string, unknown> = {};
+
+      if (fs.existsSync(instanceClaudeJson)) {
+        try {
+          instanceContent = JSON.parse(fs.readFileSync(instanceClaudeJson, 'utf8'));
+        } catch {
+          // Corrupted file, start fresh
+          instanceContent = {};
+        }
+      }
+
+      // Merge: global MCP servers as base, instance-specific overrides on top
+      const existingMcp = (instanceContent.mcpServers as Record<string, unknown> | undefined) || {};
+      instanceContent.mcpServers = { ...mcpServers, ...existingMcp };
+
+      fs.writeFileSync(instanceClaudeJson, JSON.stringify(instanceContent, null, 2), 'utf8');
+    } catch {
+      // Best-effort: don't fail instance creation if MCP sync fails
     }
   }
-  */
 
   /**
    * Sanitize profile name for filesystem

src/types/config.ts

@@ -100,6 +100,8 @@ export interface ProfileMetadata {
   context_group?: string;
   /** Shared continuity depth when context_mode='shared' */
   continuity_mode?: 'standard' | 'deeper';
+  /** Bare profile: no shared symlinks (commands, skills, agents, settings.json) */
+  bare?: boolean;
 }
 
 export interface ProfilesRegistry {