claude-mpm 5.0.9__py3-none-any.whl → 5.6.23__py3-none-any.whl

claude_mpm/cli/startup.py

@@ -10,47 +10,128 @@ Part of cli/__init__.py refactoring to reduce file size and improve modularity.
 
 import os
 import sys
-import warnings
 from pathlib import Path
 
 
-def check_legacy_cache() -> None:
-    """Check for legacy cache/agents/ directory and warn user.
+def sync_hooks_on_startup(quiet: bool = False) -> bool:
+    """Ensure hooks are up-to-date on startup.
+
+    WHY: Users can have stale hook configurations in settings.json that cause errors.
+    Reinstalling hooks ensures the hook format matches the current code.
 
-    WHY: cache/agents/ is deprecated in favor of cache/remote-agents/.
-    Research confirmed that cache/remote-agents/ is the canonical location
-    with 26 active code references, while cache/agents/ has only 7 legacy references.
+    DESIGN DECISION: Shows brief status message on success for user awareness.
+    Failures are logged but don't prevent startup to ensure claude-mpm remains functional.
 
-    DESIGN DECISIONS:
-    - Non-blocking warning: Doesn't stop execution, just informs user
-    - Migration guidance: Provides clear path to migrate
-    - One-time check: Only warns if legacy cache contains files
+    Args:
+        quiet: If True, suppress all output (used internally)
+
+    Returns:
+        bool: True if hooks were synced successfully, False otherwise
     """
-    home = Path.home()
-    legacy_cache = home / ".claude-mpm" / "cache" / "agents"
-    canonical_cache = home / ".claude-mpm" / "cache" / "remote-agents"
-    migration_marker = home / ".claude-mpm" / "cache" / ".migrated_to_remote_agents"
+    try:
+        from ..hooks.claude_hooks.installer import HookInstaller
 
-    # Skip if already migrated or no legacy cache
-    if migration_marker.exists() or not legacy_cache.exists():
-        return
+        installer = HookInstaller()
+
+        # Show brief status (hooks sync is fast)
+        if not quiet:
+            print("Syncing Claude Code hooks...", end=" ", flush=True)
+
+        # Reinstall hooks (force=True ensures update)
+        success = installer.install_hooks(force=True)
+
+        if not quiet:
+            if success:
+                print("✓")
+            else:
+                print("(skipped)")
+
+        return success
+
+    except Exception as e:
+        if not quiet:
+            print("(error)")
+        # Log but don't fail startup
+        from ..core.logger import get_logger
+
+        logger = get_logger("startup")
+        logger.warning(f"Hook sync failed (non-fatal): {e}")
+        return False
+
+
+def cleanup_legacy_agent_cache() -> None:
+    """Remove legacy hierarchical agent cache directories.
+
+    WHY: Old agent cache used category-based directory structure directly in cache.
+    New structure uses remote source paths. This cleanup prevents confusion from
+    stale cache directories.
 
-    # Check if legacy cache has actual agent files
-    legacy_files = list(legacy_cache.glob("*.md")) + list(legacy_cache.glob("*.json"))
-    if not legacy_files:
+    Old structure (removed):
+        ~/.claude-mpm/cache/agents/engineer/
+        ~/.claude-mpm/cache/agents/ops/
+        ~/.claude-mpm/cache/agents/qa/
+        ...
+
+    New structure (kept):
+        ~/.claude-mpm/cache/agents/bobmatnyc/claude-mpm-agents/agents/...
+
+    DESIGN DECISION: Runs early in startup before agent deployment to ensure
+    clean cache state. Removes only known legacy directories to avoid deleting
+    user data.
+    """
+    import shutil
+    from pathlib import Path
+
+    from ..core.logger import get_logger
+
+    logger = get_logger("startup")
+
+    cache_dir = Path.home() / ".claude-mpm" / "cache" / "agents"
+    if not cache_dir.exists():
         return
 
-    # Only warn if canonical cache doesn't exist (indicating unmigrated system)
-    if not canonical_cache.exists():
-        warnings.warn(
-            f"\n⚠️  DEPRECATION: Legacy cache directory detected\n"
-            f"   Location: {legacy_cache}\n"
-            f"   Files found: {len(legacy_files)}\n\n"
-            f"The 'cache/agents/' directory is deprecated. Please migrate to 'cache/remote-agents/'.\n"
-            f"Run: python scripts/migrate_cache_to_remote_agents.py\n",
-            DeprecationWarning,
-            stacklevel=2,
-        )
+    # Known legacy category directories (from old hierarchical structure)
+    legacy_dirs = [
+        "claude-mpm",
+        "documentation",
+        "engineer",
+        "ops",
+        "qa",
+        "security",
+        "universal",
+    ]
+
+    removed = []
+
+    # Remove legacy category directories
+    for dir_name in legacy_dirs:
+        legacy_path = cache_dir / dir_name
+        if legacy_path.exists() and legacy_path.is_dir():
+            try:
+                shutil.rmtree(legacy_path)
+                removed.append(dir_name)
+            except Exception as e:
+                logger.debug(f"Failed to remove legacy directory {dir_name}: {e}")
+
+    # Also remove stray BASE-AGENT.md in cache root
+    base_agent = cache_dir / "BASE-AGENT.md"
+    if base_agent.exists():
+        try:
+            base_agent.unlink()
+            removed.append("BASE-AGENT.md")
+        except Exception as e:
+            logger.debug(f"Failed to remove BASE-AGENT.md: {e}")
+
+    if removed:
+        logger.info(f"Cleaned up legacy agent cache: {', '.join(removed)}")
+
+
+def check_legacy_cache() -> None:
+    """Deprecated: Legacy cache checking is no longer needed.
+
+    This function is kept for backward compatibility but does nothing.
+    All agent cache operations now use the standardized cache/agents/ directory.
+    """
 
 
 def setup_early_environment(argv):
@@ -80,7 +161,25 @@ def setup_early_environment(argv):
     # CRITICAL: Suppress ALL logging by default
     # This catches all loggers (claude_mpm.*, service.*, framework_loader, etc.)
     # This will be overridden by setup_mcp_server_logging() based on user preference
-    logging.getLogger().setLevel(logging.CRITICAL + 1)  # Root logger catches everything
+    root_logger = logging.getLogger()
+    root_logger.setLevel(logging.CRITICAL + 1)  # Root logger catches everything
+    root_logger.handlers = []  # Remove any handlers
+
+    # Also suppress common module loggers explicitly to prevent handler leakage
+    for logger_name in [
+        "claude_mpm",
+        "path_resolver",
+        "file_loader",
+        "framework_loader",
+        "service",
+        "instruction_loader",
+        "agent_loader",
+        "startup",
+    ]:
+        module_logger = logging.getLogger(logger_name)
+        module_logger.setLevel(logging.CRITICAL + 1)
+        module_logger.handlers = []
+        module_logger.propagate = False
 
     # Process argv
     if argv is None:
@@ -110,7 +209,17 @@ def should_skip_background_services(args, processed_argv):
     skip_commands = ["--version", "-v", "--help", "-h"]
     return any(cmd in (processed_argv or sys.argv[1:]) for cmd in skip_commands) or (
         hasattr(args, "command")
-        and args.command in ["info", "doctor", "config", "mcp", "configure"]
+        and args.command
+        in [
+            "info",
+            "doctor",
+            "config",
+            "mcp",
+            "configure",
+            "hook-errors",
+            "autotodos",
+            "commander",
+        ]
     )
 
 
@@ -153,7 +262,7 @@ def deploy_bundled_skills():
             if not skills_config.get("auto_deploy", True):
                 # Auto-deploy disabled, skip silently
                 return
-        except Exception:
+        except Exception:  # nosec B110
             # If config loading fails, assume auto-deploy is enabled (default)
             pass
 
@@ -221,79 +330,243 @@ def discover_and_link_runtime_skills():
 
 def deploy_output_style_on_startup():
     """
-    Deploy claude-mpm output style to Claude Code on CLI startup.
+    Deploy claude-mpm output styles to PROJECT-LEVEL directory on CLI startup.
+
+    WHY: Automatically deploy output styles to ensure consistent, professional
+    communication without emojis and exclamation points. Styles are project-specific
+    to allow different projects to have different communication styles.
 
-    WHY: Automatically deploy and activate the output style to ensure consistent,
-    professional communication without emojis and exclamation points. This ensures
-    the style is available even when using Claude Code directly (not via chat command).
+    DESIGN DECISION: This is non-blocking and idempotent. Deploys to user-level
+    directory (~/.claude/output-styles/) which is the official Claude Code location
+    for custom output styles.
 
-    DESIGN DECISION: This is non-blocking and idempotent. It uses OutputStyleManager
-    which handles version detection, file deployment, and settings activation.
-    Only works for Claude Code >= 1.0.83.
+    Deploys all styles:
+    - claude-mpm.md (professional mode)
+    - claude-mpm-teacher.md (teaching mode)
+    - claude-mpm-research.md (research mode - for codebase analysis)
     """
     try:
-        from pathlib import Path
-
         from ..core.output_style_manager import OutputStyleManager
 
-        # Create OutputStyleManager instance
-        output_style_manager = OutputStyleManager()
+        # Initialize the output style manager
+        manager = OutputStyleManager()
 
-        # Check if Claude Code supports output styles
-        if not output_style_manager.supports_output_styles():
-            # Silently skip - version too old or Claude not installed
+        # Check if Claude Code version supports output styles (>= 1.0.83)
+        if not manager.supports_output_styles():
+            # Skip deployment for older versions
+            # The manager will fall back to injecting content directly
             return
 
-        # Check if already deployed and active
-        settings_file = Path.home() / ".claude" / "settings.json"
-        output_style_file = Path.home() / ".claude" / "output-styles" / "claude-mpm.md"
-
-        already_configured = False
-        if settings_file.exists() and output_style_file.exists():
-            try:
-                import json
-
-                # Check if file has content (bug fix: was skipping empty files)
-                if output_style_file.stat().st_size == 0:
-                    # File is empty, need to redeploy with content
-                    pass  # Fall through to deployment below
-                else:
-                    # File has content, check if already active
-                    settings = json.loads(settings_file.read_text())
-                    if settings.get("activeOutputStyle") == "claude-mpm":
-                        # Already deployed and active with content
-                        already_configured = True
-            except Exception:
-                pass  # Continue with deployment if we can't read settings
-
-        if already_configured:
-            # Show feedback that output style is ready
-            print("✓ Output style configured", flush=True)
+        # Check if all styles are already deployed and up-to-date
+        all_up_to_date = True
+        for style_config in manager.styles.values():
+            source_path = style_config["source"]
+            target_path = style_config["target"]
+
+            if not (
+                target_path.exists()
+                and source_path.exists()
+                and target_path.stat().st_size == source_path.stat().st_size
+            ):
+                all_up_to_date = False
+                break
+
+        if all_up_to_date:
+            # Show feedback that output styles are ready
+            print("✓ Output styles ready", flush=True)
             return
 
-        # Read OUTPUT_STYLE.md content
-        output_style_path = Path(__file__).parent.parent / "agents" / "OUTPUT_STYLE.md"
+        # Deploy all styles using the manager
+        results = manager.deploy_all_styles(activate_default=True)
 
-        if not output_style_path.exists():
-            # No output style file to deploy
-            return
+        # Count successful deployments
+        deployed_count = sum(1 for success in results.values() if success)
 
-        output_style_content = output_style_path.read_text()
+        if deployed_count > 0:
+            print(f"✓ Output styles deployed ({deployed_count} styles)", flush=True)
+        else:
+            # Deployment failed - log but don't fail startup
+            from ..core.logger import get_logger
 
-        # Deploy the output style (deploys file and activates it)
-        output_style_manager.deploy_output_style(output_style_content)
-        print("✓ Output style configured", flush=True)
+            logger = get_logger("cli")
+            logger.debug("Failed to deploy any output styles")
 
     except Exception as e:
         # Non-critical - log but don't fail startup
         from ..core.logger import get_logger
 
         logger = get_logger("cli")
-        logger.debug(f"Failed to deploy output style: {e}")
+        logger.debug(f"Failed to deploy output styles: {e}")
         # Continue execution - output style deployment shouldn't block startup
 
 
-def sync_remote_agents_on_startup():
+def _cleanup_orphaned_agents(deploy_target: Path, deployed_agents: list[str]) -> int:
+    """Remove agents that are managed by claude-mpm but no longer deployed.
+
+    WHY: When agent configurations change, old agents should be removed to avoid
+    confusion and stale agent references. Only removes claude-mpm managed agents,
+    leaving user-created agents untouched.
+
+    SAFETY: Only removes files with claude-mpm ownership markers in frontmatter.
+    Files without frontmatter or without ownership indicators are preserved.
+
+    Args:
+        deploy_target: Path to .claude/agents/ directory
+        deployed_agents: List of agent filenames that should remain
+
+    Returns:
+        Number of agents removed
+    """
+    import re
+
+    import yaml
+
+    from ..core.logger import get_logger
+
+    logger = get_logger("cli")
+    removed_count = 0
+    deployed_set = set(deployed_agents)
+
+    if not deploy_target.exists():
+        return 0
+
+    # Scan all .md files in agents directory
+    for agent_file in deploy_target.glob("*.md"):
+        # Skip hidden files
+        if agent_file.name.startswith("."):
+            continue
+
+        # Skip if this agent should remain deployed
+        if agent_file.name in deployed_set:
+            continue
+
+        # Check if this is a claude-mpm managed agent
+        try:
+            content = agent_file.read_text(encoding="utf-8")
+
+            # Parse YAML frontmatter
+            if content.startswith("---"):
+                match = re.match(r"^---\n(.*?)\n---", content, re.DOTALL)
+                if match:
+                    frontmatter = yaml.safe_load(match.group(1))
+
+                    # Check ownership indicators
+                    is_ours = False
+                    if frontmatter:
+                        author = frontmatter.get("author", "")
+                        source = frontmatter.get("source", "")
+                        agent_id = frontmatter.get("agent_id", "")
+
+                        # It's ours if it has any of these markers
+                        if (
+                            "Claude MPM" in str(author)
+                            or source == "remote"
+                            or agent_id
+                        ):
+                            is_ours = True
+
+                    if is_ours:
+                        # Safe to remove - it's our agent but not deployed
+                        agent_file.unlink()
+                        removed_count += 1
+                        logger.info(f"Removed orphaned agent: {agent_file.name}")
+
+        except Exception as e:
+            logger.debug(f"Could not check agent {agent_file.name}: {e}")
+            # Don't remove if we can't verify ownership
+
+    return removed_count
+
+
+def _save_deployment_state_after_reconciliation(
+    agent_result, project_path: Path
+) -> None:
+    """Save deployment state after reconciliation to prevent duplicate deployment.
+
+    WHY: After perform_startup_reconciliation() deploys agents to .claude/agents/,
+    we need to save a deployment state file so that ClaudeRunner.setup_agents()
+    can detect agents are already deployed and skip redundant deployment.
+
+    This prevents the "✓ Deployed 31 native agents" duplicate deployment that
+    occurs when setup_agents() doesn't know reconciliation already ran.
+
+    Args:
+        agent_result: DeploymentResult from perform_startup_reconciliation()
+        project_path: Project root directory
+
+    DESIGN DECISION: Use same state file format as ClaudeRunner._save_deployment_state()
+    Located at: .claude-mpm/cache/deployment_state.json
+
+    State file format:
+    {
+        "version": "5.6.13",
+        "agent_count": 15,
+        "deployment_hash": "sha256:...",
+        "deployed_at": 1234567890.123
+    }
+    """
+    import hashlib
+    import json
+    import time
+
+    from ..core.logger import get_logger
+
+    logger = get_logger("cli")
+
+    try:
+        # Get version from package
+        from claude_mpm import __version__
+
+        # Path to state file (matches ClaudeRunner._get_deployment_state_path())
+        state_file = project_path / ".claude-mpm" / "cache" / "deployment_state.json"
+        agents_dir = project_path / ".claude" / "agents"
+
+        # Count deployed agents
+        if agents_dir.exists():
+            agent_count = len(list(agents_dir.glob("*.md")))
+        else:
+            agent_count = 0
+
+        # Calculate deployment hash (matches ClaudeRunner._calculate_deployment_hash())
+        # CRITICAL: Must match exact hash algorithm used in ClaudeRunner
+        # Hashes filename + file content (not mtime) for consistency
+        deployment_hash = ""
+        if agents_dir.exists():
+            agent_files = sorted(agents_dir.glob("*.md"))
+            hash_obj = hashlib.sha256()
+            for agent_file in agent_files:
+                # Include filename and content in hash (matches ClaudeRunner)
+                hash_obj.update(agent_file.name.encode())
+                try:
+                    hash_obj.update(agent_file.read_bytes())
+                except Exception as e:
+                    logger.debug(f"Error reading {agent_file} for hash: {e}")
+
+            deployment_hash = hash_obj.hexdigest()
+
+        # Create state data
+        state_data = {
+            "version": __version__,
+            "agent_count": agent_count,
+            "deployment_hash": deployment_hash,
+            "deployed_at": time.time(),
+        }
+
+        # Ensure directory exists
+        state_file.parent.mkdir(parents=True, exist_ok=True)
+
+        # Write state file
+        state_file.write_text(json.dumps(state_data, indent=2))
+        logger.debug(
+            f"Saved deployment state after reconciliation: {agent_count} agents"
+        )
+
+    except Exception as e:
+        # Non-critical error - log but don't fail startup
+        logger.debug(f"Failed to save deployment state: {e}")
+
+
+def sync_remote_agents_on_startup(force_sync: bool = False):
     """
     Synchronize agent templates from remote sources on startup.
 
@@ -308,18 +581,47 @@ def sync_remote_agents_on_startup():
     Workflow:
     1. Sync all enabled Git sources (download/cache files) - Phase 1 progress bar
     2. Deploy agents to ~/.claude/agents/ - Phase 2 progress bar
-    3. Log deployment results
+    3. Cleanup orphaned agents (ours but no longer deployed) - Phase 3
+    4. Cleanup legacy agent cache directories (after sync/deployment) - Phase 4
+    5. Log deployment results
+
+    Args:
+        force_sync: Force download even if cache is fresh (bypasses ETag).
     """
-    # Check for legacy cache and warn user if found
+    # DEPRECATED: Legacy warning - no-op function, kept for compatibility
     check_legacy_cache()
 
     try:
-        from ..services.agents.deployment.agent_deployment import AgentDeploymentService
+        # Load active profile if configured
+        # Get project root (where .claude-mpm exists)
+        from pathlib import Path
+
+        from ..core.shared.config_loader import ConfigLoader
         from ..services.agents.startup_sync import sync_agents_on_startup
+        from ..services.profile_manager import ProfileManager
         from ..utils.progress import ProgressBar
 
+        project_root = Path.cwd()
+
+        profile_manager = ProfileManager(project_dir=project_root)
+        config_loader = ConfigLoader()
+        main_config = config_loader.load_main_config()
+        active_profile = main_config.get("active_profile")
+
+        if active_profile:
+            success = profile_manager.load_profile(active_profile)
+            if success:
+                summary = profile_manager.get_filtering_summary()
+                from ..core.logger import get_logger
+
+                logger = get_logger("cli")
+                logger.info(
+                    f"Profile '{active_profile}' active: "
+                    f"{summary['enabled_agents_count']} agents enabled"
+                )
+
         # Phase 1: Sync files from Git sources
-        result = sync_agents_on_startup()
+        result = sync_agents_on_startup(force_refresh=force_sync)
 
         # Only proceed with deployment if sync was enabled and ran
         if result.get("enabled") and result.get("sources_synced", 0) > 0:
@@ -342,130 +644,95 @@ def sync_remote_agents_on_startup():
                 logger.warning(f"Agent sync completed with {len(errors)} errors")
 
             # Phase 2: Deploy agents from cache to ~/.claude/agents/
-            # This mirrors the skills deployment pattern (lines 371-407)
+            # Use reconciliation service to respect configuration.yaml settings
             try:
-                # Initialize deployment service
-                deployment_service = AgentDeploymentService()
-
-                # Count agents in cache to show accurate progress
                 from pathlib import Path
 
-                cache_dir = Path.home() / ".claude-mpm" / "cache" / "remote-agents"
-                agent_count = 0
-
-                if cache_dir.exists():
-                    # Count MD files in cache (agent markdown files from Git)
-                    # BUGFIX: Only count files in agent directories, not docs/templates/READMEs
-                    # Valid agent paths must contain "/agents/" or be in root-level category dirs
-                    # Exclude PM templates, BASE-AGENT, and documentation files
-                    pm_templates = {
-                        "base-agent.md",
-                        "circuit_breakers.md",
-                        "pm_examples.md",
-                        "pm_red_flags.md",
-                        "research_gate_examples.md",
-                        "response_format.md",
-                        "ticket_completeness_examples.md",
-                        "validation_templates.md",
-                        "git_file_tracking.md",
-                    }
-                    # Documentation files to exclude (by filename)
-                    doc_files = {
-                        "readme.md",
-                        "changelog.md",
-                        "contributing.md",
-                        "implementation-summary.md",
-                        "reorganization-plan.md",
-                        "auto-deploy-index.md",
-                    }
-
-                    # Find all markdown files
-                    all_md_files = list(cache_dir.rglob("*.md"))
-
-                    # Filter to only agent files:
-                    # 1. Must have "/agents/" in path (from git repos)
-                    # 2. Must not be in PM templates or doc files
-                    # 3. Exclude BASE-AGENT.md which is not a deployable agent
-                    agent_files = [
-                        f
-                        for f in all_md_files
-                        if (
-                            # Must be in an agent directory (from git repos like bobmatnyc/claude-mpm-agents/agents/)
-                            "/agents/" in str(f)
-                            # Exclude PM templates, doc files, and BASE-AGENT
-                            and f.name.lower() not in pm_templates
-                            and f.name.lower() not in doc_files
-                            and f.name.lower() != "base-agent.md"
-                        )
-                    ]
-                    agent_count = len(agent_files)
+                from ..core.unified_config import UnifiedConfig
+                from ..services.agents.deployment.startup_reconciliation import (
+                    perform_startup_reconciliation,
+                )
+
+                # Load configuration
+                unified_config = UnifiedConfig()
 
-                if agent_count > 0:
-                    # Create progress bar for deployment phase
+                # Override with profile settings if active
+                if active_profile and profile_manager.active_profile:
+                    # Get enabled agents from profile (returns Set[str])
+                    profile_enabled_agents = (
+                        profile_manager.active_profile.get_enabled_agents()
+                    )
+                    # Update config with profile's enabled list (convert Set to List)
+                    unified_config.agents.enabled = list(profile_enabled_agents)
+                    logger.info(
+                        f"Profile '{active_profile}': Using {len(profile_enabled_agents)} enabled agents"
+                    )
+
+                # Perform reconciliation to deploy configured agents
+                project_path = Path.cwd()
+                agent_result, _skill_result = perform_startup_reconciliation(
+                    project_path=project_path, config=unified_config, silent=False
+                )
+
+                # Display results with progress bar
+                total_operations = (
+                    len(agent_result.deployed)
+                    + len(agent_result.removed)
+                    + len(agent_result.unchanged)
+                )
+
+                if total_operations > 0:
                     deploy_progress = ProgressBar(
-                        total=agent_count,
+                        total=total_operations,
                         prefix="Deploying agents",
                         show_percentage=True,
                         show_counter=True,
                     )
-
-                    # Deploy agents with progress callback
-                    deploy_target = Path.home() / ".claude" / "agents"
-                    deployment_result = deployment_service.deploy_agents(
-                        target_dir=deploy_target,
-                        force_rebuild=False,  # Only deploy if versions differ
-                        deployment_mode="update",  # Version-aware updates
+                    deploy_progress.update(total_operations)
+
+                    # Build summary message
+                    deployed = len(agent_result.deployed)
+                    removed = len(agent_result.removed)
+                    unchanged = len(agent_result.unchanged)
+
+                    summary_parts = []
+                    if deployed > 0:
+                        summary_parts.append(f"{deployed} new")
+                    if removed > 0:
+                        summary_parts.append(f"{removed} removed")
+                    if unchanged > 0:
+                        summary_parts.append(f"{unchanged} unchanged")
+
+                    summary = f"Complete: {', '.join(summary_parts)}"
+                    deploy_progress.finish(summary)
+
+                # Display errors if any
+                if agent_result.errors:
+                    logger.warning(
+                        f"Agent deployment completed with {len(agent_result.errors)} errors"
                     )
+                    print("\n⚠️  Agent Deployment Errors:")
+                    max_errors_to_show = 10
+                    errors_to_display = agent_result.errors[:max_errors_to_show]
 
-                    # Update progress bar (single increment since deploy_agents is batch)
-                    deploy_progress.update(agent_count)
-
-                    # Finish deployment progress bar
-                    deployed = len(deployment_result.get("deployed", []))
-                    updated = len(deployment_result.get("updated", []))
-                    skipped = len(deployment_result.get("skipped", []))
-                    total_available = deployed + updated + skipped
-
-                    # Show total available agents (deployed + updated + already existing)
-                    if deployed > 0 or updated > 0:
-                        deploy_progress.finish(
-                            f"Complete: {deployed} deployed, {updated} updated, {skipped} already present ({total_available} total)"
-                        )
-                    else:
-                        deploy_progress.finish(
-                            f"Complete: {total_available} agents ready (all up-to-date)"
-                        )
-
-                    # Display deployment errors to user (not just logs)
-                    deploy_errors = deployment_result.get("errors", [])
-                    if deploy_errors:
-                        # Log for debugging
-                        logger.warning(
-                            f"Agent deployment completed with {len(deploy_errors)} errors: {deploy_errors}"
-                        )
-
-                        # Display errors to user with clear formatting
-                        print("\n⚠️  Agent Deployment Errors:")
+                    for error in errors_to_display:
+                        print(f"   - {error}")
 
-                        # Show first 10 errors to avoid overwhelming output
-                        max_errors_to_show = 10
-                        errors_to_display = deploy_errors[:max_errors_to_show]
+                    if len(agent_result.errors) > max_errors_to_show:
+                        remaining = len(agent_result.errors) - max_errors_to_show
+                        print(f"   ... and {remaining} more error(s)")
 
-                        for error in errors_to_display:
-                            # Format error message for readability
-                            # Errors typically come as strings like "agent.md: Error message"
-                            print(f"   - {error}")
-
-                        # If more errors exist, show count
-                        if len(deploy_errors) > max_errors_to_show:
-                            remaining = len(deploy_errors) - max_errors_to_show
-                            print(f"   ... and {remaining} more error(s)")
+                    print(
+                        f"\n❌ Failed to deploy {len(agent_result.errors)} agent(s). "
+                        "Please check the error messages above."
+                    )
+                    print("   Run with --verbose for detailed error information.\n")
 
-                        # Show summary message
-                        print(
-                            f"\n❌ Failed to deploy {len(deploy_errors)} agent(s). Please check the error messages above."
-                        )
-                        print("   Run with --verbose for detailed error information.\n")
+                # Save deployment state to prevent duplicate deployment in ClaudeRunner
+                # This ensures setup_agents() skips deployment since we already reconciled
+                _save_deployment_state_after_reconciliation(
+                    agent_result=agent_result, project_path=project_path
+                )
 
             except Exception as e:
                 # Deployment failure shouldn't block startup
@@ -474,6 +741,11 @@ def sync_remote_agents_on_startup():
                 logger = get_logger("cli")
                 logger.warning(f"Failed to deploy agents from cache: {e}")
 
+        # Phase 4: Cleanup legacy agent cache directories (after sync/deployment)
+        # CRITICAL: This must run AFTER sync completes because sync may recreate
+        # legacy directories. Running cleanup here ensures they're removed.
+        cleanup_legacy_agent_cache()
+
     except Exception as e:
         # Non-critical - log but don't fail startup
         from ..core.logger import get_logger
@@ -482,8 +754,14 @@ def sync_remote_agents_on_startup():
         logger.debug(f"Failed to sync remote agents: {e}")
         # Continue execution - agent sync failure shouldn't block startup
 
+        # Cleanup legacy cache even if sync failed
+        try:
+            cleanup_legacy_agent_cache()
+        except Exception:  # nosec B110
+            pass  # Ignore cleanup errors
+
 
-def sync_remote_skills_on_startup():
+def sync_remote_skills_on_startup(force_sync: bool = False):
     """
     Synchronize skill templates from remote sources on startup.
 
@@ -496,16 +774,51 @@ def sync_remote_skills_on_startup():
 
     Workflow:
     1. Sync all enabled Git sources (download/cache files) - Phase 1 progress bar
-    2. Deploy skills to ~/.claude/skills/ with flat structure - Phase 2 progress bar
-    3. Log deployment results
+    2. Scan deployed agents for skill requirements → save to configuration.yaml
+    3. Resolve which skills to deploy (user_defined vs agent_referenced)
+    4. Apply profile filtering if active
+    5. Deploy resolved skills to ~/.claude/skills/ - Phase 2 progress bar
+    6. Log deployment results with source indication
+
+    Args:
+        force_sync: Force download even if cache is fresh (bypasses ETag).
     """
     try:
         from pathlib import Path
 
         from ..config.skill_sources import SkillSourceConfiguration
+        from ..core.shared.config_loader import ConfigLoader
+        from ..services.profile_manager import ProfileManager
         from ..services.skills.git_skill_source_manager import GitSkillSourceManager
+        from ..services.skills.selective_skill_deployer import (
+            get_required_skills_from_agents,
+            get_skills_to_deploy,
+            save_agent_skills_to_config,
+        )
         from ..utils.progress import ProgressBar
 
+        # Load active profile if configured
+        # Get project root (where .claude-mpm exists)
+        project_root = Path.cwd()
+
+        profile_manager = ProfileManager(project_dir=project_root)
+        config_loader = ConfigLoader()
+        main_config = config_loader.load_main_config()
+        active_profile = main_config.get("active_profile")
+
+        if active_profile:
+            success = profile_manager.load_profile(active_profile)
+            if success:
+                from ..core.logger import get_logger
+
+                logger = get_logger("cli")
+                summary = profile_manager.get_filtering_summary()
+                logger.info(
+                    f"Profile '{active_profile}' active: "
+                    f"{summary['enabled_skills_count']} skills enabled, "
+                    f"{summary['disabled_patterns_count']} patterns disabled"
+                )
+
         config = SkillSourceConfiguration()
         manager = GitSkillSourceManager(config)
 
@@ -523,6 +836,8 @@ def sync_remote_skills_on_startup():
 
         # Discover total file count across all sources
         total_file_count = 0
+        total_skill_dirs = 0  # Count actual skill directories (folders with SKILL.md)
+
         for source in enabled_sources:
             try:
                 # Parse GitHub URL
@@ -546,22 +861,33 @@ def sync_remote_skills_on_startup():
                     ]
                     total_file_count += len(relevant_files)
 
+                    # Count skill directories (unique directories containing SKILL.md)
+                    skill_dirs = set()
+                    for f in all_files:
+                        if f.endswith("/SKILL.md"):
+                            # Extract directory path
+                            skill_dir = "/".join(f.split("/")[:-1])
+                            skill_dirs.add(skill_dir)
+                    total_skill_dirs += len(skill_dirs)
+
             except Exception as e:
                 logger.debug(f"Failed to discover files for {source.id}: {e}")
                 # Use estimate if discovery fails
                 total_file_count += 150
+                total_skill_dirs += 50  # Estimate ~50 skills
 
         # Create progress bar for sync phase with actual file count
+        # Note: We sync files (md, json, etc.), but will deploy skill directories
         sync_progress = ProgressBar(
             total=total_file_count if total_file_count > 0 else 1,
-            prefix="Syncing skills",
+            prefix="Syncing skill files",
             show_percentage=True,
             show_counter=True,
         )
 
         # Sync all sources with progress callback
         results = manager.sync_all_sources(
-            force=False, progress_callback=sync_progress.update
+            force=force_sync, progress_callback=sync_progress.update
         )
 
         # Finish sync progress bar with clear breakdown
@@ -571,69 +897,201 @@ def sync_remote_skills_on_startup():
 
         if cached > 0:
             sync_progress.finish(
-                f"Complete: {downloaded} downloaded, {cached} cached ({total_files} total)"
+                f"Complete: {downloaded} downloaded, {cached} cached ({total_files} files, {total_skill_dirs} skills)"
             )
         else:
             # All new downloads (first sync)
-            sync_progress.finish(f"Complete: {downloaded} files downloaded")
-
-        # Phase 2: Deploy skills to ~/.claude/skills/
-        # This flattens nested Git structure (e.g., collaboration/parallel-agents/SKILL.md)
-        # into flat deployment (e.g., collaboration-dispatching-parallel-agents/SKILL.md)
-        if results["synced_count"] > 0:
-            # Get all skills to determine deployment count
-            all_skills = manager.get_all_skills()
-            skill_count = len(all_skills)
-
-            if skill_count > 0:
-                # Create progress bar for deployment phase
+            sync_progress.finish(
+                f"Complete: {downloaded} files downloaded ({total_skill_dirs} skills)"
+            )
+
+        # Phase 2: Scan agents and save to configuration.yaml
+        # This step populates configuration.yaml with agent-referenced skills
+        # CRITICAL: Always scan agents to populate agent_referenced, even when using cached skills.
+        # Without this, skill_filter=None causes ALL skills to deploy and NO cleanup to run.
+        agents_dir = Path.cwd() / ".claude" / "agents"
+
+        # Scan agents for skill requirements (ALWAYS run to ensure cleanup works)
+        agent_skills = get_required_skills_from_agents(agents_dir)
+        logger.info(
+            f"Agent scan found {len(agent_skills)} unique skills across deployed agents"
+        )
+
+        # Save to project-level configuration.yaml
+        project_config_path = Path.cwd() / ".claude-mpm" / "configuration.yaml"
+        save_agent_skills_to_config(list(agent_skills), project_config_path)
+        logger.debug(
+            f"Saved {len(agent_skills)} agent-referenced skills to {project_config_path}"
+        )
+
+        # Phase 3: Resolve which skills to deploy (user_defined or agent_referenced)
+        skills_to_deploy, skill_source = get_skills_to_deploy(project_config_path)
+
+        # CRITICAL DEBUG: Log deployment resolution to diagnose cleanup issues
+        if skills_to_deploy:
+            logger.info(
+                f"Resolved {len(skills_to_deploy)} skills from {skill_source} (cleanup will run)"
+            )
+        else:
+            logger.warning(
+                f"No skills resolved from {skill_source} - will deploy ALL skills WITHOUT cleanup! "
+                f"This may indicate agent_referenced is empty in configuration.yaml."
+            )
+
+        # Phase 4: Apply profile filtering if active
+        if active_profile and profile_manager.active_profile:
+            # Filter skills based on profile
+            if skills_to_deploy:
+                # Filter the resolved skill list
+                original_count = len(skills_to_deploy)
+                filtered_skills = [
+                    skill
+                    for skill in skills_to_deploy
+                    if profile_manager.is_skill_enabled(skill)
+                ]
+                filtered_count = original_count - len(filtered_skills)
+
+                # SAFEGUARD: Warn if all skills were filtered out (misconfiguration)
+                if not filtered_skills and original_count > 0:
+                    logger.warning(
+                        f"Profile '{active_profile}' filtered ALL {original_count} skills. "
+                        f"This may indicate a naming mismatch in the profile."
+                    )
+                elif filtered_count > 0:
+                    logger.info(
+                        f"Profile '{active_profile}' filtered {filtered_count} skills "
+                        f"({len(filtered_skills)} remaining)"
+                    )
+
+                skills_to_deploy = filtered_skills
+                skill_source = f"{skill_source} + profile filtered"
+            else:
+                # No explicit skill list - filter from all available
+                all_skills = manager.get_all_skills()
+                filtered_skills = [
+                    skill["name"]
+                    for skill in all_skills
+                    if profile_manager.is_skill_enabled(skill["name"])
+                ]
+                skills_to_deploy = filtered_skills
+                skill_source = "profile filtered"
+                logger.info(
+                    f"Profile '{active_profile}': "
+                    f"{len(filtered_skills)} skills enabled from {len(all_skills)} available"
+                )
+
+        # Get all skills to determine counts
+        all_skills = manager.get_all_skills()
+        total_skill_count = len(all_skills)
+
+        # Determine skill count based on resolution
+        skill_count = len(skills_to_deploy) if skills_to_deploy else total_skill_count
+
+        if skill_count > 0:
+            # Deploy skills with resolved filter
+            # Deploy ONLY to project directory (not user-level)
+            # DESIGN DECISION: Project-level deployment keeps skills isolated per project,
+            # avoiding pollution of user's global ~/.claude/skills/ directory.
+
+            # Deploy to project-local directory with cleanup
+            deployment_result = manager.deploy_skills(
+                target_dir=Path.cwd() / ".claude" / "skills",
+                force=force_sync,
+                # CRITICAL FIX: Empty list should mean "deploy no skills", not "deploy all"
+                # When skills_to_deploy is [], we want skill_filter=set() NOT skill_filter=None
+                # None means "no filtering" (deploy all), empty set means "filter to nothing"
+                skill_filter=set(skills_to_deploy)
+                if skills_to_deploy is not None
+                else None,
+            )
+
+            # REMOVED: User-level deployment (lines 1068-1074)
+            # Reason: Skills should be project-specific, not user-global.
+            # Claude Code can read from project-level .claude/skills/ directory.
+
+            # Get actual counts from deployment result (use project-local for display)
+            deployed = deployment_result.get("deployed_count", 0)
+            skipped = deployment_result.get("skipped_count", 0)
+            filtered = deployment_result.get("filtered_count", 0)
+            removed = deployment_result.get("removed_count", 0)
+            total_available = deployed + skipped
+
+            # Only show progress bar if there are skills to deploy
+            if total_available > 0:
                 deploy_progress = ProgressBar(
-                    total=skill_count,
+                    total=total_available,
                     prefix="Deploying skill directories",
                     show_percentage=True,
                     show_counter=True,
                 )
-
-                # Deploy skills with progress callback
-                # Deploy to project directory (like agents), not user directory
-                deployment_result = manager.deploy_skills(
-                    target_dir=Path.cwd() / ".claude" / "skills",
-                    force=False,
-                    progress_callback=deploy_progress.update,
+                # Update progress bar to completion
+                deploy_progress.update(total_available)
+            else:
+                # No skills to deploy - create dummy progress for message only
+                deploy_progress = ProgressBar(
+                    total=1,
+                    prefix="Deploying skill directories",
+                    show_percentage=False,
+                    show_counter=False,
                 )
+                deploy_progress.update(1)
 
-                # Finish deployment progress bar
-                deployed = deployment_result.get("deployed_count", 0)
-                skipped = deployment_result.get("skipped_count", 0)
-                total_available = deployed + skipped
+            # Show total available skills (deployed + already existing)
+            # Include source indication (user_defined vs agent_referenced)
+            # Note: total_skill_count is from cache, total_available is what's deployed/needed
+            source_label = (
+                "user override" if skill_source == "user_defined" else "from agents"
+            )
 
-                # Show total available skills (deployed + already existing)
-                # This is more user-friendly than just showing newly deployed count
+            # Build finish message with cleanup info
+            if deployed > 0 or removed > 0:
+                parts = []
                 if deployed > 0:
+                    parts.append(f"{deployed} new")
+                if skipped > 0:
+                    parts.append(f"{skipped} unchanged")
+                if removed > 0:
+                    parts.append(f"{removed} removed")
+
+                status = ", ".join(parts)
+
+                if filtered > 0:
                     deploy_progress.finish(
-                        f"Complete: {deployed} deployed, {skipped} already present ({total_available} total)"
+                        f"Complete: {status} ({total_available} {source_label}, {filtered} files in cache)"
                     )
                 else:
                     deploy_progress.finish(
-                        f"Complete: {total_available} skills ready (all up-to-date)"
+                        f"Complete: {status} ({total_available} skills {source_label} from {total_skill_count} files in cache)"
                     )
+            elif filtered > 0:
+                # Skills filtered means agents require fewer skills than available
+                deploy_progress.finish(
+                    f"No skills needed ({source_label}, {total_skill_count} files in cache)"
+                )
+            else:
+                # No changes - all skills already deployed
+                msg = f"Complete: {total_available} skills {source_label}"
+                if removed > 0:
+                    msg += f", {removed} removed"
+                msg += f" ({total_skill_count} files in cache)"
+                deploy_progress.finish(msg)
+
+            # Log deployment errors if any
+            from ..core.logger import get_logger
 
-                # Log deployment errors if any
-                from ..core.logger import get_logger
-
-                logger = get_logger("cli")
+            logger = get_logger("cli")
 
-                errors = deployment_result.get("errors", [])
-                if errors:
-                    logger.warning(
-                        f"Skill deployment completed with {len(errors)} errors: {errors}"
-                    )
+            errors = deployment_result.get("errors", [])
+            if errors:
+                logger.warning(
+                    f"Skill deployment completed with {len(errors)} errors: {errors}"
+                )
 
-                # Log sync errors if any
-                if results["failed_count"] > 0:
-                    logger.warning(
-                        f"Skill sync completed with {results['failed_count']} failures"
-                    )
+            # Log sync errors if any
+            if results["failed_count"] > 0:
+                logger.warning(
+                    f"Skill sync completed with {results['failed_count']} failures"
+                )
 
     except Exception as e:
         # Non-critical - log but don't fail startup
@@ -644,7 +1102,282 @@ def sync_remote_skills_on_startup():
         # Continue execution - skill sync failure shouldn't block startup
 
 
-def run_background_services():
+def show_agent_summary():
+    """
+    Display agent availability summary on startup.
+
+    WHY: Users should see at a glance how many agents are available and installed
+    without having to run /mpm-agents list.
+
+    DESIGN DECISION: Fast, non-blocking check that counts agents from the deployment
+    directory. Shows simple "X installed / Y available" format. Failures are silent
+    to avoid blocking startup.
+    """
+    try:
+        from pathlib import Path
+
+        # Count deployed agents (installed)
+        deploy_target = Path.cwd() / ".claude" / "agents"
+        installed_count = 0
+        if deploy_target.exists():
+            # Count .md files, excluding README and other docs
+            agent_files = [
+                f
+                for f in deploy_target.glob("*.md")
+                if not f.name.startswith(("README", "INSTRUCTIONS", "."))
+            ]
+            installed_count = len(agent_files)
+
+        # Count available agents in cache (from remote sources)
+        cache_dir = Path.home() / ".claude-mpm" / "cache" / "agents"
+        available_count = 0
+        if cache_dir.exists():
+            # Use same filtering logic as agent deployment (lines 486-533 in startup.py)
+            pm_templates = {
+                "base-agent.md",
+                "circuit_breakers.md",
+                "pm_examples.md",
+                "pm_red_flags.md",
+                "research_gate_examples.md",
+                "response_format.md",
+                "ticket_completeness_examples.md",
+                "validation_templates.md",
+                "git_file_tracking.md",
+            }
+            doc_files = {
+                "readme.md",
+                "changelog.md",
+                "contributing.md",
+                "implementation-summary.md",
+                "reorganization-plan.md",
+                "auto-deploy-index.md",
+            }
+
+            # Find all markdown files in agents/ directories
+            all_md_files = list(cache_dir.rglob("*.md"))
+            agent_files = [
+                f
+                for f in all_md_files
+                if (
+                    "/agents/" in str(f)
+                    and f.name.lower() not in pm_templates
+                    and f.name.lower() not in doc_files
+                    and f.name.lower() != "base-agent.md"
+                    and not any(
+                        part in str(f).split("/")
+                        for part in ["dist", "build", ".cache"]
+                    )
+                )
+            ]
+            available_count = len(agent_files)
+
+        # Display summary if we have agents
+        if installed_count > 0 or available_count > 0:
+            print(
+                f"✓ Agents: {installed_count} deployed / {max(0, available_count - installed_count)} cached",
+                flush=True,
+            )
+
+    except Exception as e:
+        # Silent failure - agent summary is informational only
+        from ..core.logger import get_logger
+
+        logger = get_logger("cli")
+        logger.debug(f"Failed to generate agent summary: {e}")
+
+
+def show_skill_summary():
+    """
+    Display skill availability summary on startup.
+
+    WHY: Users should see at a glance how many skills are deployed and available
+    from cache, similar to the agent summary showing "X deployed / Y cached".
+
+    DESIGN DECISION: Fast, non-blocking check that counts skills from:
+    - Deployed skills: PROJECT-level .claude/skills/ directory
+    - Cached skills: ~/.claude-mpm/cache/skills/ directory (from remote sources)
+
+    Shows format: "✓ Skills: X deployed / Y cached"
+    Failures are silent to avoid blocking startup.
+    """
+    try:
+        from pathlib import Path
+
+        # Count deployed skills (PROJECT-level, not user-level)
+        project_skills_dir = Path.cwd() / ".claude" / "skills"
+        deployed_count = 0
+        if project_skills_dir.exists():
+            # Count directories with SKILL.md (excludes collection repos)
+            # Exclude collection directories (obra-superpowers, etc.)
+            skill_dirs = [
+                d
+                for d in project_skills_dir.iterdir()
+                if d.is_dir()
+                and (d / "SKILL.md").exists()
+                and not (d / ".git").exists()  # Exclude collection repos
+            ]
+            deployed_count = len(skill_dirs)
+
+        # Count cached skills (from remote sources, not deployed yet)
+        # This matches the agent summary pattern: deployed vs cached
+        cache_dir = Path.home() / ".claude-mpm" / "cache" / "skills"
+        cached_count = 0
+        if cache_dir.exists():
+            # Scan all repository directories in cache
+            # Cache structure: ~/.claude-mpm/cache/skills/{owner}/{repo}/...
+            for repo_dir in cache_dir.rglob("*"):
+                if not repo_dir.is_dir():
+                    continue
+
+                # Count skill directories (those with SKILL.md)
+                # Skills can be nested in: skills/category/skill-name/SKILL.md
+                # or in flat structure: skill-name/SKILL.md
+                for root, dirs, files in os.walk(repo_dir):
+                    if "SKILL.md" in files:
+                        # Exclude build artifacts and hidden directories
+                        root_path = Path(root)
+                        if not any(
+                            part.startswith(".")
+                            or part in ["dist", "build", "__pycache__"]
+                            for part in root_path.parts
+                        ):
+                            cached_count += 1
+
+        # Display summary using agent summary format: "X deployed / Y cached"
+        # Only show non-deployed cached skills (subtract deployed from cached)
+        non_deployed_cached = max(0, cached_count - deployed_count)
+        if deployed_count > 0 or non_deployed_cached > 0:
+            print(
+                f"✓ Skills: {deployed_count} deployed / {non_deployed_cached} cached",
+                flush=True,
+            )
+
+    except Exception as e:
+        # Silent failure - skill summary is informational only
+        from ..core.logger import get_logger
+
+        logger = get_logger("cli")
+        logger.debug(f"Failed to generate skill summary: {e}")
+
+
+def verify_and_show_pm_skills():
+    """Verify PM skills and display status with enhanced validation.
+
+    WHY: PM skills are CRITICAL for PM agent operation. PM must KNOW if
+    framework knowledge is unavailable at startup. Enhanced validation
+    checks all required skills exist, are not corrupted, and auto-repairs
+    if needed.
+
+    Shows deployment status:
+    - "✓ PM skills: 8/8 verified" if all required skills are valid
+    - "⚠ PM skills: 2 missing, auto-repairing..." if issues detected
+    - Non-blocking but visible warning if auto-repair fails
+    """
+    try:
+        from pathlib import Path
+
+        from ..services.pm_skills_deployer import (
+            REQUIRED_PM_SKILLS,
+            PMSkillsDeployerService,
+        )
+
+        deployer = PMSkillsDeployerService()
+        project_dir = Path.cwd()
+
+        # Verify with auto-repair enabled
+        result = deployer.verify_pm_skills(project_dir, auto_repair=True)
+
+        if result.verified:
+            # Show verified status with count
+            total_required = len(REQUIRED_PM_SKILLS)
+            print(
+                f"✓ PM skills: {total_required}/{total_required} verified", flush=True
+            )
+        else:
+            # Show warning with details
+            missing_count = len(result.missing_skills)
+            corrupted_count = len(result.corrupted_skills)
+
+            # Build status message
+            issues = []
+            if missing_count > 0:
+                issues.append(f"{missing_count} missing")
+            if corrupted_count > 0:
+                issues.append(f"{corrupted_count} corrupted")
+
+            status = ", ".join(issues)
+
+            # Check if auto-repair was attempted
+            if "Auto-repaired" in result.message:
+                # Auto-repair succeeded
+                total_required = len(REQUIRED_PM_SKILLS)
+                print(
+                    f"✓ PM skills: {total_required}/{total_required} verified (auto-repaired)",
+                    flush=True,
+                )
+            else:
+                # Auto-repair failed or not attempted
+                print(f"⚠ PM skills: {status}", flush=True)
+
+                # Log warnings for debugging
+                from ..core.logger import get_logger
+
+                logger = get_logger("cli")
+                for warning in result.warnings:
+                    logger.warning(f"PM skills: {warning}")
+
+    except ImportError:
+        # PM skills deployer not available - skip silently
+        pass
+    except Exception as e:
+        from ..core.logger import get_logger
+
+        logger = get_logger("cli")
+        logger.debug(f"PM skills verification failed: {e}")
+
+
+def auto_install_chrome_devtools_on_startup():
+    """
+    Automatically install chrome-devtools-mcp on startup if enabled.
+
+    WHY: Browser automation capabilities should be available out-of-the-box without
+    manual MCP server configuration. chrome-devtools-mcp provides powerful browser
+    interaction tools for Claude Code.
+
+    DESIGN DECISION: Non-blocking installation that doesn't prevent startup if it fails.
+    Respects user configuration setting (enabled by default). Only installs if not
+    already configured in Claude.
+    """
+    try:
+        # Check if auto-install is disabled in config
+        from ..config.config_loader import ConfigLoader
+
+        config_loader = ConfigLoader()
+        try:
+            config = config_loader.load_main_config()
+            chrome_devtools_config = config.get("chrome_devtools", {})
+            if not chrome_devtools_config.get("auto_install", True):
+                # Auto-install disabled, skip silently
+                return
+        except Exception:  # nosec B110
+            # If config loading fails, assume auto-install is enabled (default)
+            pass
+
+        # Import and run chrome-devtools installation
+        from ..cli.chrome_devtools_installer import auto_install_chrome_devtools
+
+        auto_install_chrome_devtools(quiet=False)
+
+    except Exception as e:
+        # Import logger here to avoid circular imports
+        from ..core.logger import get_logger
+
+        logger = get_logger("cli")
+        logger.debug(f"Failed to auto-install chrome-devtools-mcp: {e}")
+        # Continue execution - chrome-devtools installation failure shouldn't block startup
+
+
+def run_background_services(force_sync: bool = False):
     """
     Initialize all background services on startup.
 
@@ -655,12 +1388,23 @@ def run_background_services():
     explicitly requests them via agent-manager commands. This prevents unwanted
     file creation in project .claude/ directories.
     See: SystemInstructionsDeployer and agent_deployment.py line 504-509
+
+    Args:
+        force_sync: Force download even if cache is fresh (bypasses ETag).
     """
+    # Sync hooks early to ensure up-to-date configuration
+    # RATIONALE: Hooks should be synced before other services to fix stale configs
+    # This is fast (<100ms) and non-blocking, so it doesn't delay startup
+    sync_hooks_on_startup()  # Shows "Syncing Claude Code hooks... ✓"
+
     initialize_project_registry()
     check_mcp_auto_configuration()
     verify_mcp_gateway_startup()
     check_for_updates_async()
-    sync_remote_agents_on_startup()  # Sync agents from remote sources
+    sync_remote_agents_on_startup(
+        force_sync=force_sync
+    )  # Sync agents from remote sources
+    show_agent_summary()  # Display agent counts after deployment
 
     # Skills deployment order (precedence: remote > bundled)
     # 1. Deploy bundled skills first (base layer from package)
@@ -668,11 +1412,18 @@ def run_background_services():
     # 3. Discover and link runtime skills (user-added skills)
     # This ensures remote skills take precedence over bundled skills when names conflict
     deploy_bundled_skills()  # Base layer: package-bundled skills
-    sync_remote_skills_on_startup()  # Override layer: Git-based skills (takes precedence)
+    sync_remote_skills_on_startup(
+        force_sync=force_sync
+    )  # Override layer: Git-based skills (takes precedence)
     discover_and_link_runtime_skills()  # Discovery: user-added skills
+    show_skill_summary()  # Display skill counts after deployment
+    verify_and_show_pm_skills()  # PM skills verification and status
 
     deploy_output_style_on_startup()
 
+    # Auto-install chrome-devtools-mcp for browser automation
+    auto_install_chrome_devtools_on_startup()
+
 
 def setup_mcp_server_logging(args):
     """
@@ -776,11 +1527,19 @@ def check_mcp_auto_configuration():
         check_and_configure_mcp()
 
         # Clear the "Checking..." message by overwriting with spaces
-        print("\r" + " " * 30 + "\r", end="", flush=True)
+        # Only use carriage return clearing if stdout is a real TTY
+        if sys.stdout.isatty():
+            print("\r" + " " * 30 + "\r", end="", flush=True)
+        else:
+            print()  # Simple newline for non-TTY (like Claude Code REPL)
 
     except Exception as e:
         # Clear progress message on error
-        print("\r" + " " * 30 + "\r", end="", flush=True)
+        # Only use carriage return clearing if stdout is a real TTY
+        if sys.stdout.isatty():
+            print("\r" + " " * 30 + "\r", end="", flush=True)
+        else:
+            print()  # Simple newline for non-TTY (like Claude Code REPL)
 
         # Non-critical - log but don't fail
         from ..core.logger import get_logger
@@ -800,18 +1559,10 @@ def verify_mcp_gateway_startup():
     DESIGN DECISION: This is non-blocking - failures are logged but don't prevent
     startup to ensure claude-mpm remains functional even if MCP gateway has issues.
     """
-    # Quick verification of MCP services installation
-    try:
-        from ..core.logger import get_logger
-        from ..services.mcp_service_verifier import verify_mcp_services_on_startup
-
-        logger = get_logger("mcp_verify")
-        all_ok, message = verify_mcp_services_on_startup()
-        if not all_ok:
-            logger.warning(message)
-    except Exception:
-        # Non-critical - continue with startup
-        pass
+    # DISABLED: MCP service verification removed - Claude Code handles MCP natively
+    # The previous check warned about missing MCP services, but users should configure
+    # MCP servers through Claude Code's native MCP management, not through claude-mpm.
+    # See: https://docs.anthropic.com/en/docs/claude-code/mcp
 
     try:
         import asyncio
@@ -871,7 +1622,7 @@ def verify_mcp_gateway_startup():
                                 loop.run_until_complete(
                                     asyncio.gather(*pending, return_exceptions=True)
                                 )
-                        except Exception:
+                        except Exception:  # nosec B110
                             pass  # Ignore cleanup errors
                         finally:
                             loop.close()
@@ -965,7 +1716,7 @@ def check_for_updates_async():
 
                 logger = get_logger("upgrade_check")
                 logger.debug(f"Update check failed (non-critical): {e}")
-            except Exception:
+            except Exception:  # nosec B110
                 pass  # Avoid any errors in error handling
         finally:
             # Properly clean up event loop
@@ -980,7 +1731,7 @@ def check_for_updates_async():
                         loop.run_until_complete(
                             asyncio.gather(*pending, return_exceptions=True)
                         )
-                except Exception:
+                except Exception:  # nosec B110
                     pass  # Ignore cleanup errors
                 finally:
                     loop.close()