moai-adk 0.8.0__py3-none-any.whl → 0.34.0__py3-none-any.whl

moai_adk/cli/commands/update.py

@@ -13,6 +13,7 @@ Includes:
 - 70-80% performance improvement for up-to-date projects
 
 ## Skill Invocation Guide (English-Only)
+# mypy: disable-error-code=return-value
 
 ### Related Skills
 - **moai-foundation-trust**: For post-update validation
@@ -25,34 +26,48 @@ Includes:
 
 ### When to Invoke Skills in Related Workflows
 1. **After successful update**:
-   - Run `Skill("moai-foundation-trust")` to validate all TRUST 5 gates
+   - Run `Skill("moai-foundation-trust")` to validate all TRUST 4 gates
    - Run `Skill("moai-foundation-langs")` to confirm language toolchain still works
    - Run project doctor command for full system validation
 
 2. **Before updating**:
    - Create backup with `python -m moai_adk backup`
-   - Run `Skill("moai-foundation-tags")` to document current TAG state
 
 3. **If update fails**:
    - Use backup to restore previous state
    - Debug with `python -m moai_adk doctor --verbose`
 """
+
+# type: ignore
+
 from __future__ import annotations
 
 import json
+import logging
+import shutil
 import subprocess
 from datetime import datetime
 from pathlib import Path
-from typing import Any, cast
+from typing import Any, Union, cast
 
 import click
+import yaml
 from packaging import version
 from rich.console import Console
 
 from moai_adk import __version__
+from moai_adk.core.merge import MergeAnalyzer
+from moai_adk.core.migration import VersionMigrator
+from moai_adk.core.migration.alfred_to_moai_migrator import AlfredToMoaiMigrator
+
+# Import new custom element restoration modules
+from moai_adk.core.migration.custom_element_scanner import create_custom_element_scanner
+from moai_adk.core.migration.selective_restorer import create_selective_restorer
+from moai_adk.core.migration.user_selection_ui import create_user_selection_ui
 from moai_adk.core.template.processor import TemplateProcessor
 
 console = Console()
+logger = logging.getLogger(__name__)
 
 # Constants for tool detection
 TOOL_DETECTION_TIMEOUT = 5  # seconds
@@ -61,33 +76,76 @@ PIPX_COMMAND = ["pipx", "upgrade", "moai-adk"]
 PIP_COMMAND = ["pip", "install", "--upgrade", "moai-adk"]
 
 
-# @CODE:UPDATE-REFACTOR-002-004
 # Custom exceptions for better error handling
 class UpdateError(Exception):
     """Base exception for update operations."""
+
     pass
 
 
 class InstallerNotFoundError(UpdateError):
     """Raised when no package installer detected."""
+
     pass
 
 
 class NetworkError(UpdateError):
     """Raised when network operation fails."""
+
     pass
 
 
 class UpgradeError(UpdateError):
     """Raised when package upgrade fails."""
+
     pass
 
 
 class TemplateSyncError(UpdateError):
     """Raised when template sync fails."""
+
     pass
 
 
+def _get_config_path(project_path: Path) -> tuple[Path, bool]:
+    """Get config file path, preferring YAML over JSON.
+
+    Returns:
+        Tuple of (config_path, is_yaml)
+    """
+    yaml_path = project_path / ".moai" / "config" / "config.yaml"
+    json_path = project_path / ".moai" / "config" / "config.json"
+
+    if yaml_path.exists():
+        return yaml_path, True
+    return json_path, False
+
+
+def _load_config(config_path: Path) -> dict[str, Any]:
+    """Load config from YAML or JSON file."""
+    if not config_path.exists():
+        return {}
+
+    is_yaml = config_path.suffix in (".yaml", ".yml")
+    content = config_path.read_text(encoding="utf-8")
+
+    if is_yaml:
+        return yaml.safe_load(content) or {}
+    return json.loads(content)
+
+
+def _save_config(config_path: Path, config_data: dict[str, Any]) -> None:
+    """Save config to YAML or JSON file."""
+    is_yaml = config_path.suffix in (".yaml", ".yml")
+
+    if is_yaml:
+        content = yaml.safe_dump(config_data, default_flow_style=False, allow_unicode=True, sort_keys=False)
+    else:
+        content = json.dumps(config_data, indent=2, ensure_ascii=False) + "\n"
+
+    config_path.write_text(content, encoding="utf-8")
+
+
 def _is_installed_via_uv_tool() -> bool:
     """Check if moai-adk installed via uv tool.
 
@@ -100,7 +158,7 @@ def _is_installed_via_uv_tool() -> bool:
             capture_output=True,
             text=True,
             timeout=TOOL_DETECTION_TIMEOUT,
-            check=False
+            check=False,
         )
         return result.returncode == 0 and "moai-adk" in result.stdout
     except (FileNotFoundError, subprocess.TimeoutExpired, OSError):
@@ -119,7 +177,7 @@ def _is_installed_via_pipx() -> bool:
             capture_output=True,
             text=True,
             timeout=TOOL_DETECTION_TIMEOUT,
-            check=False
+            check=False,
         )
         return result.returncode == 0 and "moai-adk" in result.stdout
     except (FileNotFoundError, subprocess.TimeoutExpired, OSError):
@@ -138,14 +196,13 @@ def _is_installed_via_pip() -> bool:
             capture_output=True,
             text=True,
             timeout=TOOL_DETECTION_TIMEOUT,
-            check=False
+            check=False,
         )
         return result.returncode == 0
     except (FileNotFoundError, subprocess.TimeoutExpired, OSError):
         return False
 
 
-# @CODE:UPDATE-REFACTOR-002-001
 def _detect_tool_installer() -> list[str] | None:
     """Detect which tool installed moai-adk.
 
@@ -185,7 +242,6 @@ def _detect_tool_installer() -> list[str] | None:
         return None
 
 
-# @CODE:UPDATE-REFACTOR-002-002
 def _get_current_version() -> str:
     """Get currently installed moai-adk version.
 
@@ -219,126 +275,1251 @@ def _get_latest_version() -> str:
         raise RuntimeError(f"Failed to fetch latest version from PyPI: {e}") from e
 
 
-def _compare_versions(current: str, latest: str) -> int:
-    """Compare semantic versions.
+def _compare_versions(current: str, latest: str) -> int:
+    """Compare semantic versions.
+
+    Args:
+        current: Current version string
+        latest: Latest version string
+
+    Returns:
+        -1 if current < latest (upgrade needed)
+        0 if current == latest (up to date)
+        1 if current > latest (unusual, already newer)
+    """
+    current_v = version.parse(current)
+    latest_v = version.parse(latest)
+
+    if current_v < latest_v:
+        return -1
+    elif current_v == latest_v:
+        return 0
+    else:
+        return 1
+
+
+def _get_package_config_version() -> str:
+    """Get the current package template version.
+
+    This returns the version of the currently installed moai-adk package,
+    which is the version of templates that this package provides.
+
+    Returns:
+        Version string of the installed package (e.g., "0.6.1")
+    """
+    # Package template version = current installed package version
+    # This is simple and reliable since templates are versioned with the package
+    return __version__
+
+
+def _get_project_config_version(project_path: Path) -> str:
+    """Get current project config.json template version.
+
+    This reads the project's .moai/config/config.json to determine the current
+    template version that the project is configured with.
+
+    Args:
+        project_path: Project directory path (absolute)
+
+    Returns:
+        Version string from project's config.json (e.g., "0.6.1")
+        Returns "0.0.0" if template_version field not found (indicates no prior sync)
+
+    Raises:
+        ValueError: If config file exists but cannot be parsed
+    """
+
+    def _is_placeholder_val(value: str) -> bool:
+        """Check if value contains unsubstituted template placeholders."""
+        return isinstance(value, str) and value.startswith("{{") and value.endswith("}}")
+
+    config_path, _ = _get_config_path(project_path)
+
+    if not config_path.exists():
+        # No config yet, treat as version 0.0.0 (needs initial sync)
+        return "0.0.0"
+
+    try:
+        config_data = _load_config(config_path)
+        # Check for template_version in project section
+        template_version = config_data.get("project", {}).get("template_version")
+        if template_version and not _is_placeholder_val(template_version):
+            return template_version
+
+        # Fallback to moai version if no template_version exists
+        moai_version = config_data.get("moai", {}).get("version")
+        if moai_version and not _is_placeholder_val(moai_version):
+            return moai_version
+
+        # If values are placeholders or don't exist, treat as uninitialized (0.0.0 triggers sync)
+        return "0.0.0"
+    except (json.JSONDecodeError, yaml.YAMLError) as e:
+        raise ValueError(f"Failed to parse project config: {e}") from e
+
+
+def _ask_merge_strategy(yes: bool = False) -> str:
+    """
+    Ask user to choose merge strategy via CLI prompt.
+
+    Args:
+        yes: If True, auto-select "auto" (for --yes flag)
+
+    Returns:
+        "auto" or "manual"
+    """
+    if yes:
+        return "auto"
+
+    console.print("\n[cyan]🔀 Choose merge strategy:[/cyan]")
+    console.print("[cyan]  [1] Auto-merge (default)[/cyan]")
+    console.print("[dim]     → Template installs fresh + user changes preserved + minimal conflicts[/dim]")
+    console.print("[cyan]  [2] Manual merge[/cyan]")
+    console.print("[dim]     → Backup preserved + merge guide generated + you control merging[/dim]")
+
+    response = click.prompt("Select [1 or 2]", default="1")
+    if response == "2":
+        return "manual"
+    return "auto"
+
+
+def _generate_manual_merge_guide(backup_path: Path, template_path: Path, project_path: Path) -> Path:
+    """
+    Generate comprehensive merge guide for manual merging.
+
+    Args:
+        backup_path: Path to backup directory
+        template_path: Path to template directory
+        project_path: Project root path
+
+    Returns:
+        Path to generated merge guide
+    """
+    guide_dir = project_path / ".moai" / "guides"
+    guide_dir.mkdir(parents=True, exist_ok=True)
+
+    guide_path = guide_dir / "merge-guide.md"
+
+    # Find changed files
+    changed_files = []
+    backup_claude = backup_path / ".claude"
+    backup_path / ".moai"
+
+    # Compare .claude/
+    if backup_claude.exists():
+        for file in backup_claude.rglob("*"):
+            if file.is_file():
+                rel_path = file.relative_to(backup_path)
+                current_file = project_path / rel_path
+                if current_file.exists():
+                    if file.read_text(encoding="utf-8", errors="ignore") != current_file.read_text(
+                        encoding="utf-8", errors="ignore"
+                    ):
+                        changed_files.append(f"  - {rel_path}")
+                else:
+                    changed_files.append(f"  - {rel_path} (new)")
+
+    # Generate guide
+    timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
+    guide_content = f"""# Merge Guide - Manual Merge Mode
+
+**Generated**: {timestamp}
+**Backup Location**: `{backup_path.relative_to(project_path)}/`
+
+## Summary
+
+During this update, the following files were changed:
+
+{chr(10).join(changed_files) if changed_files else "  (No changes detected)"}
+
+## How to Merge
+
+### Option 1: Using diff (Terminal)
+
+```bash
+# Compare specific files
+diff {backup_path.name}/.claude/settings.json .claude/settings.json
+
+# View all differences
+diff -r {backup_path.name}/ .
+```
+
+### Option 2: Using Visual Merge Tool
+
+```bash
+# macOS/Linux - Using meld
+meld {backup_path.relative_to(project_path)}/ .
+
+# Using VSCode
+code --diff {backup_path.relative_to(project_path)}/.claude/settings.json .claude/settings.json
+```
+
+### Option 3: Manual Line-by-Line
+
+1. Open backup file in your editor
+2. Open current file side-by-side
+3. Manually copy your customizations
+
+## Key Files to Review
+
+### .claude/settings.json
+- Contains MCP servers, hooks, environment variables
+- **Action**: Restore any custom MCP servers and environment variables
+- **Location**: {backup_path.relative_to(project_path)}/.claude/settings.json
+
+### .moai/config/config.json
+- Contains project configuration and metadata
+- **Action**: Verify user-specific settings are preserved
+- **Location**: {backup_path.relative_to(project_path)}/.moai/config/config.json
+
+### .claude/commands/, .claude/agents/, .claude/hooks/
+- Contains custom scripts and automation
+- **Action**: Restore any custom scripts outside of /moai/ folders
+- **Location**: {backup_path.relative_to(project_path)}/.claude/
+
+## Migration Checklist
+
+- [ ] Compare `.claude/settings.json`
+  - [ ] Restore custom MCP servers
+  - [ ] Restore environment variables
+  - [ ] Verify hooks are properly configured
+
+- [ ] Review `.moai/config/config.json`
+  - [ ] Check version was updated
+  - [ ] Verify user settings preserved
+
+- [ ] Restore custom scripts
+  - [ ] Any custom commands outside /moai/
+  - [ ] Any custom agents outside /moai/
+  - [ ] Any custom hooks outside /moai/
+
+- [ ] Run tests
+  ```bash
+  uv run pytest
+  moai-adk validate
+  ```
+
+- [ ] Commit changes
+  ```bash
+  git add .
+  git commit -m "merge: Update templates with manual merge"
+  ```
+
+## Rollback if Needed
+
+If you want to cancel and restore the backup:
+
+```bash
+# Restore everything from backup
+cp -r {backup_path.relative_to(project_path)}/.claude .
+cp -r {backup_path.relative_to(project_path)}/.moai .
+cp {backup_path.relative_to(project_path)}/CLAUDE.md .
+
+# Or restore specific files
+cp {backup_path.relative_to(project_path)}/.claude/settings.json .claude/
+```
+
+## Questions?
+
+If you encounter merge conflicts or issues:
+
+1. Check the backup folder for original files
+2. Compare line-by-line using diff tools
+3. Consult documentation: https://adk.mo.ai.kr/update-merge
+
+---
+
+**Backup**: `{backup_path}/`
+**Generated**: {timestamp}
+"""
+
+    guide_path.write_text(guide_content, encoding="utf-8")
+    logger.info(f"✅ Merge guide created: {guide_path}")
+    return guide_path
+
+
+def _migrate_legacy_logs(project_path: Path, dry_run: bool = False) -> bool:
+    """Migrate legacy log files to unified directory structure.
+
+    Creates new unified directory structure (.moai/docs/, .moai/logs/archive/) and
+    migrates files from legacy locations to new unified structure:
+    - .moai/memory/last-session-state.json → .moai/logs/sessions/
+    - .moai/error_logs/ → .moai/logs/errors/
+    - .moai/reports/ → .moai/docs/reports/
+
+    Args:
+        project_path: Project directory path (absolute)
+        dry_run: If True, only simulate migration without making changes
+
+    Returns:
+        True if migration succeeded or no migration needed, False otherwise
+
+    Raises:
+        Exception: If migration fails during actual execution
+    """
+    try:
+        # Define source and target directories
+        legacy_memory = project_path / ".moai" / "memory"
+        legacy_error_logs = project_path / ".moai" / "error_logs"
+        legacy_reports = project_path / ".moai" / "reports"
+
+        # Create new unified directory structure
+        new_logs_dir = project_path / ".moai" / "logs"
+        new_docs_dir = project_path / ".moai" / "docs"
+        new_sessions_dir = new_logs_dir / "sessions"
+        new_errors_dir = new_logs_dir / "errors"
+        new_archive_dir = new_logs_dir / "archive"
+        new_docs_reports_dir = new_docs_dir / "reports"
+
+        migration_log = []
+        files_migrated = 0
+        files_skipped = 0
+
+        # Check if any legacy directories exist
+        has_legacy_files = legacy_memory.exists() or legacy_error_logs.exists() or legacy_reports.exists()
+
+        if not has_legacy_files:
+            if not dry_run:
+                # Create new directory structure anyway for consistency
+                new_logs_dir.mkdir(parents=True, exist_ok=True)
+                new_docs_dir.mkdir(parents=True, exist_ok=True)
+                new_sessions_dir.mkdir(parents=True, exist_ok=True)
+                new_errors_dir.mkdir(parents=True, exist_ok=True)
+                new_archive_dir.mkdir(parents=True, exist_ok=True)
+                new_docs_reports_dir.mkdir(parents=True, exist_ok=True)
+            return True
+
+        if dry_run:
+            console.print("[cyan]🔍 Legacy log migration (dry run):[/cyan]")
+
+        # Create new directories if not dry run
+        if not dry_run:
+            new_logs_dir.mkdir(parents=True, exist_ok=True)
+            new_docs_dir.mkdir(parents=True, exist_ok=True)
+            new_sessions_dir.mkdir(parents=True, exist_ok=True)
+            new_errors_dir.mkdir(parents=True, exist_ok=True)
+            new_archive_dir.mkdir(parents=True, exist_ok=True)
+            new_docs_reports_dir.mkdir(parents=True, exist_ok=True)
+
+        # Migration 1: .moai/memory/last-session-state.json → .moai/logs/sessions/
+        if legacy_memory.exists():
+            session_file = legacy_memory / "last-session-state.json"
+            if session_file.exists():
+                target_file = new_sessions_dir / "last-session-state.json"
+
+                if target_file.exists():
+                    files_skipped += 1
+                    migration_log.append(f"Skipped: {session_file.relative_to(project_path)} (target already exists)")
+                else:
+                    if not dry_run:
+                        shutil.copy2(session_file, target_file)
+                        # Preserve original timestamp
+                        shutil.copystat(session_file, target_file)
+                        src_path = session_file.relative_to(project_path)
+                        dst_path = target_file.relative_to(project_path)
+                        migration_log.append(f"Migrated: {src_path} → {dst_path}")
+                    else:
+                        src_path = session_file.relative_to(project_path)
+                        dst_path = target_file.relative_to(project_path)
+                        migration_log.append(f"Would migrate: {src_path} → {dst_path}")
+                    files_migrated += 1
+
+        # Migration 2: .moai/error_logs/ → .moai/logs/errors/
+        if legacy_error_logs.exists() and legacy_error_logs.is_dir():
+            for error_file in legacy_error_logs.rglob("*"):
+                if error_file.is_file():
+                    relative_path = error_file.relative_to(legacy_error_logs)
+                    target_file = new_errors_dir / relative_path
+
+                    # Ensure target directory exists
+                    if not dry_run:
+                        target_file.parent.mkdir(parents=True, exist_ok=True)
+
+                    if target_file.exists():
+                        files_skipped += 1
+                        error_path = error_file.relative_to(project_path)
+                        migration_log.append(f"Skipped: {error_path} (target already exists)")
+                    else:
+                        if not dry_run:
+                            shutil.copy2(error_file, target_file)
+                            shutil.copystat(error_file, target_file)
+                            error_path = error_file.relative_to(project_path)
+                            target_path = target_file.relative_to(project_path)
+                            migration_log.append(f"Migrated: {error_path} → {target_path}")
+                        else:
+                            error_path = error_file.relative_to(project_path)
+                            target_path = target_file.relative_to(project_path)
+                            migration_log.append(f"Would migrate: {error_path} → {target_path}")
+                        files_migrated += 1
+
+        # Migration 3: .moai/reports/ → .moai/docs/reports/
+        if legacy_reports.exists() and legacy_reports.is_dir():
+            for report_file in legacy_reports.rglob("*"):
+                if report_file.is_file():
+                    relative_path = report_file.relative_to(legacy_reports)
+                    target_file = new_docs_reports_dir / relative_path
+
+                    # Ensure target directory exists
+                    if not dry_run:
+                        target_file.parent.mkdir(parents=True, exist_ok=True)
+
+                    if target_file.exists():
+                        files_skipped += 1
+                        report_path = report_file.relative_to(project_path)
+                        migration_log.append(f"Skipped: {report_path} (target already exists)")
+                    else:
+                        if not dry_run:
+                            shutil.copy2(report_file, target_file)
+                            shutil.copystat(report_file, target_file)
+                            report_path = report_file.relative_to(project_path)
+                            target_path = target_file.relative_to(project_path)
+                            migration_log.append(f"Migrated: {report_path} → {target_path}")
+                        else:
+                            report_path = report_file.relative_to(project_path)
+                            target_path = target_file.relative_to(project_path)
+                            migration_log.append(f"Would migrate: {report_path} → {target_path}")
+                        files_migrated += 1
+
+        # Create migration log
+        migration_log_path = new_logs_dir / "migration-log.json"
+        if not dry_run and files_migrated > 0:
+            migration_data = {
+                "migration_timestamp": datetime.now().isoformat(),
+                "moai_adk_version": __version__,
+                "files_migrated": files_migrated,
+                "files_skipped": files_skipped,
+                "migration_log": migration_log,
+                "legacy_directories_found": [
+                    str(d.relative_to(project_path))
+                    for d in [legacy_memory, legacy_error_logs, legacy_reports]
+                    if d.exists()
+                ],
+            }
+            json_content = json.dumps(migration_data, indent=2, ensure_ascii=False)
+            migration_log_path.write_text(json_content + "\n", encoding="utf-8")
+
+        # Display results
+        if files_migrated > 0 or files_skipped > 0:
+            if dry_run:
+                console.print(f"   [yellow]Would migrate {files_migrated} files, skip {files_skipped} files[/yellow]")
+            else:
+                console.print(f"   [green]✓ Migrated {files_migrated} legacy log files[/green]")
+                if files_skipped > 0:
+                    console.print(f"   [yellow]⚠ Skipped {files_skipped} files (already exist)[/yellow]")
+                console.print(f"   [dim]   Migration log: {migration_log_path.relative_to(project_path)}[/dim]")
+        elif has_legacy_files:
+            console.print("   [dim]   No files to migrate[/dim]")
+
+        return True
+
+    except Exception as e:
+        console.print(f"   [red]✗ Log migration failed: {e}[/red]")
+        logger.error(f"Legacy log migration failed: {e}", exc_info=True)
+        return False
+
+
+def _detect_stale_cache(upgrade_output: str, current_version: str, latest_version: str) -> bool:
+    """
+    Detect if uv cache is stale by comparing versions.
+
+    A stale cache occurs when PyPI metadata is outdated, causing uv to incorrectly
+    report "Nothing to upgrade" even though a newer version exists. This function
+    detects this condition by:
+    1. Checking if upgrade output contains "Nothing to upgrade"
+    2. Verifying that latest version is actually newer than current version
+
+    Uses packaging.version.parse() for robust semantic version comparison that
+    handles pre-releases, dev versions, and other PEP 440 version formats correctly.
+
+    Args:
+        upgrade_output: Output from uv tool upgrade command
+        current_version: Currently installed version (string, e.g., "0.8.3")
+        latest_version: Latest version available on PyPI (string, e.g., "0.9.0")
+
+    Returns:
+        True if cache is stale (output shows "Nothing to upgrade" but current < latest),
+        False otherwise
+
+    Examples:
+        >>> _detect_stale_cache("Nothing to upgrade", "0.8.3", "0.9.0")
+        True
+        >>> _detect_stale_cache("Updated moai-adk", "0.8.3", "0.9.0")
+        False
+        >>> _detect_stale_cache("Nothing to upgrade", "0.9.0", "0.9.0")
+        False
+    """
+    # Check if output indicates no upgrade needed
+    if not upgrade_output or "Nothing to upgrade" not in upgrade_output:
+        return False
+
+    # Compare versions using packaging.version
+    try:
+        current_v = version.parse(current_version)
+        latest_v = version.parse(latest_version)
+        return current_v < latest_v
+    except (version.InvalidVersion, TypeError) as e:
+        # Graceful degradation: if version parsing fails, assume cache is not stale
+        logger.debug(f"Version parsing failed: {e}")
+        return False
+
+
+def _clear_uv_package_cache(package_name: str = "moai-adk") -> bool:
+    """
+    Clear uv cache for specific package.
+
+    Executes `uv cache clean <package>` with 10-second timeout to prevent
+    hanging on network issues. Provides user-friendly error handling for
+    various failure scenarios (timeout, missing uv, etc.).
+
+    Args:
+        package_name: Package name to clear cache for (default: "moai-adk")
+
+    Returns:
+        True if cache cleared successfully, False otherwise
+
+    Exceptions:
+        - subprocess.TimeoutExpired: Logged as warning, returns False
+        - FileNotFoundError: Logged as warning, returns False
+        - Exception: Logged as warning, returns False
+
+    Examples:
+        >>> _clear_uv_package_cache("moai-adk")
+        True  # If uv cache clean succeeds
+    """
+    try:
+        result = subprocess.run(
+            ["uv", "cache", "clean", package_name],
+            capture_output=True,
+            text=True,
+            timeout=10,  # 10 second timeout
+            check=False,
+        )
+
+        if result.returncode == 0:
+            logger.debug(f"UV cache cleared for {package_name}")
+            return True
+        else:
+            logger.warning(f"Failed to clear UV cache: {result.stderr}")
+            return False
+
+    except subprocess.TimeoutExpired:
+        logger.warning(f"UV cache clean timed out for {package_name}")
+        return False
+    except FileNotFoundError:
+        logger.warning("UV command not found. Is uv installed?")
+        return False
+    except Exception as e:
+        logger.warning(f"Unexpected error clearing cache: {e}")
+        return False
+
+
+def _execute_upgrade_with_retry(installer_cmd: list[str], package_name: str = "moai-adk") -> bool:
+    """
+    Execute upgrade with automatic cache retry on stale detection.
+
+    Implements a robust 7-stage upgrade flow that handles PyPI cache staleness:
+
+    Stage 1: First upgrade attempt (up to 60 seconds)
+    Stage 2: Check success condition (returncode=0 AND no "Nothing to upgrade")
+    Stage 3: Detect stale cache using _detect_stale_cache()
+    Stage 4: Show user feedback if stale cache detected
+    Stage 5: Clear cache using _clear_uv_package_cache()
+    Stage 6: Retry upgrade with same command
+    Stage 7: Return final result (success or failure)
+
+    Retry Logic:
+    - Only ONE retry is performed to prevent infinite loops
+    - Retry only happens if stale cache is detected AND cache clear succeeds
+    - Cache clear failures are reported to user with manual workaround
+
+    User Feedback:
+    - Shows emoji-based status messages for each stage
+    - Clear guidance on manual workaround if automatic retry fails
+    - All errors logged at WARNING level for debugging
+
+    Args:
+        installer_cmd: Command list from _detect_tool_installer()
+                      e.g., ["uv", "tool", "upgrade", "moai-adk"]
+        package_name: Package name for cache clearing (default: "moai-adk")
+
+    Returns:
+        True if upgrade succeeded (either first attempt or after retry),
+        False otherwise
+
+    Examples:
+        >>> # First attempt succeeds
+        >>> _execute_upgrade_with_retry(["uv", "tool", "upgrade", "moai-adk"])
+        True
+
+        >>> # First attempt stale, retry succeeds
+        >>> _execute_upgrade_with_retry(["uv", "tool", "upgrade", "moai-adk"])
+        True  # After cache clear and retry
+
+    Raises:
+        subprocess.TimeoutExpired: Re-raised if upgrade command times out
+    """
+    # Stage 1: First upgrade attempt
+    try:
+        result = subprocess.run(installer_cmd, capture_output=True, text=True, timeout=60, check=False)
+    except subprocess.TimeoutExpired:
+        raise  # Re-raise timeout for caller to handle
+    except Exception:
+        return False
+
+    # Stage 2: Check if upgrade succeeded without stale cache
+    if result.returncode == 0 and "Nothing to upgrade" not in result.stdout:
+        return True
+
+    # Stage 3: Detect stale cache
+    try:
+        current_version = _get_current_version()
+        latest_version = _get_latest_version()
+    except RuntimeError:
+        # If version check fails, return original result
+        return result.returncode == 0
+
+    if _detect_stale_cache(result.stdout, current_version, latest_version):
+        # Stage 4: User feedback
+        console.print("[yellow]⚠️ Cache outdated, refreshing...[/yellow]")
+
+        # Stage 5: Clear cache
+        if _clear_uv_package_cache(package_name):
+            console.print("[cyan]♻️ Cache cleared, retrying upgrade...[/cyan]")
+
+            # Stage 6: Retry upgrade
+            try:
+                result = subprocess.run(
+                    installer_cmd,
+                    capture_output=True,
+                    text=True,
+                    timeout=60,
+                    check=False,
+                )
+
+                if result.returncode == 0:
+                    return True
+                else:
+                    console.print("[red]✗ Upgrade failed after retry[/red]")
+                    return False
+            except subprocess.TimeoutExpired:
+                raise  # Re-raise timeout
+            except Exception:
+                return False
+        else:
+            # Cache clear failed
+            console.print("[red]✗ Cache clear failed. Manual workaround:[/red]")
+            console.print("  [cyan]uv cache clean moai-adk && moai-adk update[/cyan]")
+            return False
+
+    # Stage 7: Cache is not stale, return original result
+    return result.returncode == 0
+
+
+def _execute_upgrade(installer_cmd: list[str]) -> bool:
+    """Execute package upgrade using detected installer.
+
+    Args:
+        installer_cmd: Command list from _detect_tool_installer()
+                      e.g., ["uv", "tool", "upgrade", "moai-adk"]
+
+    Returns:
+        True if upgrade succeeded, False otherwise
+
+    Raises:
+        subprocess.TimeoutExpired: If upgrade times out
+    """
+    try:
+        result = subprocess.run(installer_cmd, capture_output=True, text=True, timeout=60, check=False)
+        return result.returncode == 0
+    except subprocess.TimeoutExpired:
+        raise  # Re-raise timeout for caller to handle
+    except Exception:
+        return False
+
+
+def _preserve_user_settings(project_path: Path) -> dict[str, Path | None]:
+    """Back up user-specific settings files before template sync.
+
+    Args:
+        project_path: Project directory path
+
+    Returns:
+        Dictionary with backup paths of preserved files
+    """
+    preserved = {}
+    claude_dir = project_path / ".claude"
+
+    # Preserve settings.local.json (user MCP and GLM configuration)
+    settings_local = claude_dir / "settings.local.json"
+    if settings_local.exists():
+        try:
+            backup_dir = project_path / ".moai-backups" / "settings-backup"
+            backup_dir.mkdir(parents=True, exist_ok=True)
+            backup_path = backup_dir / "settings.local.json"
+            backup_path.write_text(settings_local.read_text(encoding="utf-8"))
+            preserved["settings.local.json"] = backup_path
+            console.print("   [cyan]💾 Backed up user settings[/cyan]")
+        except Exception as e:
+            logger.warning(f"Failed to backup settings.local.json: {e}")
+            preserved["settings.local.json"] = None
+    else:
+        preserved["settings.local.json"] = None
+
+    return preserved
+
+
+def _restore_user_settings(project_path: Path, preserved: dict[str, Path | None]) -> bool:
+    """Restore user-specific settings files after template sync.
+
+    Args:
+        project_path: Project directory path
+        preserved: Dictionary of backup paths from _preserve_user_settings()
+
+    Returns:
+        True if restoration succeeded, False otherwise
+    """
+    claude_dir = project_path / ".claude"
+    claude_dir.mkdir(parents=True, exist_ok=True)
+
+    success = True
+
+    # Restore settings.local.json
+    if preserved.get("settings.local.json"):
+        try:
+            backup_path = preserved["settings.local.json"]
+            settings_local = claude_dir / "settings.local.json"
+            settings_local.write_text(backup_path.read_text(encoding="utf-8"))
+            console.print("   [cyan]✓ Restored user settings[/cyan]")
+        except Exception as e:
+            console.print(f"   [yellow]⚠️ Failed to restore settings.local.json: {e}[/yellow]")
+            logger.warning(f"Failed to restore settings.local.json: {e}")
+            success = False
+
+    return success
+
+
+def _get_template_skill_names() -> set[str]:
+    """Get set of skill folder names from installed template.
+
+    Returns:
+        Set of skill folder names that are part of the template package.
+    """
+    template_path = Path(__file__).parent.parent.parent / "templates"
+    skills_path = template_path / ".claude" / "skills"
+
+    if not skills_path.exists():
+        return set()
+
+    return {d.name for d in skills_path.iterdir() if d.is_dir()}
+
+
+def _get_template_command_names() -> set[str]:
+    """Get set of command file names from installed template.
+
+    Returns:
+        Set of .md command file names from .claude/commands/moai/ in template.
+    """
+    template_path = Path(__file__).parent.parent.parent / "templates"
+    commands_path = template_path / ".claude" / "commands" / "moai"
+
+    if not commands_path.exists():
+        return set()
+
+    return {f.name for f in commands_path.iterdir() if f.is_file() and f.suffix == ".md"}
+
+
+def _get_template_agent_names() -> set[str]:
+    """Get set of agent file names from installed template.
+
+    Returns:
+        Set of agent file names from .claude/agents/ in template.
+    """
+    template_path = Path(__file__).parent.parent.parent / "templates"
+    agents_path = template_path / ".claude" / "agents"
+
+    if not agents_path.exists():
+        return set()
+
+    return {f.name for f in agents_path.iterdir() if f.is_file()}
+
+
+def _get_template_hook_names() -> set[str]:
+    """Get set of hook file names from installed template.
+
+    Returns:
+        Set of .py hook file names from .claude/hooks/moai/ in template.
+    """
+    template_path = Path(__file__).parent.parent.parent / "templates"
+    hooks_path = template_path / ".claude" / "hooks" / "moai"
+
+    if not hooks_path.exists():
+        return set()
+
+    return {f.name for f in hooks_path.iterdir() if f.is_file() and f.suffix == ".py"}
+
+
+def _detect_custom_commands(project_path: Path, template_commands: set[str]) -> list[str]:
+    """Detect custom commands NOT in template (user-created).
+
+    Args:
+        project_path: Project path (absolute)
+        template_commands: Set of template command file names
+
+    Returns:
+        Sorted list of custom command file names.
+    """
+    commands_path = project_path / ".claude" / "commands" / "moai"
+
+    if not commands_path.exists():
+        return []
+
+    project_commands = {f.name for f in commands_path.iterdir() if f.is_file() and f.suffix == ".md"}
+    custom_commands = project_commands - template_commands
+
+    return sorted(custom_commands)
+
+
+def _detect_custom_agents(project_path: Path, template_agents: set[str]) -> list[str]:
+    """Detect custom agents NOT in template (user-created).
+
+    Args:
+        project_path: Project path (absolute)
+        template_agents: Set of template agent file names
+
+    Returns:
+        Sorted list of custom agent file names.
+    """
+    agents_path = project_path / ".claude" / "agents"
+
+    if not agents_path.exists():
+        return []
+
+    project_agents = {f.name for f in agents_path.iterdir() if f.is_file()}
+    custom_agents = project_agents - template_agents
+
+    return sorted(custom_agents)
+
+
+def _detect_custom_hooks(project_path: Path, template_hooks: set[str]) -> list[str]:
+    """Detect custom hooks NOT in template (user-created).
+
+    Args:
+        project_path: Project path (absolute)
+        template_hooks: Set of template hook file names
+
+    Returns:
+        Sorted list of custom hook file names.
+    """
+    hooks_path = project_path / ".claude" / "hooks" / "moai"
+
+    if not hooks_path.exists():
+        return []
+
+    project_hooks = {f.name for f in hooks_path.iterdir() if f.is_file() and f.suffix == ".py"}
+    custom_hooks = project_hooks - template_hooks
+
+    return sorted(custom_hooks)
+
+
+def _group_custom_files_by_type(
+    custom_commands: list[str],
+    custom_agents: list[str],
+    custom_hooks: list[str],
+) -> dict[str, list[str]]:
+    """Group custom files by type for UI display.
+
+    Args:
+        custom_commands: List of custom command file names
+        custom_agents: List of custom agent file names
+        custom_hooks: List of custom hook file names
+
+    Returns:
+        Dictionary with keys: commands, agents, hooks
+    """
+    return {
+        "commands": custom_commands,
+        "agents": custom_agents,
+        "hooks": custom_hooks,
+    }
+
+
+def _prompt_custom_files_restore(
+    custom_commands: list[str],
+    custom_agents: list[str],
+    custom_hooks: list[str],
+    yes: bool = False,
+) -> dict[str, list[str]]:
+    """Interactive fuzzy checkbox for custom files restore with search support.
+
+    Args:
+        custom_commands: List of custom command file names
+        custom_agents: List of custom agent file names
+        custom_hooks: List of custom hook file names
+        yes: Auto-confirm flag (skips restoration in CI/CD mode)
+
+    Returns:
+        Dictionary with selected files grouped by type.
+    """
+    # If no custom files, skip UI
+    if not (custom_commands or custom_agents or custom_hooks):
+        return {
+            "commands": [],
+            "agents": [],
+            "hooks": [],
+        }
+
+    # In --yes mode, skip restoration (safest default)
+    if yes:
+        console.print("\n[dim]   Skipping custom files restoration (--yes mode)[/dim]\n")
+        return {
+            "commands": [],
+            "agents": [],
+            "hooks": [],
+        }
+
+    # Try to use new UI, fallback to questionary if import fails
+    try:
+        from moai_adk.cli.ui.prompts import create_grouped_choices, fuzzy_checkbox
+
+        # Build grouped choices for fuzzy checkbox
+        groups: dict[str, list[dict[str, str]]] = {}
+
+        if custom_commands:
+            groups["Commands (.claude/commands/moai/)"] = [
+                {"name": cmd, "value": f"cmd:{cmd}"} for cmd in custom_commands
+            ]
+
+        if custom_agents:
+            groups["Agents (.claude/agents/)"] = [{"name": agent, "value": f"agent:{agent}"} for agent in custom_agents]
+
+        if custom_hooks:
+            groups["Hooks (.claude/hooks/moai/)"] = [{"name": hook, "value": f"hook:{hook}"} for hook in custom_hooks]
+
+        choices = create_grouped_choices(groups)
+
+        console.print("\n[#DA7756]📦 Custom files detected in backup:[/#DA7756]")
+        console.print("[dim]   Use fuzzy search to find files quickly[/dim]\n")
+
+        selected = fuzzy_checkbox(
+            "Select custom files to restore:",
+            choices=choices,
+            instruction="[Space] Toggle  [Tab] All  [Enter] Confirm  [Type to search]",
+        )
+
+    except ImportError:
+        # Fallback to questionary if new UI not available
+        import questionary
+        from questionary import Choice, Separator
+
+        choices_legacy: list[Union[Separator, Choice]] = []
+
+        if custom_commands:
+            choices_legacy.append(Separator("Commands (.claude/commands/moai/)"))
+            for cmd in custom_commands:
+                choices_legacy.append(Choice(title=cmd, value=f"cmd:{cmd}"))
+
+        if custom_agents:
+            choices_legacy.append(Separator("Agents (.claude/agents/)"))
+            for agent in custom_agents:
+                choices_legacy.append(Choice(title=agent, value=f"agent:{agent}"))
+
+        if custom_hooks:
+            choices_legacy.append(Separator("Hooks (.claude/hooks/moai/)"))
+            for hook in custom_hooks:
+                choices_legacy.append(Choice(title=hook, value=f"hook:{hook}"))
+
+        console.print("\n[cyan]📦 Custom files detected in backup:[/cyan]")
+        console.print("[dim]   Select files to restore (none selected by default)[/dim]\n")
+
+        selected = questionary.checkbox(
+            "Select custom files to restore:",
+            choices=choices_legacy,
+        ).ask()
+
+    # Parse results
+    result_commands = []
+    result_agents = []
+    result_hooks = []
+
+    if selected:
+        for item in selected:
+            if item.startswith("cmd:"):
+                result_commands.append(item[4:])
+            elif item.startswith("agent:"):
+                result_agents.append(item[6:])
+            elif item.startswith("hook:"):
+                result_hooks.append(item[5:])
+
+    return {
+        "commands": result_commands,
+        "agents": result_agents,
+        "hooks": result_hooks,
+    }
+
+
+def _restore_custom_files(
+    project_path: Path,
+    backup_path: Path,
+    selected_commands: list[str],
+    selected_agents: list[str],
+    selected_hooks: list[str],
+) -> bool:
+    """Restore selected custom files from backup to project.
+
+    Args:
+        project_path: Project directory path
+        backup_path: Backup directory path
+        selected_commands: List of command files to restore
+        selected_agents: List of agent files to restore
+        selected_hooks: List of hook files to restore
+
+    Returns:
+        True if all restorations succeeded, False otherwise.
+    """
+    import shutil
+
+    success = True
+
+    # Restore commands
+    if selected_commands:
+        commands_dst = project_path / ".claude" / "commands" / "moai"
+        commands_dst.mkdir(parents=True, exist_ok=True)
+
+        for cmd_file in selected_commands:
+            src = backup_path / ".claude" / "commands" / "moai" / cmd_file
+            dst = commands_dst / cmd_file
+
+            if src.exists():
+                try:
+                    shutil.copy2(src, dst)
+                except Exception as e:
+                    logger.warning(f"Failed to restore command {cmd_file}: {e}")
+                    success = False
+            else:
+                logger.warning(f"Command file not in backup: {cmd_file}")
+                success = False
+
+    # Restore agents
+    if selected_agents:
+        agents_dst = project_path / ".claude" / "agents"
+        agents_dst.mkdir(parents=True, exist_ok=True)
+
+        for agent_file in selected_agents:
+            src = backup_path / ".claude" / "agents" / agent_file
+            dst = agents_dst / agent_file
+
+            if src.exists():
+                try:
+                    shutil.copy2(src, dst)
+                except Exception as e:
+                    logger.warning(f"Failed to restore agent {agent_file}: {e}")
+                    success = False
+            else:
+                logger.warning(f"Agent file not in backup: {agent_file}")
+                success = False
+
+    # Restore hooks
+    if selected_hooks:
+        hooks_dst = project_path / ".claude" / "hooks" / "moai"
+        hooks_dst.mkdir(parents=True, exist_ok=True)
+
+        for hook_file in selected_hooks:
+            src = backup_path / ".claude" / "hooks" / "moai" / hook_file
+            dst = hooks_dst / hook_file
+
+            if src.exists():
+                try:
+                    shutil.copy2(src, dst)
+                except Exception as e:
+                    logger.warning(f"Failed to restore hook {hook_file}: {e}")
+                    success = False
+            else:
+                logger.warning(f"Hook file not in backup: {hook_file}")
+                success = False
+
+    return success
+
+
+def _detect_custom_skills(project_path: Path, template_skills: set[str]) -> list[str]:
+    """Detect skills NOT in template (user-created).
 
     Args:
-        current: Current version string
-        latest: Latest version string
+        project_path: Project path (absolute)
+        template_skills: Set of template skill names
 
     Returns:
-        -1 if current < latest (upgrade needed)
-        0 if current == latest (up to date)
-        1 if current > latest (unusual, already newer)
+        Sorted list of custom skill names.
     """
-    current_v = version.parse(current)
-    latest_v = version.parse(latest)
+    skills_path = project_path / ".claude" / "skills"
 
-    if current_v < latest_v:
-        return -1
-    elif current_v == latest_v:
-        return 0
-    else:
-        return 1
+    if not skills_path.exists():
+        return []
 
+    project_skills = {d.name for d in skills_path.iterdir() if d.is_dir()}
+    custom_skills = project_skills - template_skills
 
-# @CODE:UPDATE-REFACTOR-002-006
-def _get_package_config_version() -> str:
-    """Get the current package template version.
+    return sorted(custom_skills)
 
-    This returns the version of the currently installed moai-adk package,
-    which is the version of templates that this package provides.
+
+def _prompt_skill_restore(custom_skills: list[str], yes: bool = False) -> list[str]:
+    """Interactive fuzzy checkbox for skill restore with search support.
+
+    Args:
+        custom_skills: List of custom skill names
+        yes: Auto-confirm flag (skips restoration in CI/CD mode)
 
     Returns:
-        Version string of the installed package (e.g., "0.6.1")
+        List of skills user selected to restore.
     """
-    # Package template version = current installed package version
-    # This is simple and reliable since templates are versioned with the package
-    return __version__
+    if not custom_skills:
+        return []
 
+    console.print("\n[#DA7756]📦 Custom skills detected in backup:[/#DA7756]")
+    for skill in custom_skills:
+        console.print(f"   • {skill}")
+    console.print()
 
-# @CODE:UPDATE-REFACTOR-002-007
-def _get_project_config_version(project_path: Path) -> str:
-    """Get current project config.json template version.
+    if yes:
+        console.print("[dim]   Skipping restoration (--yes mode)[/dim]\n")
+        return []
+
+    # Try new UI, fallback to questionary
+    try:
+        from moai_adk.cli.ui.prompts import fuzzy_checkbox
+
+        choices = [{"name": skill, "value": skill} for skill in custom_skills]
+
+        selected = fuzzy_checkbox(
+            "Select skills to restore (type to search):",
+            choices=choices,
+            instruction="[Space] Toggle  [Tab] All  [Enter] Confirm  [Type to search]",
+        )
+
+    except ImportError:
+        import questionary
+
+        selected = questionary.checkbox(
+            "Select skills to restore (none selected by default):",
+            choices=[questionary.Choice(title=skill, checked=False) for skill in custom_skills],
+        ).ask()
+
+    return selected if selected else []
 
-    This reads the project's .moai/config.json to determine the current
-    template version that the project is configured with.
+
+def _restore_selected_skills(skills: list[str], backup_path: Path, project_path: Path) -> bool:
+    """Restore selected skills from backup.
 
     Args:
-        project_path: Project directory path (absolute)
+        skills: List of skill names to restore
+        backup_path: Backup directory path
+        project_path: Project path (absolute)
 
     Returns:
-        Version string from project's config.json (e.g., "0.6.1")
-        Returns "0.0.0" if template_version field not found (indicates no prior sync)
-
-    Raises:
-        ValueError: If config.json exists but cannot be parsed
+        True if all restorations succeeded.
     """
-    config_path = project_path / ".moai" / "config.json"
-
-    if not config_path.exists():
-        # No config yet, treat as version 0.0.0 (needs initial sync)
-        return "0.0.0"
+    import shutil
 
-    try:
-        config_data = json.loads(config_path.read_text(encoding="utf-8"))
-        # Check for template_version in project section
-        template_version = config_data.get("project", {}).get("template_version")
-        if template_version:
-            return template_version
+    if not skills:
+        return True
 
-        # Fallback to moai version if no template_version exists
-        moai_version = config_data.get("moai", {}).get("version")
-        if moai_version:
-            return moai_version
+    console.print("\n[cyan]📥 Restoring selected skills...[/cyan]")
+    skills_dst = project_path / ".claude" / "skills"
+    skills_dst.mkdir(parents=True, exist_ok=True)
 
-        # If neither exists, this is a new/old project
-        return "0.0.0"
-    except json.JSONDecodeError as e:
-        raise ValueError(f"Failed to parse project config.json: {e}") from e
+    success = True
+    for skill_name in skills:
+        src = backup_path / ".claude" / "skills" / skill_name
+        dst = skills_dst / skill_name
 
+        if src.exists():
+            try:
+                shutil.copytree(src, dst, dirs_exist_ok=True)
+                console.print(f"   [green]✓ Restored: {skill_name}[/green]")
+            except Exception as e:
+                console.print(f"   [red]✗ Failed: {skill_name} - {e}[/red]")
+                success = False
+        else:
+            console.print(f"   [yellow]⚠ Not in backup: {skill_name}[/yellow]")
+            success = False
 
-def _execute_upgrade(installer_cmd: list[str]) -> bool:
-    """Execute package upgrade using detected installer.
+    return success
 
-    Args:
-        installer_cmd: Command list from _detect_tool_installer()
-                      e.g., ["uv", "tool", "upgrade", "moai-adk"]
 
-    Returns:
-        True if upgrade succeeded, False otherwise
+def _show_post_update_guidance(backup_path: Path) -> None:
+    """Show post-update guidance for running /moai:0-project update.
 
-    Raises:
-        subprocess.TimeoutExpired: If upgrade times out
+    Args:
+        backup_path: Backup directory path for reference
     """
-    try:
-        result = subprocess.run(
-            installer_cmd,
-            capture_output=True,
-            text=True,
-            timeout=60,
-            check=False
-        )
-        return result.returncode == 0
-    except subprocess.TimeoutExpired:
-        raise  # Re-raise timeout for caller to handle
-    except Exception:
-        return False
+    console.print("\n" + "[cyan]" + "=" * 60 + "[/cyan]")
+    console.print("[green]✅ Update complete![/green]")
+    console.print("\n[yellow]📝 IMPORTANT - Next step:[/yellow]")
+    console.print("   Run [cyan]/moai:0-project update[/cyan] in Claude Code")
+    console.print("\n   This will:")
+    console.print("   • Merge your settings with new templates")
+    console.print("   • Validate configuration compatibility")
+    console.print("\n[dim]💡 Personal instructions should go in CLAUDE.local.md[/dim]")
+    console.print(f"[dim]📂 Backup location: {backup_path}[/dim]")
+    console.print("[cyan]" + "=" * 60 + "[/cyan]\n")
 
 
-def _sync_templates(project_path: Path, force: bool = False) -> bool:
-    """Sync templates to project.
+def _sync_templates(project_path: Path, force: bool = False, yes: bool = False) -> bool:
+    """Sync templates to project with rollback mechanism.
 
     Args:
         project_path: Project path (absolute)
         force: Force update without backup
+        yes: Auto-confirm flag (skips interactive prompts)
 
     Returns:
         True if sync succeeded, False otherwise
     """
+    from moai_adk.core.template.backup import TemplateBackup
+
+    backup_path = None
     try:
+        # NEW: Detect custom files and skills BEFORE backup/sync
+        template_skills = _get_template_skill_names()
+        _detect_custom_skills(project_path, template_skills)
+
+        # Detect custom commands, agents, and hooks
+        template_commands = _get_template_command_names()
+        _detect_custom_commands(project_path, template_commands)
+
+        template_agents = _get_template_agent_names()
+        _detect_custom_agents(project_path, template_agents)
+
+        template_hooks = _get_template_hook_names()
+        _detect_custom_hooks(project_path, template_hooks)
+
         processor = TemplateProcessor(project_path)
 
+        # Create pre-sync backup for rollback
+        if not force:
+            backup = TemplateBackup(project_path)
+            if backup.has_existing_files():
+                backup_path = backup.create_backup()
+                console.print(f"💾 Created backup: {backup_path.name}")
+
+                # Merge analysis using Claude Code headless mode
+                try:
+                    analyzer = MergeAnalyzer(project_path)
+                    # Template source path from installed package
+                    template_path = Path(__file__).parent.parent.parent / "templates"
+
+                    console.print("\n[cyan]🔍 Starting merge analysis (max 2 mins)...[/cyan]")
+                    console.print("[dim]   Analyzing intelligent merge with Claude Code.[/dim]")
+                    console.print("[dim]   Please wait...[/dim]\n")
+                    analysis = analyzer.analyze_merge(backup_path, template_path)
+
+                    # Ask user confirmation
+                    if not analyzer.ask_user_confirmation(analysis):
+                        console.print("[yellow]⚠️  User cancelled the update.[/yellow]")
+                        backup.restore_backup(backup_path)
+                        return False
+                except Exception as e:
+                    console.print(f"[yellow]⚠️  Merge analysis failed: {e}[/yellow]")
+                    console.print("[yellow]Proceeding with automatic merge.[/yellow]")
+
         # Load existing config
         existing_config = _load_existing_config(project_path)
 
@@ -347,9 +1528,37 @@ def _sync_templates(project_path: Path, force: bool = False) -> bool:
         if context:
             processor.set_context(context)
 
-        # Copy templates
+        # Copy templates (including moai folder)
         processor.copy_templates(backup=False, silent=True)
 
+        # Stage 1.5: Alfred → Moai migration (AFTER template sync)
+        # Execute migration after template copy (moai folders must exist first)
+        migrator = AlfredToMoaiMigrator(project_path)
+        if migrator.needs_migration():
+            console.print("\n[cyan]🔄 Migrating folder structure: Alfred → Moai[/cyan]")
+            try:
+                if not migrator.execute_migration(backup_path):
+                    console.print("[red]❌ Alfred → Moai migration failed[/red]")
+                    if backup_path:
+                        console.print("[yellow]🔄 Restoring from backup...[/yellow]")
+                        backup = TemplateBackup(project_path)
+                        backup.restore_backup(backup_path)
+                    return False
+            except Exception as e:
+                console.print(f"[red]❌ Error during migration: {e}[/red]")
+                if backup_path:
+                    backup = TemplateBackup(project_path)
+                    backup.restore_backup(backup_path)
+                return False
+
+        # Validate template substitution
+        validation_passed = _validate_template_substitution_with_rollback(project_path, backup_path)
+        if not validation_passed:
+            if backup_path:
+                console.print(f"[yellow]🔄 Rolling back to backup: {backup_path.name}[/yellow]")
+                backup.restore_backup(backup_path)
+            return False
+
         # Preserve metadata
         _preserve_project_metadata(project_path, context, existing_config, __version__)
         _apply_context_to_file(processor, project_path / "CLAUDE.md")
@@ -357,8 +1566,56 @@ def _sync_templates(project_path: Path, force: bool = False) -> bool:
         # Set optimized=false
         set_optimized_false(project_path)
 
+        # Update companyAnnouncements in settings.local.json
+        try:
+            import sys
+
+            utils_dir = (
+                Path(__file__).parent.parent.parent / "templates" / ".claude" / "hooks" / "moai" / "shared" / "utils"
+            )
+
+            if utils_dir.exists():
+                sys.path.insert(0, str(utils_dir))
+                try:
+                    from announcement_translator import auto_translate_and_update
+
+                    console.print("[cyan]Updating announcements...[/cyan]")
+                    auto_translate_and_update(project_path)
+                    console.print("[green]✓ Announcements updated[/green]")
+                except Exception as e:
+                    console.print(f"[yellow]⚠️  Announcement update failed: {e}[/yellow]")
+                finally:
+                    sys.path.remove(str(utils_dir))
+
+        except Exception as e:
+            console.print(f"[yellow]⚠️  Announcement module not available: {e}[/yellow]")
+
+        # NEW: Interactive custom element restore using new system
+        _handle_custom_element_restoration(project_path, backup_path, yes)
+
+        # NEW: Migrate legacy logs to unified structure
+        console.print("\n[cyan]📁 Migrating legacy log files...[/cyan]")
+        if not _migrate_legacy_logs(project_path):
+            console.print("[yellow]⚠️ Legacy log migration failed, but update continuing[/yellow]")
+
+        # Clean up legacy presets directory
+        _cleanup_legacy_presets(project_path)
+
+        # NEW: Show post-update guidance
+        if backup_path:
+            _show_post_update_guidance(backup_path)
+
         return True
-    except Exception:
+    except Exception as e:
+        console.print(f"[red]✗ Template sync failed: {e}[/red]")
+        if backup_path:
+            console.print(f"[yellow]🔄 Rolling back to backup: {backup_path.name}[/yellow]")
+            try:
+                backup = TemplateBackup(project_path)
+                backup.restore_backup(backup_path)
+                console.print("[green]✅ Rollback completed[/green]")
+            except Exception as rollback_error:
+                console.print(f"[red]✗ Rollback failed: {rollback_error}[/red]")
         return False
 
 
@@ -379,35 +1636,32 @@ def get_latest_version() -> str | None:
 
 
 def set_optimized_false(project_path: Path) -> None:
-    """Set config.json's optimized field to false.
+    """Set config's optimized field to false.
 
     Args:
         project_path: Project path (absolute).
     """
-    config_path = project_path / ".moai" / "config.json"
+    config_path, _ = _get_config_path(project_path)
     if not config_path.exists():
         return
 
     try:
-        config_data = json.loads(config_path.read_text(encoding="utf-8"))
+        config_data = _load_config(config_path)
         config_data.setdefault("project", {})["optimized"] = False
-        config_path.write_text(
-            json.dumps(config_data, indent=2, ensure_ascii=False) + "\n",
-            encoding="utf-8"
-        )
-    except (json.JSONDecodeError, KeyError):
-        # Ignore errors if config.json is invalid
+        _save_config(config_path, config_data)
+    except (json.JSONDecodeError, yaml.YAMLError, KeyError):
+        # Ignore errors if config is invalid
         pass
 
 
 def _load_existing_config(project_path: Path) -> dict[str, Any]:
-    """Load existing config.json if available."""
-    config_path = project_path / ".moai" / "config.json"
+    """Load existing config (YAML or JSON) if available."""
+    config_path, _ = _get_config_path(project_path)
     if config_path.exists():
         try:
-            return json.loads(config_path.read_text(encoding="utf-8"))
-        except json.JSONDecodeError:
-            console.print("[yellow]⚠ Existing config.json could not be parsed. Proceeding with defaults.[/yellow]")
+            return _load_config(config_path)
+        except (json.JSONDecodeError, yaml.YAMLError):
+            console.print("[yellow]⚠ Existing config could not be parsed. Proceeding with defaults.[/yellow]")
     return {}
 
 
@@ -445,6 +1699,8 @@ def _build_template_context(
     version_for_config: str,
 ) -> dict[str, str]:
     """Build substitution context for template files."""
+    import platform
+
     project_section = _extract_project_section(existing_config)
 
     project_name = _coalesce(
@@ -474,13 +1730,106 @@ def _build_template_context(
         default=datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
     )
 
+    # Detect OS for cross-platform Hook path configuration
+    hook_project_dir = "%CLAUDE_PROJECT_DIR%" if platform.system() == "Windows" else "$CLAUDE_PROJECT_DIR"
+
+    # Extract and resolve language configuration using centralized resolver
+    try:
+        from moai_adk.core.language_config_resolver import get_resolver
+
+        # Use language resolver to get complete configuration
+        resolver = get_resolver(str(project_path))
+        resolved_config = resolver.resolve_config()
+
+        # Extract language configuration with environment variable priority
+        language_config = {
+            "conversation_language": resolved_config.get("conversation_language", "en"),
+            "conversation_language_name": resolved_config.get("conversation_language_name", "English"),
+            "agent_prompt_language": resolved_config.get("agent_prompt_language", "en"),
+        }
+
+        # Extract user personalization
+        user_name = resolved_config.get("user_name", "")
+        personalized_greeting = resolver.get_personalized_greeting(resolved_config)
+        config_source = resolved_config.get("config_source", "config_file")
+
+    except ImportError:
+        # Fallback to basic language config extraction if resolver not available
+        language_config = existing_config.get("language", {})
+        if not isinstance(language_config, dict):
+            language_config = {}
+
+        user_name = existing_config.get("user", {}).get("name", "")
+        conv_lang = language_config.get("conversation_language")
+        personalized_greeting = f"{user_name}님" if user_name and conv_lang == "ko" else user_name
+        config_source = "config_file"
+
+    # Enhanced version formatting (matches TemplateProcessor.get_enhanced_version_context)
+    def format_short_version(v: str) -> str:
+        """Remove 'v' prefix if present."""
+        return v[1:] if v.startswith("v") else v
+
+    def format_display_version(v: str) -> str:
+        """Format display version with proper formatting."""
+        if v == "unknown":
+            return "MoAI-ADK unknown version"
+        elif v.startswith("v"):
+            return f"MoAI-ADK {v}"
+        else:
+            return f"MoAI-ADK v{v}"
+
+    def format_trimmed_version(v: str, max_length: int = 10) -> str:
+        """Format version with maximum length for UI displays."""
+        if v == "unknown":
+            return "unknown"
+        clean_version = v[1:] if v.startswith("v") else v
+        if len(clean_version) > max_length:
+            return clean_version[:max_length]
+        return clean_version
+
+    def format_semver_version(v: str) -> str:
+        """Format version as semantic version."""
+        if v == "unknown":
+            return "0.0.0"
+        clean_version = v[1:] if v.startswith("v") else v
+        import re
+
+        semver_match = re.match(r"^(\d+\.\d+\.\d+)", clean_version)
+        if semver_match:
+            return semver_match.group(1)
+        return "0.0.0"
+
     return {
         "MOAI_VERSION": version_for_config,
+        "MOAI_VERSION_SHORT": format_short_version(version_for_config),
+        "MOAI_VERSION_DISPLAY": format_display_version(version_for_config),
+        "MOAI_VERSION_TRIMMED": format_trimmed_version(version_for_config),
+        "MOAI_VERSION_SEMVER": format_semver_version(version_for_config),
+        "MOAI_VERSION_VALID": "true" if version_for_config != "unknown" else "false",
+        "MOAI_VERSION_SOURCE": "config_cached",
         "PROJECT_NAME": project_name,
         "PROJECT_MODE": project_mode,
         "PROJECT_DESCRIPTION": project_description,
         "PROJECT_VERSION": project_version,
         "CREATION_TIMESTAMP": created_at,
+        "PROJECT_DIR": hook_project_dir,
+        "CONVERSATION_LANGUAGE": language_config.get("conversation_language", "en"),
+        "CONVERSATION_LANGUAGE_NAME": language_config.get("conversation_language_name", "English"),
+        "AGENT_PROMPT_LANGUAGE": language_config.get("agent_prompt_language", "en"),
+        "GIT_COMMIT_MESSAGES_LANGUAGE": language_config.get("git_commit_messages", "en"),
+        "CODE_COMMENTS_LANGUAGE": language_config.get("code_comments", "en"),
+        "DOCUMENTATION_LANGUAGE": language_config.get(
+            "documentation", language_config.get("conversation_language", "en")
+        ),
+        "ERROR_MESSAGES_LANGUAGE": language_config.get(
+            "error_messages", language_config.get("conversation_language", "en")
+        ),
+        "USER_NAME": user_name,
+        "PERSONALIZED_GREETING": personalized_greeting,
+        "LANGUAGE_CONFIG_SOURCE": config_source,
+        "CODEBASE_LANGUAGE": project_section.get("language", "generic"),
+        "PROJECT_OWNER": project_section.get("author", "@user"),
+        "AUTHOR": project_section.get("author", "@user"),
     }
 
 
@@ -490,18 +1839,18 @@ def _preserve_project_metadata(
     existing_config: dict[str, Any],
     version_for_config: str,
 ) -> None:
-    """Restore project-specific metadata in the new config.json.
+    """Restore project-specific metadata in the new config (YAML or JSON).
 
     Also updates template_version to track which template version is synchronized.
     """
-    config_path = project_path / ".moai" / "config.json"
+    config_path, _ = _get_config_path(project_path)
     if not config_path.exists():
         return
 
     try:
-        config_data = json.loads(config_path.read_text(encoding="utf-8"))
-    except json.JSONDecodeError:
-        console.print("[red]✗ Failed to parse config.json after template copy[/red]")
+        config_data = _load_config(config_path)
+    except (json.JSONDecodeError, yaml.YAMLError):
+        console.print("[red]✗ Failed to parse config after template copy[/red]")
         return
 
     project_data = config_data.setdefault("project", {})
@@ -528,14 +1877,10 @@ def _preserve_project_metadata(
     config_data.setdefault("moai", {})
     config_data["moai"]["version"] = version_for_config
 
-    # @CODE:UPDATE-REFACTOR-002-008: Update template_version to track sync status
     # This allows Stage 2 to compare package vs project template versions
     project_data["template_version"] = version_for_config
 
-    config_path.write_text(
-        json.dumps(config_data, indent=2, ensure_ascii=False) + "\n",
-        encoding="utf-8"
-    )
+    _save_config(config_path, config_data)
 
 
 def _apply_context_to_file(processor: TemplateProcessor, target_path: Path) -> None:
@@ -557,7 +1902,88 @@ def _apply_context_to_file(processor: TemplateProcessor, target_path: Path) -> N
     target_path.write_text(substituted, encoding="utf-8")
 
 
-# @CODE:UPDATE-REFACTOR-002-003
+def _validate_template_substitution(project_path: Path) -> None:
+    """Validate that all template variables have been properly substituted."""
+    import re
+
+    # Files to check for unsubstituted variables
+    files_to_check = [
+        project_path / ".claude" / "settings.json",
+        project_path / "CLAUDE.md",
+    ]
+
+    issues_found = []
+
+    for file_path in files_to_check:
+        if not file_path.exists():
+            continue
+
+        try:
+            content = file_path.read_text(encoding="utf-8")
+            # Look for unsubstituted template variables
+            unsubstituted = re.findall(r"\{\{([A-Z_]+)\}\}", content)
+            if unsubstituted:
+                unique_vars = sorted(set(unsubstituted))
+                issues_found.append(f"{file_path.relative_to(project_path)}: {', '.join(unique_vars)}")
+        except Exception as e:
+            console.print(f"[yellow]⚠️ Could not validate {file_path.relative_to(project_path)}: {e}[/yellow]")
+
+    if issues_found:
+        console.print("[red]✗ Template substitution validation failed:[/red]")
+        for issue in issues_found:
+            console.print(f"   {issue}")
+        console.print("[yellow]💡 Run '/moai:0-project' to fix template variables[/yellow]")
+    else:
+        console.print("[green]✅ Template substitution validation passed[/green]")
+
+
+def _validate_template_substitution_with_rollback(project_path: Path, backup_path: Path | None) -> bool:
+    """Validate template substitution with rollback capability.
+
+    Returns:
+        True if validation passed, False if failed (rollback handled by caller)
+    """
+    import re
+
+    # Files to check for unsubstituted variables
+    files_to_check = [
+        project_path / ".claude" / "settings.json",
+        project_path / "CLAUDE.md",
+    ]
+
+    issues_found = []
+
+    for file_path in files_to_check:
+        if not file_path.exists():
+            continue
+
+        try:
+            content = file_path.read_text(encoding="utf-8")
+            # Look for unsubstituted template variables
+            unsubstituted = re.findall(r"\{\{([A-Z_]+)\}\}", content)
+            if unsubstituted:
+                unique_vars = sorted(set(unsubstituted))
+                issues_found.append(f"{file_path.relative_to(project_path)}: {', '.join(unique_vars)}")
+        except Exception as e:
+            console.print(f"[yellow]⚠️ Could not validate {file_path.relative_to(project_path)}: {e}[/yellow]")
+
+    if issues_found:
+        console.print("[red]✗ Template substitution validation failed:[/red]")
+        for issue in issues_found:
+            console.print(f"   {issue}")
+
+        if backup_path:
+            console.print("[yellow]🔄 Rolling back due to validation failure...[/yellow]")
+        else:
+            console.print("[yellow]💡 Run '/moai:0-project' to fix template variables[/yellow]")
+            console.print("[red]⚠️ No backup available - manual fix required[/red]")
+
+        return False
+    else:
+        console.print("[green]✅ Template substitution validation passed[/green]")
+        return True
+
+
 def _show_version_info(current: str, latest: str) -> None:
     """Display version information.
 
@@ -570,7 +1996,6 @@ def _show_version_info(current: str, latest: str) -> None:
     console.print(f"   Latest version:  {latest}")
 
 
-# @CODE:UPDATE-REFACTOR-002-005
 def _show_installer_not_found_help() -> None:
     """Show help when installer not found."""
     console.print("[red]❌ Cannot detect package installer[/red]\n")
@@ -624,35 +2049,94 @@ def _show_timeout_error_help() -> None:
     console.print("  [cyan]moai-adk update --yes --force[/cyan]")
 
 
+def _execute_migration_if_needed(project_path: Path, yes: bool = False) -> bool:
+    """Check and execute migration if needed.
+
+    Args:
+        project_path: Project directory path
+        yes: Auto-confirm without prompting
+
+    Returns:
+        True if no migration needed or migration succeeded, False if migration failed
+    """
+    try:
+        migrator = VersionMigrator(project_path)
+
+        # Check if migration is needed
+        if not migrator.needs_migration():
+            return True
+
+        # Get migration info
+        info = migrator.get_migration_info()
+        console.print("\n[cyan]🔄 Migration Required[/cyan]")
+        console.print(f"   Current version: {info['current_version']}")
+        console.print(f"   Target version:  {info['target_version']}")
+        console.print(f"   Files to migrate: {info['file_count']}")
+        console.print()
+        console.print("   This will migrate configuration files to new locations:")
+        console.print("   • .moai/config.json → .moai/config/config.json")
+        console.print("   • .claude/statusline-config.yaml → .moai/config/statusline-config.yaml")
+        console.print()
+        console.print("   A backup will be created automatically.")
+        console.print()
+
+        # Confirm with user (unless --yes)
+        if not yes:
+            if not click.confirm("Do you want to proceed with migration?", default=True):
+                console.print("[yellow]⚠️  Migration skipped. Some features may not work correctly.[/yellow]")
+                console.print("[cyan]💡 Run 'moai-adk migrate' manually when ready[/cyan]")
+                return False
+
+        # Execute migration
+        console.print("[cyan]🚀 Starting migration...[/cyan]")
+        success = migrator.migrate_to_v024(dry_run=False, cleanup=True)
+
+        if success:
+            console.print("[green]✅ Migration completed successfully![/green]")
+            return True
+        else:
+            console.print("[red]❌ Migration failed[/red]")
+            console.print("[cyan]💡 Use 'moai-adk migrate --rollback' to restore from backup[/cyan]")
+            return False
+
+    except Exception as e:
+        console.print(f"[red]❌ Migration error: {e}[/red]")
+        logger.error(f"Migration failed: {e}", exc_info=True)
+        return False
+
+
 @click.command()
 @click.option(
     "--path",
     type=click.Path(exists=True),
     default=".",
-    help="Project path (default: current directory)"
-)
-@click.option(
-    "--force",
-    is_flag=True,
-    help="Skip backup and force the update"
-)
-@click.option(
-    "--check",
-    is_flag=True,
-    help="Only check version (do not update)"
+    help="Project path (default: current directory)",
 )
+@click.option("--force", is_flag=True, help="Skip backup and force the update")
+@click.option("--check", is_flag=True, help="Only check version (do not update)")
+@click.option("--templates-only", is_flag=True, help="Skip package upgrade, sync templates only")
+@click.option("--yes", is_flag=True, help="Auto-confirm all prompts (CI/CD mode)")
 @click.option(
-    "--templates-only",
-    is_flag=True,
-    help="Skip package upgrade, sync templates only"
+    "--merge",
+    "merge_strategy",
+    flag_value="auto",
+    help="Auto-merge: Apply template + preserve user changes",
 )
 @click.option(
-    "--yes",
-    is_flag=True,
-    help="Auto-confirm all prompts (CI/CD mode)"
+    "--manual",
+    "merge_strategy",
+    flag_value="manual",
+    help="Manual merge: Preserve backup, generate merge guide",
 )
-def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool) -> None:
-    """Update command with 3-stage workflow (v0.6.3+).
+def update(
+    path: str,
+    force: bool,
+    check: bool,
+    templates_only: bool,
+    yes: bool,
+    merge_strategy: str | None,
+) -> None:
+    """Update command with 3-stage workflow + merge strategy selection (v0.26.0+).
 
     Stage 1 (Package Version Check):
     - Fetches current and latest versions from PyPI
@@ -664,18 +2148,34 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
     - If versions match: skips Stage 3 (already up-to-date)
     - Performance improvement: 70-80% faster for unchanged projects (3-4s vs 12-18s)
 
-    Stage 3 (Template Sync):
+    Stage 3 (Template Sync with Merge Strategy - NEW in v0.26.0):
     - Syncs templates only if versions differ
+    - User chooses merge strategy:
+      * Auto-merge (default): Template + preserved user changes
+      * Manual merge: Backup + comprehensive merge guide (full control)
     - Updates .claude/, .moai/, CLAUDE.md, config.json
     - Preserves specs and reports
     - Saves new template_version to config.json
 
     Examples:
-        python -m moai_adk update                    # auto 3-stage workflow
-        python -m moai_adk update --force            # force template sync
+        python -m moai_adk update                    # interactive merge strategy selection
+        python -m moai_adk update --merge            # auto-merge (template + user changes)
+        python -m moai_adk update --manual           # manual merge (backup + guide)
+        python -m moai_adk update --force            # force template sync (no backup)
         python -m moai_adk update --check            # check version only
         python -m moai_adk update --templates-only   # skip package upgrade
-        python -m moai_adk update --yes              # CI/CD mode (auto-confirm)
+        python -m moai_adk update --yes              # CI/CD mode (auto-confirm + auto-merge)
+
+    Merge Strategies:
+        --merge:  Auto-merge applies template + preserves your changes (default)
+                  Generated files: backup, merge report
+        --manual: Manual merge preserves backup + generates comprehensive guide
+                  Generated files: backup, merge guide
+
+    Generated Files:
+        - Backup: .moai-backups/pre-update-backup_{timestamp}/
+        - Report: .moai/reports/merge-report.md (auto-merge only)
+        - Guide:  .moai/guides/merge-guide.md (manual merge only)
     """
     try:
         project_path = Path(path).resolve()
@@ -689,8 +2189,20 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
         # Note: If --check is used, always fetch versions even if --templates-only is also present
         if check or not templates_only:
             try:
-                current = _get_current_version()
-                latest = _get_latest_version()
+                # Try to use new spinner UI
+                try:
+                    from moai_adk.cli.ui.progress import SpinnerContext
+
+                    with SpinnerContext("Checking for updates...") as spinner:
+                        current = _get_current_version()
+                        spinner.update("Fetching latest version from PyPI...")
+                        latest = _get_latest_version()
+                        spinner.success("Version check complete")
+                except ImportError:
+                    # Fallback to simple console output
+                    console.print("[dim]Checking for updates...[/dim]")
+                    current = _get_current_version()
+                    latest = _get_latest_version()
             except RuntimeError as e:
                 console.print(f"[red]Error: {e}[/red]")
                 if not force:
@@ -717,8 +2229,13 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
         # Step 2: Handle --templates-only (skip upgrade, go straight to sync)
         if templates_only:
             console.print("[cyan]📄 Syncing templates only...[/cyan]")
+
+            # Preserve user-specific settings before sync
+            console.print("   [cyan]💾 Preserving user settings...[/cyan]")
+            preserved_settings = _preserve_user_settings(project_path)
+
             try:
-                if not _sync_templates(project_path, force):
+                if not _sync_templates(project_path, force, yes):
                     raise TemplateSyncError("Template sync returned False")
             except TemplateSyncError:
                 console.print("[red]Error: Template sync failed[/red]")
@@ -729,6 +2246,9 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
                 _show_template_sync_failure_help()
                 raise click.Abort()
 
+            # Restore user-specific settings after sync
+            _restore_user_settings(project_path, preserved_settings)
+
             console.print("   [green]✅ .claude/ update complete[/green]")
             console.print("   [green]✅ .moai/ update complete (specs/reports preserved)[/green]")
             console.print("   [green]🔄 CLAUDE.md merge complete[/green]")
@@ -740,7 +2260,6 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
         comparison = _compare_versions(current, latest)
 
         # Stage 1: Package Upgrade (if current < latest)
-        # @CODE:UPDATE-REFACTOR-002-009: Stage 1 - Package version check and upgrade
         if comparison < 0:
             console.print(f"\n[cyan]📦 Upgrading: {current} → {latest}[/cyan]")
 
@@ -779,10 +2298,20 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
             console.print("[cyan]📢 Run 'moai-adk update' again to sync templates[/cyan]")
             return
 
-        # Stage 2: Config Version Comparison
-        # @CODE:UPDATE-REFACTOR-002-010: Stage 2 - Compare template versions to determine if sync needed
+        # Stage 1.5: Migration Check (NEW in v0.24.0)
         console.print(f"✓ Package already up to date ({current})")
 
+        # Execute migration if needed
+        if not _execute_migration_if_needed(project_path, yes):
+            console.print("[yellow]⚠️  Update continuing without migration[/yellow]")
+            console.print("[cyan]💡 Some features may require migration to work correctly[/cyan]")
+
+        # Migrate config.json → config.yaml (v0.32.0+)
+        console.print("\n[cyan]🔍 Checking for config format migration...[/cyan]")
+        if not _migrate_config_json_to_yaml(project_path):
+            console.print("[yellow]⚠️  Config migration failed, continuing with existing format[/yellow]")
+
+        # Stage 2: Config Version Comparison
         try:
             package_config_version = _get_package_config_version()
             project_config_version = _get_project_config_version(project_path)
@@ -796,7 +2325,14 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
         console.print(f"   Package template: {package_config_version}")
         console.print(f"   Project config:   {project_config_version}")
 
-        config_comparison = _compare_versions(package_config_version, project_config_version)
+        try:
+            config_comparison = _compare_versions(package_config_version, project_config_version)
+        except version.InvalidVersion as e:
+            # Handle invalid version strings (e.g., unsubstituted template placeholders, corrupted configs)
+            console.print(f"[yellow]⚠ Invalid version format in config: {e}[/yellow]")
+            console.print("[cyan]ℹ️  Forcing template sync to repair configuration...[/cyan]")
+            # Force template sync by treating project version as outdated
+            config_comparison = 1  # package_config_version > project_config_version
 
         # If versions are equal, no sync needed
         if config_comparison <= 0:
@@ -805,9 +2341,52 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
             return
 
         # Stage 3: Template Sync (Only if package_config_version > project_config_version)
-        # @CODE:UPDATE-REFACTOR-002-011: Stage 3 - Template sync only if versions differ
         console.print(f"\n[cyan]📄 Syncing templates ({project_config_version} → {package_config_version})...[/cyan]")
 
+        # Determine merge strategy (default: auto-merge)
+        final_merge_strategy = merge_strategy or "auto"
+
+        # Handle merge strategy
+        if final_merge_strategy == "manual":
+            # Manual merge mode: Create full backup + generate guide, no template sync
+            console.print("\n[cyan]🔀 Manual merge mode selected[/cyan]")
+
+            # Create full project backup
+            console.print("   [cyan]💾 Creating full project backup...[/cyan]")
+            try:
+                from moai_adk.core.migration.backup_manager import BackupManager
+
+                backup_manager = BackupManager(project_path)
+                full_backup_path = backup_manager.create_full_project_backup(description="pre-update-backup")
+                console.print(f"   [green]✓ Backup: {full_backup_path.relative_to(project_path)}/[/green]")
+
+                # Generate merge guide
+                console.print("   [cyan]📋 Generating merge guide...[/cyan]")
+                template_path = Path(__file__).parent.parent.parent / "templates"
+                guide_path = _generate_manual_merge_guide(full_backup_path, template_path, project_path)
+                console.print(f"   [green]✓ Guide: {guide_path.relative_to(project_path)}[/green]")
+
+                # Summary
+                console.print("\n[green]✓ Manual merge setup complete![/green]")
+                console.print(f"[cyan]📍 Backup location: {full_backup_path.relative_to(project_path)}/[/cyan]")
+                console.print(f"[cyan]📋 Merge guide: {guide_path.relative_to(project_path)}[/cyan]")
+                console.print("\n[yellow]⚠️  Next steps:[/yellow]")
+                console.print("[yellow]  1. Review the merge guide[/yellow]")
+                console.print("[yellow]  2. Compare files using diff or visual tools[/yellow]")
+                console.print("[yellow]  3. Manually merge your customizations[/yellow]")
+                console.print("[yellow]  4. Test and commit changes[/yellow]")
+
+            except Exception as e:
+                console.print(f"[red]Error: Manual merge setup failed - {e}[/red]")
+                raise click.Abort()
+
+            return
+
+        # Auto merge mode: Preserve user-specific settings before sync
+        console.print("\n[cyan]🔀 Auto-merge mode selected[/cyan]")
+        console.print("   [cyan]💾 Preserving user settings...[/cyan]")
+        preserved_settings = _preserve_user_settings(project_path)
+
         # Create backup unless --force
         if not force:
             console.print("   [cyan]💾 Creating backup...[/cyan]")
@@ -821,10 +2400,14 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
         else:
             console.print("   [yellow]⚠ Skipping backup (--force)[/yellow]")
 
-        # Sync templates
+        # Sync templates (NO spinner - user interaction may be required)
+        # SpinnerContext blocks stdin, causing hang when click.confirm() is called
         try:
-            if not _sync_templates(project_path, force):
+            console.print("   [cyan]Syncing templates...[/cyan]")
+            if not _sync_templates(project_path, force, yes):
                 raise TemplateSyncError("Template sync returned False")
+            _restore_user_settings(project_path, preserved_settings)
+            console.print("   [green]✓ Template sync complete[/green]")
         except TemplateSyncError:
             console.print("[red]Error: Template sync failed[/red]")
             _show_template_sync_failure_help()
@@ -841,8 +2424,254 @@ def update(path: str, force: bool, check: bool, templates_only: bool, yes: bool)
         console.print("   [yellow]⚙️  Set optimized=false (optimization needed)[/yellow]")
 
         console.print("\n[green]✓ Update complete![/green]")
-        console.print("[cyan]ℹ️  Next step: Run /alfred:0-project update to optimize template changes[/cyan]")
+        console.print("[cyan]ℹ️  Next step: Run /moai:0-project update to optimize template changes[/cyan]")
 
     except Exception as e:
         console.print(f"[red]✗ Update failed: {e}[/red]")
         raise click.ClickException(str(e)) from e
+
+
+def _handle_custom_element_restoration(project_path: Path, backup_path: Path | None, yes: bool = False) -> None:
+    """Handle custom element restoration using the enhanced system.
+
+    This function provides an improved interface for restoring user-created custom elements
+    (agents, commands, skills, hooks) from backup during MoAI-ADK updates.
+
+    Key improvements:
+    - Preserves unselected elements (fixes disappearing issue)
+    - Only overwrites/creates selected elements from backup
+    - Interactive checkbox selection with arrow key navigation
+    - Includes all categories (Agents, Commands, Skills, Hooks)
+
+    Args:
+        project_path: Path to the MoAI-ADK project directory
+        backup_path: Path to the backup directory (None if no backup)
+        yes: Whether to automatically accept defaults (non-interactive mode)
+    """
+    if not backup_path:
+        # No backup available, cannot restore
+        return
+
+    try:
+        # Create scanner to find custom elements in backup (not current project)
+        backup_scanner = create_custom_element_scanner(backup_path)
+
+        # Get count of custom elements in backup
+        backup_element_count = backup_scanner.get_element_count()
+
+        if backup_element_count == 0:
+            # No custom elements found in backup
+            console.print("[green]✓ No custom elements found in backup to restore[/green]")
+            return
+
+        # Create enhanced user selection UI
+        ui = create_user_selection_ui(project_path)
+
+        console.print(f"\n[cyan]🔍 Found {backup_element_count} custom elements in backup[/cyan]")
+
+        # If yes mode is enabled, restore all elements automatically
+        if yes:
+            console.print(f"[cyan]🔄 Auto-restoring {backup_element_count} custom elements...[/cyan]")
+            backup_custom_elements = backup_scanner.scan_custom_elements()
+            selected_elements = []
+
+            # Collect all element paths from backup
+            for element_type, elements in backup_custom_elements.items():
+                if element_type == "skills":
+                    for skill in elements:
+                        selected_elements.append(str(skill.path))
+                else:
+                    for element_path in elements:
+                        selected_elements.append(str(element_path))
+        else:
+            # Interactive mode - prompt user for selection using enhanced UI
+            selected_elements = ui.prompt_user_selection(backup_available=True)
+
+            if not selected_elements:
+                console.print("[yellow]⚠ No elements selected for restoration[/yellow]")
+                console.print("[green]✓ All existing custom elements will be preserved[/green]")
+                return
+
+            # Confirm selection
+            if not ui.confirm_selection(selected_elements):
+                console.print("[yellow]⚠ Restoration cancelled by user[/yellow]")
+                console.print("[green]✓ All existing custom elements will be preserved[/green]")
+                return
+
+        # Perform selective restoration - ONLY restore selected elements
+        if selected_elements:
+            console.print(f"[cyan]🔄 Restoring {len(selected_elements)} selected elements from backup...[/cyan]")
+            restorer = create_selective_restorer(project_path, backup_path)
+            success, stats = restorer.restore_elements(selected_elements)
+
+            if success:
+                console.print(f"[green]✅ Successfully restored {stats['success']} custom elements[/green]")
+                console.print("[green]✓ All unselected elements remain preserved[/green]")
+            else:
+                console.print(f"[yellow]⚠️ Partial restoration: {stats['success']}/{stats['total']} elements[/yellow]")
+                if stats["failed"] > 0:
+                    console.print(f"[red]❌ Failed to restore {stats['failed']} elements[/red]")
+                console.print("[yellow]⚠️ All other elements remain preserved[/yellow]")
+        else:
+            console.print("[green]✓ No elements selected, all custom elements preserved[/green]")
+
+    except Exception as e:
+        console.print(f"[yellow]⚠️ Custom element restoration failed: {e}[/yellow]")
+        logger.warning(f"Custom element restoration error: {e}")
+        console.print("[yellow]⚠️ All existing custom elements remain as-is[/yellow]")
+        # Don't fail the entire update process, just log the error
+        pass
+
+
+def _cleanup_legacy_presets(project_path: Path) -> None:
+    """Remove legacy presets directory entirely.
+
+    This function removes the entire .moai/config/presets/ directory as it is
+    no longer used. All preset settings are now consolidated in sections/git-strategy.yaml.
+
+    Args:
+        project_path: Project directory path (absolute)
+    """
+    import shutil
+
+    presets_dir = project_path / ".moai" / "config" / "presets"
+
+    if not presets_dir.exists() or not presets_dir.is_dir():
+        return
+
+    try:
+        # Remove entire presets directory (no longer needed)
+        shutil.rmtree(presets_dir)
+        console.print("   [cyan]🧹 Removed legacy presets directory (now in sections/git-strategy.yaml)[/cyan]")
+        logger.info(f"Removed legacy presets directory: {presets_dir}")
+    except Exception as e:
+        logger.warning(f"Failed to remove legacy presets directory {presets_dir}: {e}")
+
+
+def _migrate_config_json_to_yaml(project_path: Path) -> bool:
+    """Migrate legacy config.json to config.yaml format.
+
+    This function:
+    1. Checks if config.json exists
+    2. Converts it to config.yaml using YAML format
+    3. Removes the old config.json file
+    4. Also migrates preset files from JSON to YAML
+
+    Args:
+        project_path: Project directory path (absolute)
+
+    Returns:
+        bool: True if migration successful or not needed, False on error
+    """
+    try:
+        import yaml
+    except ImportError:
+        console.print("   [yellow]⚠️ PyYAML not available, skipping config migration[/yellow]")
+        return True  # Not a critical error
+
+    config_dir = project_path / ".moai" / "config"
+    json_path = config_dir / "config.json"
+    yaml_path = config_dir / "config.yaml"
+
+    # Check if migration needed
+    if not json_path.exists():
+        # No JSON file, migration not needed
+        return True
+
+    if yaml_path.exists():
+        # YAML already exists, just remove JSON
+        try:
+            json_path.unlink()
+            console.print("   [cyan]🔄 Removed legacy config.json (YAML version exists)[/cyan]")
+            logger.info(f"Removed legacy config.json: {json_path}")
+            return True
+        except Exception as e:
+            console.print(f"   [yellow]⚠️ Failed to remove legacy config.json: {e}[/yellow]")
+            logger.warning(f"Failed to remove {json_path}: {e}")
+            return True  # Not critical
+
+    # Perform migration
+    try:
+        # Read JSON config
+        with open(json_path, "r", encoding="utf-8") as f:
+            config_data = json.load(f)
+
+        # Write YAML config
+        with open(yaml_path, "w", encoding="utf-8") as f:
+            yaml.safe_dump(
+                config_data,
+                f,
+                default_flow_style=False,
+                allow_unicode=True,
+                sort_keys=False,
+            )
+
+        # Remove old JSON file
+        json_path.unlink()
+
+        console.print("   [green]✓ Migrated config.json → config.yaml[/green]")
+        logger.info(f"Migrated config from JSON to YAML: {json_path} → {yaml_path}")
+
+        # Migrate preset files if they exist
+        _migrate_preset_files_to_yaml(config_dir)
+
+        return True
+
+    except Exception as e:
+        console.print(f"   [red]✗ Config migration failed: {e}[/red]")
+        logger.error(f"Failed to migrate config.json to YAML: {e}")
+        return False
+
+
+def _migrate_preset_files_to_yaml(config_dir: Path) -> None:
+    """Migrate preset files from JSON to YAML format.
+
+    Args:
+        config_dir: .moai/config directory path
+    """
+    try:
+        import yaml
+    except ImportError:
+        return
+
+    presets_dir = config_dir / "presets"
+    if not presets_dir.exists():
+        return
+
+    migrated_count = 0
+    for json_file in presets_dir.glob("*.json"):
+        yaml_file = json_file.with_suffix(".yaml")
+
+        # Skip if YAML already exists
+        if yaml_file.exists():
+            # Just remove the JSON file
+            try:
+                json_file.unlink()
+                migrated_count += 1
+            except Exception as e:
+                logger.warning(f"Failed to remove {json_file}: {e}")
+            continue
+
+        # Migrate JSON → YAML
+        try:
+            with open(json_file, "r", encoding="utf-8") as f:
+                preset_data = json.load(f)
+
+            with open(yaml_file, "w", encoding="utf-8") as f:
+                yaml.safe_dump(
+                    preset_data,
+                    f,
+                    default_flow_style=False,
+                    allow_unicode=True,
+                    sort_keys=False,
+                )
+
+            json_file.unlink()
+            migrated_count += 1
+
+        except Exception as e:
+            logger.warning(f"Failed to migrate preset {json_file}: {e}")
+
+    if migrated_count > 0:
+        console.print(f"   [cyan]🔄 Migrated {migrated_count} preset file(s) to YAML[/cyan]")
+        logger.info(f"Migrated {migrated_count} preset files to YAML")