claude-mpm 4.24.0__py3-none-any.whl → 5.4.41__py3-none-any.whl

claude_mpm/cli/startup.py

@@ -10,6 +10,128 @@ Part of cli/__init__.py refactoring to reduce file size and improve modularity.
 
 import os
 import sys
+from pathlib import Path
+
+
+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.
+
+    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.
+
+    Args:
+        quiet: If True, suppress all output (used internally)
+
+    Returns:
+        bool: True if hooks were synced successfully, False otherwise
+    """
+    try:
+        from ..hooks.claude_hooks.installer import HookInstaller
+
+        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.
+
+    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
+
+    # 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):
@@ -19,23 +141,34 @@ def setup_early_environment(argv):
     WHY: Some commands need special environment handling before any logging
     or service initialization occurs.
 
+    CRITICAL: Suppress ALL logging by default until setup_mcp_server_logging()
+    configures the user's preference. This prevents early loggers (like
+    ProjectInitializer and service.* loggers) from logging at INFO level before
+    we know the user's logging preference.
+
     Args:
         argv: Command line arguments
 
     Returns:
         Processed argv list
     """
+    import logging
+
     # Disable telemetry and set cleanup flags early
     os.environ.setdefault("DISABLE_TELEMETRY", "1")
     os.environ.setdefault("CLAUDE_MPM_SKIP_CLEANUP", "0")
 
-    # EARLY CHECK: Suppress logging for configure command
+    # 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
+
+    # Process argv
     if argv is None:
         argv = sys.argv[1:]
-    if "configure" in argv or (len(argv) > 0 and argv[0] == "configure"):
-        import logging
 
-        logging.getLogger("claude_mpm").setLevel(logging.WARNING)
+    # EARLY CHECK: Additional suppression for configure command
+    if "configure" in argv or (len(argv) > 0 and argv[0] == "configure"):
         os.environ["CLAUDE_MPM_SKIP_CLEANUP"] = "1"
 
     return argv
@@ -86,7 +219,7 @@ def deploy_bundled_skills():
     WHY: Automatically deploy skills from the bundled/ directory to .claude/skills/
     to ensure skills are available for agents without manual intervention.
 
-    DESIGN DECISION: Deployment happens silently on startup with logging only.
+    DESIGN DECISION: Deployment happens with minimal feedback (checkmark on success).
     Failures are logged but don't block startup to ensure claude-mpm remains
     functional even if skills deployment fails. Respects auto_deploy config setting.
     """
@@ -117,9 +250,13 @@ def deploy_bundled_skills():
         logger = get_logger("cli")
 
         if deployment_result.get("deployed"):
-            logger.info(
-                f"Skills: Deployed {len(deployment_result['deployed'])} skill(s)"
-            )
+            # Show simple feedback for deployed skills
+            deployed_count = len(deployment_result["deployed"])
+            print(f"✓ Bundled skills ready ({deployed_count} deployed)", flush=True)
+            logger.info(f"Skills: Deployed {deployed_count} skill(s)")
+        elif not deployment_result.get("errors"):
+            # No deployment needed, skills already present
+            print("✓ Bundled skills ready", flush=True)
 
         if deployment_result.get("errors"):
             logger.warning(
@@ -142,7 +279,8 @@ def discover_and_link_runtime_skills():
     WHY: Automatically discover and link skills added to .claude/skills/
     without requiring manual configuration.
 
-    DESIGN DECISION: Failures are logged but don't block startup to ensure
+    DESIGN DECISION: Provides simple feedback on completion.
+    Failures are logged but don't block startup to ensure
     claude-mpm remains functional even if skills discovery fails.
     """
     try:
@@ -151,6 +289,8 @@ def discover_and_link_runtime_skills():
         )
 
         discover_skills()
+        # Show simple success feedback
+        print("✓ Runtime skills linked", flush=True)
     except Exception as e:
         # Import logger here to avoid circular imports
         from ..core.logger import get_logger
@@ -160,18 +300,1116 @@ def discover_and_link_runtime_skills():
         # Continue execution - skills discovery failure shouldn't block startup
 
 
+def deploy_output_style_on_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.
+
+    DESIGN DECISION: This is non-blocking and idempotent. Deploys to project-level
+    directory (.claude/settings/output-styles/) instead of user-level to maintain
+    project isolation.
+
+    Deploys two styles:
+    - claude-mpm-style.md (professional mode)
+    - claude-mpm-teacher.md (teaching mode)
+    """
+    try:
+        import shutil
+        from pathlib import Path
+
+        # Source files (in framework package)
+        package_dir = Path(__file__).parent.parent / "agents"
+        professional_source = package_dir / "CLAUDE_MPM_OUTPUT_STYLE.md"
+        teacher_source = package_dir / "CLAUDE_MPM_TEACHER_OUTPUT_STYLE.md"
+
+        # Target directory (PROJECT-LEVEL, not user-level)
+        project_dir = Path.cwd()
+        output_styles_dir = project_dir / ".claude" / "settings" / "output-styles"
+        professional_target = output_styles_dir / "claude-mpm-style.md"
+        teacher_target = output_styles_dir / "claude-mpm-teacher.md"
+
+        # Create directory if it doesn't exist
+        output_styles_dir.mkdir(parents=True, exist_ok=True)
+
+        # Check if already deployed (both files exist and have content)
+        already_deployed = (
+            professional_target.exists()
+            and teacher_target.exists()
+            and professional_target.stat().st_size > 0
+            and teacher_target.stat().st_size > 0
+        )
+
+        if already_deployed:
+            # Show feedback that output styles are ready
+            print("✓ Output styles ready", flush=True)
+            return
+
+        # Deploy both styles
+        deployed_count = 0
+        if professional_source.exists():
+            shutil.copy2(professional_source, professional_target)
+            deployed_count += 1
+
+        if teacher_source.exists():
+            shutil.copy2(teacher_source, teacher_target)
+            deployed_count += 1
+
+        if deployed_count > 0:
+            print(f"✓ Output styles deployed ({deployed_count} styles)", flush=True)
+        else:
+            # Source files missing - log but don't fail
+            from ..core.logger import get_logger
+
+            logger = get_logger("cli")
+            logger.debug("Output style source files not found")
+
+    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 styles: {e}")
+        # Continue execution - output style deployment shouldn't block 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 sync_remote_agents_on_startup():
+    """
+    Synchronize agent templates from remote sources on startup.
+
+    WHY: Ensures agents are up-to-date from remote Git sources (GitHub)
+    without manual intervention. Uses ETag-based caching for efficient
+    updates (95%+ bandwidth reduction).
+
+    DESIGN DECISION: Non-blocking synchronization that doesn't prevent
+    startup if network is unavailable. Failures are logged but don't
+    block startup to ensure claude-mpm remains functional.
+
+    Workflow:
+    1. Cleanup legacy agent cache directories (if any)
+    2. Sync all enabled Git sources (download/cache files) - Phase 1 progress bar
+    3. Deploy agents to ~/.claude/agents/ - Phase 2 progress bar
+    4. Cleanup orphaned agents (ours but no longer deployed) - Phase 3
+    5. Log deployment results
+    """
+    # Cleanup legacy cache directories first (before syncing)
+    cleanup_legacy_agent_cache()
+
+    # DEPRECATED: Legacy warning - replaced by automatic cleanup above
+    check_legacy_cache()
+
+    try:
+        from ..core.shared.config_loader import ConfigLoader
+        from ..services.agents.deployment.agent_deployment import AgentDeploymentService
+        from ..services.agents.startup_sync import sync_agents_on_startup
+        from ..services.profile_manager import ProfileManager
+        from ..utils.progress import ProgressBar
+
+        # Load active profile if configured
+        # Get project root (where .claude-mpm exists)
+        from pathlib import Path
+        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()
+
+        # Only proceed with deployment if sync was enabled and ran
+        if result.get("enabled") and result.get("sources_synced", 0) > 0:
+            from ..core.logger import get_logger
+
+            logger = get_logger("cli")
+
+            downloaded = result.get("total_downloaded", 0)
+            cached = result.get("cache_hits", 0)
+            duration = result.get("duration_ms", 0)
+
+            if downloaded > 0 or cached > 0:
+                logger.debug(
+                    f"Agent sync: {downloaded} updated, {cached} cached ({duration}ms)"
+                )
+
+            # Log errors if any
+            errors = result.get("errors", [])
+            if errors:
+                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)
+            try:
+                # Initialize deployment service with profile-filtered configuration
+                from ..core.config import Config
+
+                deploy_config = None
+                if active_profile and profile_manager.active_profile:
+                    # Create config with excluded agents based on profile
+                    # Get all agents that should be excluded (not in enabled list)
+                    from pathlib import Path
+
+                    cache_dir = Path.home() / ".claude-mpm" / "cache" / "agents"
+                    if cache_dir.exists():
+                        # Find all agent files
+                        all_agent_files = [
+                            f
+                            for f in cache_dir.rglob("*.md")
+                            if "/agents/" in str(f)
+                            and str(f).count("/agents/") == 1
+                            and f.stem.lower() != "base-agent"
+                        ]
+
+                        # Build exclusion list for agents not in profile
+                        excluded_agents = []
+                        for agent_file in all_agent_files:
+                            agent_name = agent_file.stem
+                            if not profile_manager.is_agent_enabled(agent_name):
+                                excluded_agents.append(agent_name)
+
+                        if excluded_agents:
+                            # Get singleton config and update with profile settings
+                            # BUGFIX: Config is a singleton that ignores dict parameter if already initialized.
+                            # Creating Config({...}) doesn't store excluded_agents - use set() instead.
+                            deploy_config = Config()
+                            deploy_config.set("agent_deployment.excluded_agents", excluded_agents)
+                            deploy_config.set("agent_deployment.filter_non_mpm_agents", False)
+                            deploy_config.set("agent_deployment.case_sensitive", False)
+                            deploy_config.set("agent_deployment.exclude_dependencies", False)
+                            logger.info(
+                                f"Profile '{active_profile}': Excluding {len(excluded_agents)} agents from deployment"
+                            )
+
+                deployment_service = AgentDeploymentService(config=deploy_config)
+
+                # Count agents in cache to show accurate progress
+                from pathlib import Path
+
+                cache_dir = Path.home() / ".claude-mpm" / "cache" / "agents"
+                agent_count = 0
+
+                if cache_dir.exists():
+                    # BUGFIX (cache-count-inflation): Clean up stale cache files
+                    # from old repositories before counting to prevent inflated counts.
+                    # Issue: Old caches like bobmatnyc/claude-mpm-agents/agents/
+                    # were counted alongside current agents, inflating count
+                    # from 44 to 85.
+                    #
+                    # Solution: Remove files with nested /agents/ paths
+                    # (e.g., cache/agents/user/repo/agents/...)
+                    # Keep only current agents (e.g., cache/agents/engineer/...)
+                    removed_count = 0
+                    stale_dirs = set()
+
+                    for md_file in cache_dir.rglob("*.md"):
+                        # Stale cache files have multiple /agents/ in their path
+                        # Current: ~/.claude-mpm/cache/agents/engineer/...
+                        #          (1 occurrence)
+                        # Old: ~/.claude-mpm/cache/agents/bobmatnyc/.../agents/...
+                        #      (2+ occurrences)
+                        if str(md_file).count("/agents/") > 1:
+                            # Track parent directory for cleanup
+                            # Extract subdirectory under cache/agents/
+                            # (e.g., "bobmatnyc")
+                            parts = md_file.parts
+                            cache_agents_idx = parts.index("agents")
+                            if cache_agents_idx + 1 < len(parts):
+                                stale_subdir = parts[cache_agents_idx + 1]
+                                # Only remove if it's not a known category directory
+                                if stale_subdir not in [
+                                    "engineer",
+                                    "ops",
+                                    "qa",
+                                    "universal",
+                                    "documentation",
+                                    "claude-mpm",
+                                    "security",
+                                ]:
+                                    stale_dirs.add(cache_dir / stale_subdir)
+
+                            md_file.unlink()
+                            removed_count += 1
+
+                    # Remove empty stale directories
+                    for stale_dir in stale_dirs:
+                        if stale_dir.exists() and stale_dir.is_dir():
+                            try:
+                                # Remove directory and all contents
+                                import shutil
+
+                                shutil.rmtree(stale_dir)
+                            except Exception:
+                                pass  # Ignore cleanup errors
+
+                    if removed_count > 0:
+                        from loguru import logger
+
+                        logger.info(
+                            f"Cleaned up {removed_count} stale cache files "
+                            f"from old repositories"
+                        )
+
+                    # Count MD files in cache (agent markdown files from
+                    # current repos)
+                    # BUGFIX: Only count files in agent directories,
+                    # not docs/templates/READMEs
+                    # Valid agent paths must contain "/agents/" exactly ONCE
+                    # (current structure)
+                    # 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 (after cleanup)
+                    all_md_files = list(cache_dir.rglob("*.md"))
+
+                    # Filter to only agent files:
+                    # 1. Must have "/agents/" in path exactly ONCE
+                    #    (current structure)
+                    # 2. Must not be in PM templates or doc files
+                    # 3. Exclude BASE-AGENT.md which is not a deployable agent
+                    # 4. Exclude build artifacts (dist/, build/, .cache/)
+                    #    to prevent double-counting
+                    agent_files = [
+                        f
+                        for f in all_md_files
+                        if (
+                            # Must be in an agent directory (from current
+                            # cache structure)
+                            "/agents/" in str(f)
+                            # NEW: Only ONE /agents/ in path (excludes old
+                            # nested repos)
+                            # This prevents counting old caches like
+                            # bobmatnyc/claude-mpm-agents/agents/...
+                            and str(f).count("/agents/") == 1
+                            # 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"
+                            # Exclude build artifacts (prevents double-counting
+                            # source + built files)
+                            and not any(
+                                part in str(f).split("/")
+                                for part in ["dist", "build", ".cache"]
+                            )
+                        )
+                    ]
+                    agent_count = len(agent_files)
+
+                if agent_count > 0:
+                    # Deploy agents to project-level directory where Claude Code expects them
+                    deploy_target = Path.cwd() / ".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
+                        config=deploy_config,  # Pass config to respect profile filtering
+                    )
+
+                    # Get actual counts from deployment result (reflects configured agents)
+                    deployed = len(deployment_result.get("deployed", []))
+                    updated = len(deployment_result.get("updated", []))
+                    skipped = len(deployment_result.get("skipped", []))
+                    total_configured = deployed + updated + skipped
+
+                    # FALLBACK: If deployment result doesn't track skipped agents (async path),
+                    # count existing agents in target directory as "already deployed"
+                    # This ensures accurate reporting when agents are already up-to-date
+                    if total_configured == 0 and deploy_target.exists():
+                        existing_agents = list(deploy_target.glob("*.md"))
+                        # Filter out non-agent files (e.g., README.md, INSTRUCTIONS.md)
+                        agent_count_in_target = len(
+                            [
+                                f
+                                for f in existing_agents
+                                if not f.name.startswith(("README", "INSTRUCTIONS"))
+                            ]
+                        )
+                        if agent_count_in_target > 0:
+                            # All agents already deployed - count them as skipped
+                            skipped = agent_count_in_target
+                            total_configured = agent_count_in_target
+
+                    # Create progress bar with actual configured agent count (not raw file count)
+                    deploy_progress = ProgressBar(
+                        total=total_configured if total_configured > 0 else 1,
+                        prefix="Deploying agents",
+                        show_percentage=True,
+                        show_counter=True,
+                    )
+
+                    # Update progress bar to completion
+                    deploy_progress.update(
+                        total_configured if total_configured > 0 else 1
+                    )
+
+                    # Cleanup orphaned agents (ours but no longer deployed)
+                    # Get list of deployed agent filenames (what should remain)
+                    deployed_filenames = []
+                    for agent_name in deployment_result.get("deployed", []):
+                        deployed_filenames.append(f"{agent_name}.md")
+                    for agent_name in deployment_result.get("updated", []):
+                        deployed_filenames.append(f"{agent_name}.md")
+                    for agent_name in deployment_result.get("skipped", []):
+                        deployed_filenames.append(f"{agent_name}.md")
+
+                    # Run cleanup and get count of removed agents
+                    removed = _cleanup_orphaned_agents(
+                        deploy_target, deployed_filenames
+                    )
+
+                    # Show total configured agents (deployed + updated + already existing)
+                    # Include cache count for context and removed count if any
+                    if deployed > 0 or updated > 0:
+                        if removed > 0:
+                            deploy_progress.finish(
+                                f"Complete: {deployed} new, {updated} updated, {skipped} unchanged, "
+                                f"{removed} removed ({total_configured} configured from {agent_count} files in cache)"
+                            )
+                        else:
+                            deploy_progress.finish(
+                                f"Complete: {deployed} new, {updated} updated, {skipped} unchanged "
+                                f"({total_configured} configured from {agent_count} files in cache)"
+                            )
+                    elif removed > 0:
+                        deploy_progress.finish(
+                            f"Complete: {total_configured} agents deployed, "
+                            f"{removed} removed ({agent_count} files in cache)"
+                        )
+                    else:
+                        deploy_progress.finish(
+                            f"Complete: {total_configured} agents deployed "
+                            f"({agent_count} files in cache)"
+                        )
+
+                    # 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:")
+
+                        # Show first 10 errors to avoid overwhelming output
+                        max_errors_to_show = 10
+                        errors_to_display = deploy_errors[:max_errors_to_show]
+
+                        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)")
+
+                        # 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")
+
+            except Exception as e:
+                # Deployment failure shouldn't block startup
+                from ..core.logger import get_logger
+
+                logger = get_logger("cli")
+                logger.warning(f"Failed to deploy agents from cache: {e}")
+
+    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 sync remote agents: {e}")
+        # Continue execution - agent sync failure shouldn't block startup
+
+
+def sync_remote_skills_on_startup():
+    """
+    Synchronize skill templates from remote sources on startup.
+
+    WHY: Ensures skills are up-to-date from remote Git sources (GitHub)
+    without manual intervention. Provides consistency with agent syncing.
+
+    DESIGN DECISION: Non-blocking synchronization that doesn't prevent
+    startup if network is unavailable. Failures are logged but don't
+    block startup to ensure claude-mpm remains functional.
+
+    Workflow:
+    1. Sync all enabled Git sources (download/cache files) - Phase 1 progress bar
+    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
+    """
+    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)
+
+        # Get enabled sources
+        enabled_sources = config.get_enabled_sources()
+        if not enabled_sources:
+            return  # No sources enabled, nothing to sync
+
+        # Phase 1: Sync files from Git sources
+        # We need to discover file count first to show accurate progress
+        # This requires pre-scanning repositories via GitHub API
+        from ..core.logger import get_logger
+
+        logger = get_logger("cli")
+
+        # 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
+                url_parts = (
+                    source.url.rstrip("/").replace(".git", "").split("github.com/")
+                )
+                if len(url_parts) == 2:
+                    repo_path = url_parts[1].strip("/")
+                    owner_repo = "/".join(repo_path.split("/")[:2])
+
+                    # Use Tree API to discover all files
+                    all_files = manager._discover_repository_files_via_tree_api(
+                        owner_repo, source.branch
+                    )
+
+                    # Count relevant files (markdown, JSON)
+                    relevant_files = [
+                        f
+                        for f in all_files
+                        if f.endswith(".md") or f.endswith(".json") or f == ".gitignore"
+                    ]
+                    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 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
+        )
+
+        # Finish sync progress bar with clear breakdown
+        downloaded = results["total_files_updated"]
+        cached = results["total_files_cached"]
+        total_files = downloaded + cached
+
+        if cached > 0:
+            sync_progress.finish(
+                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 ({total_skill_dirs} skills)"
+            )
+
+        # Phase 2: Scan agents and save to configuration.yaml
+        # This step populates configuration.yaml with agent-referenced skills
+        if results["synced_count"] > 0:
+            agents_dir = Path.cwd() / ".claude" / "agents"
+
+            # Scan agents for skill requirements
+            agent_skills = get_required_skills_from_agents(agents_dir)
+
+            # 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)
+
+            # Phase 3: Resolve which skills to deploy (user_defined or agent_referenced)
+            skills_to_deploy, skill_source = get_skills_to_deploy(project_config_path)
+
+            # 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 to project directory (like agents), not user directory
+                deployment_result = manager.deploy_skills(
+                    target_dir=Path.cwd() / ".claude" / "skills",
+                    force=False,
+                    skill_filter=set(skills_to_deploy) if skills_to_deploy else None,
+                )
+
+                # Get actual counts from deployment result
+                deployed = deployment_result.get("deployed_count", 0)
+                skipped = deployment_result.get("skipped_count", 0)
+                filtered = deployment_result.get("filtered_count", 0)
+                total_available = deployed + skipped
+
+                # Only show progress bar if there are skills to deploy
+                if total_available > 0:
+                    deploy_progress = ProgressBar(
+                        total=total_available,
+                        prefix="Deploying skill directories",
+                        show_percentage=True,
+                        show_counter=True,
+                    )
+                    # 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)
+
+                # 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"
+                )
+
+                if deployed > 0:
+                    if filtered > 0:
+                        deploy_progress.finish(
+                            f"Complete: {deployed} new, {skipped} unchanged "
+                            f"({total_available} {source_label}, {filtered} files in cache)"
+                        )
+                    else:
+                        deploy_progress.finish(
+                            f"Complete: {deployed} new, {skipped} unchanged "
+                            f"({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:
+                    deploy_progress.finish(
+                        f"Complete: {total_available} skills {source_label} "
+                        f"({total_skill_count} files in cache)"
+                    )
+
+                # Log deployment errors if any
+                from ..core.logger import get_logger
+
+                logger = get_logger("cli")
+
+                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"
+                    )
+
+    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 sync remote skills: {e}")
+        # Continue execution - skill sync failure shouldn't block startup
+
+
+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 / {available_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 collections, similar to the agent summary.
+
+    DESIGN DECISION: Fast, non-blocking check that counts skills from deployment
+    directory and collection repos. Shows "X installed (Y available)" format.
+    Failures are silent to avoid blocking startup.
+    """
+    try:
+        from pathlib import Path
+
+        # Count deployed skills (installed)
+        skills_dir = Path.home() / ".claude" / "skills"
+        installed_count = 0
+        if skills_dir.exists():
+            # Count directories with SKILL.md (excludes collection repos)
+            # Exclude collection directories (obra-superpowers, etc.)
+            skill_dirs = [
+                d
+                for d in skills_dir.iterdir()
+                if d.is_dir()
+                and (d / "SKILL.md").exists()
+                and not (d / ".git").exists()  # Exclude collection repos
+            ]
+            installed_count = len(skill_dirs)
+
+        # Count available skills in collections
+        available_count = 0
+        if skills_dir.exists():
+            # Scan all collection directories (those with .git)
+            for collection_dir in skills_dir.iterdir():
+                if (
+                    not collection_dir.is_dir()
+                    or not (collection_dir / ".git").exists()
+                ):
+                    continue
+
+                # Count skill directories in this collection
+                # 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(collection_dir):
+                    if "SKILL.md" in files:
+                        # Exclude build artifacts and hidden directories (within the collection)
+                        # Get relative path from collection_dir to avoid excluding based on .claude parent
+                        root_path = Path(root)
+                        relative_parts = root_path.relative_to(collection_dir).parts
+                        if not any(
+                            part.startswith(".")
+                            or part in ["dist", "build", "__pycache__"]
+                            for part in relative_parts
+                        ):
+                            available_count += 1
+
+        # Display summary if we have skills
+        if installed_count > 0 or available_count > 0:
+            print(
+                f"✓ Skills: {installed_count} installed ({available_count} available)",
+                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.
+
+    WHY: PM skills are essential for PM agent operation.
+    Shows deployment status and auto-deploys if missing.
+    """
+    try:
+        from pathlib import Path
+
+        from ..services.pm_skills_deployer import PMSkillsDeployerService
+
+        deployer = PMSkillsDeployerService()
+        project_dir = Path.cwd()
+
+        result = deployer.verify_pm_skills(project_dir)
+
+        if result.verified:
+            # Show verified status
+            print(f"✓ PM skills: {result.skill_count} verified", flush=True)
+        else:
+            # Auto-deploy if missing
+            print("Deploying PM skills...", end="", flush=True)
+            deploy_result = deployer.deploy_pm_skills(project_dir)
+            if deploy_result.success:
+                total = len(deploy_result.deployed) + len(deploy_result.skipped)
+                print(f"\r✓ PM skills: {total} deployed" + " " * 20, flush=True)
+            else:
+                print(f"\r⚠ PM skills: deployment failed" + " " * 20, flush=True)
+
+    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:
+            # 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():
     """
     Initialize all background services on startup.
 
     WHY: Centralizes all startup service initialization for cleaner main().
+
+    NOTE: System instructions (PM_INSTRUCTIONS.md, WORKFLOW.md, MEMORY.md) and
+    templates do NOT deploy automatically on startup. They only deploy when user
+    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
     """
+    # 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()
-    deploy_bundled_skills()
-    discover_and_link_runtime_skills()
+    sync_remote_agents_on_startup()  # 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)
+    # 2. Sync and deploy remote skills (Git sources, can override bundled)
+    # 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)
+    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):
@@ -247,12 +1485,26 @@ def check_mcp_auto_configuration():
     user consent.
 
     DESIGN DECISION: This is blocking but quick - it only runs once and has
-    a 10-second timeout. We want to catch users on first run for the best
-    experience.
+    a 10-second timeout. Shows progress feedback during checks to avoid
+    appearing frozen.
+
+    OPTIMIZATION: Skip ALL MCP checks for doctor and configure commands to avoid
+    duplicate checks (doctor performs its own comprehensive check, configure
+    allows users to select services).
     """
+    # Skip MCP service checks for the doctor and configure commands
+    # The doctor command performs its own comprehensive MCP service check
+    # The configure command allows users to configure which services to enable
+    # Running both would cause duplicate checks and log messages (9 seconds apart)
+    if len(sys.argv) > 1 and sys.argv[1] in ("doctor", "configure"):
+        return
+
     try:
         from ..services.mcp_gateway.auto_configure import check_and_configure_mcp
 
+        # Show progress feedback - this operation can take 10+ seconds
+        print("Checking MCP configuration...", end="", flush=True)
+
         # This function handles all the logic:
         # - Checks if already configured
         # - Checks if pipx installation
@@ -261,45 +1513,18 @@ def check_mcp_auto_configuration():
         # - Configures if user agrees
         check_and_configure_mcp()
 
-    except Exception as e:
-        # Non-critical - log but don't fail
-        from ..core.logger import get_logger
-
-        logger = get_logger("cli")
-        logger.debug(f"MCP auto-configuration check failed: {e}")
-
-    # Skip MCP service fixes for the doctor and configure commands
-    # The doctor command performs its own comprehensive MCP service check
-    # The configure command allows users to configure which services to enable
-    # Running both would cause duplicate checks and log messages (9 seconds apart)
-    if len(sys.argv) > 1 and sys.argv[1] in ("doctor", "configure"):
-        return
-
-    # Also ensure MCP services are properly configured in ~/.claude.json
-    # This fixes incorrect paths and adds missing services
-    try:
-        from ..core.logger import get_logger
-        from ..services.mcp_config_manager import MCPConfigManager
-
-        logger = get_logger("cli")
-        mcp_manager = MCPConfigManager()
-
-        # Fix any corrupted installations first
-        _fix_success, fix_message = mcp_manager.fix_mcp_service_issues()
-        if fix_message and "Fixed:" in fix_message:
-            logger.info(f"MCP service fixes applied: {fix_message}")
-
-        # Ensure all services are configured correctly
-        _config_success, config_message = mcp_manager.ensure_mcp_services_configured()
-        if config_message and "Added MCP services" in config_message:
-            logger.info(f"MCP services configured: {config_message}")
+        # Clear the "Checking..." message by overwriting with spaces
+        print("\r" + " " * 30 + "\r", end="", flush=True)
 
     except Exception as e:
+        # Clear progress message on error
+        print("\r" + " " * 30 + "\r", end="", flush=True)
+
         # Non-critical - log but don't fail
         from ..core.logger import get_logger
 
         logger = get_logger("cli")
-        logger.debug(f"MCP services configuration update failed: {e}")
+        logger.debug(f"MCP auto-configuration check failed: {e}")
 
 
 def verify_mcp_gateway_startup():
@@ -313,22 +1538,13 @@ 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
-        import time
 
         from ..core.logger import get_logger
         from ..services.mcp_gateway.core.startup_verification import (
@@ -343,68 +1559,14 @@ def verify_mcp_gateway_startup():
 
         # DISABLED: Pre-warming MCP servers can interfere with Claude Code's MCP management
         # This was causing issues with MCP server initialization and stderr handling
-        # def run_pre_warming():
-        #     loop = None
-        #     try:
-        #         start_time = time.time()
-        #         loop = asyncio.new_event_loop()
-        #         asyncio.set_event_loop(loop)
-        #
-        #         # Pre-warm MCP servers (especially vector search)
-        #         logger.info("Pre-warming MCP servers to eliminate startup delay...")
-        #         loop.run_until_complete(pre_warm_mcp_servers())
-        #
-        #         pre_warm_time = time.time() - start_time
-        #         if pre_warm_time > 1.0:
-        #             logger.info(f"MCP servers pre-warmed in {pre_warm_time:.2f}s")
-
-        # Dummy function to maintain structure
-        def run_pre_warming():
-            loop = None
-            try:
-                time.time()
-                loop = asyncio.new_event_loop()
-                asyncio.set_event_loop(loop)
+        # Pre-warming functionality has been removed. Gateway verification only runs
+        # if MCP gateway is not already configured.
 
-                # Also run gateway verification if needed
-                if not gateway_configured:
-                    loop.run_until_complete(verify_mcp_gateway_on_startup())
-
-            except Exception as e:
-                # Non-blocking - log but don't fail
-                logger.debug(f"MCP pre-warming error (non-critical): {e}")
-            finally:
-                # Properly clean up event loop to prevent kqueue warnings
-                if loop is not None:
-                    try:
-                        # Cancel all running tasks
-                        pending = asyncio.all_tasks(loop)
-                        for task in pending:
-                            task.cancel()
-                        # Wait for tasks to complete cancellation
-                        if pending:
-                            loop.run_until_complete(
-                                asyncio.gather(*pending, return_exceptions=True)
-                            )
-                    except Exception:
-                        pass  # Ignore cleanup errors
-                    finally:
-                        loop.close()
-                        # Clear the event loop reference to help with cleanup
-                        asyncio.set_event_loop(None)
-
-        # Run pre-warming in background thread
-        import threading
-
-        pre_warm_thread = threading.Thread(target=run_pre_warming, daemon=True)
-        pre_warm_thread.start()
-
-        return
-
-        # Run detailed verification in background if not configured
+        # Run gateway verification in background if not configured
         if not gateway_configured:
-            # Note: We don't await this to avoid blocking startup
+
             def run_verification():
+                """Background thread to verify MCP gateway configuration."""
                 loop = None
                 try:
                     loop = asyncio.new_event_loop()