foundry-mcp 0.3.3__py3-none-any.whl → 0.8.10__py3-none-any.whl

foundry_mcp/core/spec.py

@@ -9,16 +9,59 @@ import shutil
 import subprocess
 from datetime import datetime, timezone
 from pathlib import Path
-from typing import Optional, Dict, Any, List, Tuple
+from typing import Optional, Dict, Any, List, Tuple, Union
 
 # Valid templates and categories for spec creation
-TEMPLATES = ("simple", "medium", "complex", "security")
+# Note: Only 'empty' template is supported. Use phase templates to add structure.
+TEMPLATES = ("empty",)
+TEMPLATE_DESCRIPTIONS = {
+    "empty": "Blank spec with no phases - use phase templates to add structure",
+}
 CATEGORIES = ("investigation", "implementation", "refactoring", "decision", "research")
 
 # Valid verification types for verify nodes
-# - test: Automated tests via mcp__foundry-mcp__test-run
+# - run-tests: Automated tests via mcp__foundry-mcp__test-run
 # - fidelity: Implementation-vs-spec comparison via mcp__foundry-mcp__spec-review-fidelity
-VERIFICATION_TYPES = ("test", "fidelity")
+# - manual: Manual verification steps
+VERIFICATION_TYPES = ("run-tests", "fidelity", "manual")
+
+# Valid phase templates for reusable phase structures
+PHASE_TEMPLATES = ("planning", "implementation", "testing", "security", "documentation")
+
+
+def _requires_rich_task_fields(spec_data: Dict[str, Any]) -> bool:
+    """Check if spec requires rich task fields based on explicit complexity metadata."""
+    metadata = spec_data.get("metadata", {})
+    if not isinstance(metadata, dict):
+        return False
+
+    # Only check explicit complexity metadata (template no longer indicates complexity)
+    complexity = metadata.get("complexity")
+    if isinstance(complexity, str) and complexity.strip().lower() in {
+        "medium",
+        "complex",
+        "high",
+    }:
+        return True
+
+    return False
+
+
+def _normalize_acceptance_criteria(value: Any) -> Optional[List[str]]:
+    if value is None:
+        return None
+    if isinstance(value, str):
+        cleaned = value.strip()
+        return [cleaned] if cleaned else []
+    if isinstance(value, list):
+        cleaned_items = []
+        for item in value:
+            if isinstance(item, str):
+                cleaned = item.strip()
+                if cleaned:
+                    cleaned_items.append(cleaned)
+        return cleaned_items
+    return []
 
 
 def find_git_root() -> Optional[Path]:
@@ -161,6 +204,36 @@ def resolve_spec_file(
     return find_spec_file(search_name, specs_dir)
 
 
+def _migrate_spec_fields(spec_data: Dict[str, Any]) -> Dict[str, Any]:
+    """
+    Migrate spec from dual-field format to canonical format.
+
+    Moves status, progress_percentage, and current_phase from metadata
+    to top-level (their canonical location). This handles specs created
+    before the field deduplication.
+
+    Args:
+        spec_data: Spec data dictionary (modified in place)
+
+    Returns:
+        The modified spec_data
+    """
+    if not spec_data:
+        return spec_data
+
+    metadata = spec_data.get("metadata", {})
+    computed_fields = ("status", "progress_percentage", "current_phase")
+
+    for field in computed_fields:
+        # If field exists in metadata but not at top-level, migrate it
+        if field in metadata and field not in spec_data:
+            spec_data[field] = metadata[field]
+        # Remove from metadata (canonical location is top-level)
+        metadata.pop(field, None)
+
+    return spec_data
+
+
 def load_spec(
     spec_id: str, specs_dir: Optional[Path] = None
 ) -> Optional[Dict[str, Any]]:
@@ -181,7 +254,9 @@ def load_spec(
 
     try:
         with open(spec_file, "r") as f:
-            return json.load(f)
+            spec_data = json.load(f)
+            # Migrate old specs to canonical field locations
+            return _migrate_spec_fields(spec_data)
     except (json.JSONDecodeError, IOError):
         return None
 
@@ -234,13 +309,34 @@ def save_spec(
         return False
 
 
-def backup_spec(spec_id: str, specs_dir: Optional[Path] = None) -> Optional[Path]:
+# Default retention policy for versioned backups
+DEFAULT_MAX_BACKUPS = 10
+
+
+def backup_spec(
+    spec_id: str,
+    specs_dir: Optional[Path] = None,
+    max_backups: int = DEFAULT_MAX_BACKUPS,
+) -> Optional[Path]:
     """
-    Create a backup copy of the JSON spec file in the .backups/ directory.
+    Create a versioned backup of the JSON spec file.
+
+    Creates timestamped backups in .backups/{spec_id}/ directory with a
+    configurable retention policy. Also maintains a latest.json copy for
+    quick access to the most recent backup.
+
+    Directory structure:
+        .backups/
+          └── {spec_id}/
+              ├── 2025-12-26T18-20-13.456789.json   # Timestamped backups (μs precision)
+              ├── 2025-12-26T18-30-45.123456.json
+              └── latest.json                       # Copy of most recent
 
     Args:
         spec_id: Specification ID or path to spec file
         specs_dir: Path to specs directory (optional, auto-detected if not provided)
+        max_backups: Maximum number of versioned backups to retain (default: 10).
+                     Set to 0 for unlimited backups.
 
     Returns:
         Path to backup file if created, None otherwise
@@ -256,18 +352,556 @@ def backup_spec(spec_id: str, specs_dir: Optional[Path] = None) -> Optional[Path
     if not specs_dir:
         return None
 
-    backups_dir = specs_dir / ".backups"
-    backups_dir.mkdir(parents=True, exist_ok=True)
+    # Create versioned backup directory: .backups/{spec_id}/
+    spec_backups_dir = specs_dir / ".backups" / spec_id
+    spec_backups_dir.mkdir(parents=True, exist_ok=True)
 
-    backup_file = backups_dir / f"{spec_id}.backup"
+    # Generate timestamp filename (ISO format with safe characters)
+    # Include full microseconds to handle rapid successive saves
+    now = datetime.now(timezone.utc)
+    timestamp = now.strftime("%Y-%m-%dT%H-%M-%S")
+    micros = now.strftime("%f")  # Full 6-digit microseconds
+    backup_file = spec_backups_dir / f"{timestamp}.{micros}.json"
 
     try:
+        # Create the timestamped backup
         shutil.copy2(spec_file, backup_file)
+
+        # Update latest.json to point to the newest backup
+        latest_file = spec_backups_dir / "latest.json"
+        shutil.copy2(backup_file, latest_file)
+
+        # Apply retention policy
+        if max_backups > 0:
+            _apply_backup_retention(spec_backups_dir, max_backups)
+
         return backup_file
     except (IOError, OSError):
         return None
 
 
+def _apply_backup_retention(backups_dir: Path, max_backups: int) -> int:
+    """
+    Apply retention policy by removing oldest backups exceeding the limit.
+
+    Args:
+        backups_dir: Path to the spec's backup directory
+        max_backups: Maximum number of backups to retain
+
+    Returns:
+        Number of backups deleted
+    """
+    # List all timestamped backup files (exclude latest.json)
+    backup_files = sorted(
+        [
+            f for f in backups_dir.glob("*.json")
+            if f.name != "latest.json" and f.is_file()
+        ],
+        key=lambda p: p.name,  # Sort by filename (timestamp order)
+    )
+
+    deleted_count = 0
+    while len(backup_files) > max_backups:
+        oldest = backup_files.pop(0)
+        try:
+            oldest.unlink()
+            deleted_count += 1
+        except (IOError, OSError):
+            pass  # Best effort deletion
+
+    return deleted_count
+
+
+# Default pagination settings for backup listing
+DEFAULT_BACKUP_PAGE_SIZE = 50
+MAX_BACKUP_PAGE_SIZE = 100
+
+
+def list_spec_backups(
+    spec_id: str,
+    specs_dir: Optional[Path] = None,
+    cursor: Optional[str] = None,
+    limit: Optional[int] = None,
+) -> Dict[str, Any]:
+    """
+    List backups for a spec with cursor-based pagination.
+
+    Lists timestamped backup files chronologically (newest first) from the
+    .backups/{spec_id}/ directory. Returns file metadata including timestamp,
+    path, and size. Designed for use with spec.history action.
+
+    Args:
+        spec_id: Specification ID to list backups for
+        specs_dir: Base specs directory (uses find_specs_directory if None)
+        cursor: Pagination cursor from previous call (base64-encoded JSON)
+        limit: Maximum backups per page (default: 50, max: 100)
+
+    Returns:
+        Dict with structure:
+            {
+                "spec_id": str,
+                "backups": [
+                    {
+                        "timestamp": str,      # ISO-ish format from filename
+                        "file_path": str,      # Absolute path to backup file
+                        "file_size_bytes": int # File size
+                    },
+                    ...
+                ],
+                "count": int,
+                "pagination": {
+                    "cursor": Optional[str],
+                    "has_more": bool,
+                    "page_size": int
+                }
+            }
+
+        Returns empty backups list if spec or backup directory doesn't exist.
+    """
+    # Import pagination helpers
+    from foundry_mcp.core.pagination import (
+        CursorError,
+        decode_cursor,
+        encode_cursor,
+        normalize_page_size,
+    )
+
+    # Resolve specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
+
+    # Normalize page size
+    page_size = normalize_page_size(
+        limit, default=DEFAULT_BACKUP_PAGE_SIZE, maximum=MAX_BACKUP_PAGE_SIZE
+    )
+
+    result: Dict[str, Any] = {
+        "spec_id": spec_id,
+        "backups": [],
+        "count": 0,
+        "pagination": {
+            "cursor": None,
+            "has_more": False,
+            "page_size": page_size,
+        },
+    }
+
+    if not specs_dir:
+        return result
+
+    # Locate backup directory: .backups/{spec_id}/
+    backups_dir = specs_dir / ".backups" / spec_id
+    if not backups_dir.is_dir():
+        return result
+
+    # List all timestamped backup files (exclude latest.json)
+    backup_files = sorted(
+        [
+            f
+            for f in backups_dir.glob("*.json")
+            if f.name != "latest.json" and f.is_file()
+        ],
+        key=lambda p: p.name,
+        reverse=True,  # Newest first
+    )
+
+    if not backup_files:
+        return result
+
+    # Handle cursor-based pagination
+    start_after_timestamp: Optional[str] = None
+    if cursor:
+        try:
+            cursor_data = decode_cursor(cursor)
+            start_after_timestamp = cursor_data.get("last_id")
+        except CursorError:
+            # Invalid cursor - return from beginning
+            pass
+
+    # Find start position based on cursor
+    if start_after_timestamp:
+        start_index = 0
+        for idx, backup_file in enumerate(backup_files):
+            # Filename without extension is the timestamp
+            timestamp = backup_file.stem
+            if timestamp == start_after_timestamp:
+                start_index = idx + 1
+                break
+        backup_files = backup_files[start_index:]
+
+    # Fetch one extra to check for more pages
+    page_files = backup_files[: page_size + 1]
+    has_more = len(page_files) > page_size
+    if has_more:
+        page_files = page_files[:page_size]
+
+    # Build backup entries with metadata
+    backups = []
+    for backup_file in page_files:
+        try:
+            file_stat = backup_file.stat()
+            backups.append(
+                {
+                    "timestamp": backup_file.stem,
+                    "file_path": str(backup_file.absolute()),
+                    "file_size_bytes": file_stat.st_size,
+                }
+            )
+        except OSError:
+            # Skip files we can't stat
+            continue
+
+    # Generate next cursor if more pages exist
+    next_cursor = None
+    if has_more and backups:
+        next_cursor = encode_cursor({"last_id": backups[-1]["timestamp"]})
+
+    result["backups"] = backups
+    result["count"] = len(backups)
+    result["pagination"] = {
+        "cursor": next_cursor,
+        "has_more": has_more,
+        "page_size": page_size,
+    }
+
+    return result
+
+
+# Default settings for diff operations
+DEFAULT_DIFF_MAX_RESULTS = 100
+
+
+def _load_spec_source(
+    source: Union[str, Path, Dict[str, Any]],
+    specs_dir: Optional[Path] = None,
+) -> Optional[Dict[str, Any]]:
+    """
+    Load a spec from various source types.
+
+    Args:
+        source: Spec ID, file path, or already-loaded dict
+        specs_dir: Base specs directory for ID lookups
+
+    Returns:
+        Loaded spec dict, or None if not found/invalid
+    """
+    # Already a dict - return as-is
+    if isinstance(source, dict):
+        return source
+
+    # Path object or string path
+    source_path = Path(source) if isinstance(source, str) else source
+
+    # If it's an existing file path, load directly
+    if source_path.is_file():
+        try:
+            with open(source_path, "r") as f:
+                return json.load(f)
+        except (IOError, json.JSONDecodeError):
+            return None
+
+    # Otherwise treat as spec_id and use resolve_spec_file
+    if isinstance(source, str):
+        return load_spec(source, specs_dir)
+
+    return None
+
+
+def _diff_node(
+    old_node: Dict[str, Any],
+    new_node: Dict[str, Any],
+    node_id: str,
+) -> Optional[Dict[str, Any]]:
+    """
+    Compare two nodes and return field-level changes.
+
+    Args:
+        old_node: Original node data
+        new_node: Updated node data
+        node_id: Node identifier for the result
+
+    Returns:
+        Dict with node info and field_changes list, or None if no changes
+    """
+    # Fields to compare (excluding computed/transient fields)
+    compare_fields = ["title", "status", "type", "parent", "children", "metadata", "dependencies"]
+
+    field_changes = []
+    for field in compare_fields:
+        old_val = old_node.get(field)
+        new_val = new_node.get(field)
+
+        if old_val != new_val:
+            field_changes.append({
+                "field": field,
+                "old": old_val,
+                "new": new_val,
+            })
+
+    if not field_changes:
+        return None
+
+    return {
+        "node_id": node_id,
+        "type": new_node.get("type", old_node.get("type")),
+        "title": new_node.get("title", old_node.get("title")),
+        "field_changes": field_changes,
+    }
+
+
+def diff_specs(
+    source: Union[str, Path, Dict[str, Any]],
+    target: Union[str, Path, Dict[str, Any]],
+    specs_dir: Optional[Path] = None,
+    max_results: Optional[int] = None,
+) -> Dict[str, Any]:
+    """
+    Compare two specs and categorize changes as added, removed, or modified.
+
+    Compares hierarchy nodes between source (base/older) and target (comparison/newer)
+    specs, identifying structural and content changes at the task level.
+
+    Args:
+        source: Base spec - spec_id, file path (including backup), or loaded dict
+        target: Comparison spec - spec_id, file path, or loaded dict
+        specs_dir: Base specs directory (auto-detected if None)
+        max_results: Maximum changes to return per category (default: 100)
+
+    Returns:
+        Dict with structure:
+            {
+                "summary": {
+                    "added_count": int,
+                    "removed_count": int,
+                    "modified_count": int,
+                    "total_changes": int
+                },
+                "changes": {
+                    "added": [{"node_id": str, "type": str, "title": str}, ...],
+                    "removed": [{"node_id": str, "type": str, "title": str}, ...],
+                    "modified": [{
+                        "node_id": str,
+                        "type": str,
+                        "title": str,
+                        "field_changes": [{"field": str, "old": Any, "new": Any}, ...]
+                    }, ...]
+                },
+                "partial": bool,  # True if results truncated
+                "source_spec_id": Optional[str],
+                "target_spec_id": Optional[str]
+            }
+
+        Returns error structure if specs cannot be loaded:
+            {"error": str, "success": False}
+    """
+    # Resolve specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
+
+    # Load source spec
+    source_spec = _load_spec_source(source, specs_dir)
+    if source_spec is None:
+        return {
+            "error": f"Could not load source spec: {source}",
+            "success": False,
+        }
+
+    # Load target spec
+    target_spec = _load_spec_source(target, specs_dir)
+    if target_spec is None:
+        return {
+            "error": f"Could not load target spec: {target}",
+            "success": False,
+        }
+
+    # Get hierarchies
+    source_hierarchy = source_spec.get("hierarchy", {})
+    target_hierarchy = target_spec.get("hierarchy", {})
+
+    source_ids = set(source_hierarchy.keys())
+    target_ids = set(target_hierarchy.keys())
+
+    # Categorize changes
+    added_ids = target_ids - source_ids
+    removed_ids = source_ids - target_ids
+    common_ids = source_ids & target_ids
+
+    # Apply max_results limit
+    limit = max_results if max_results is not None else DEFAULT_DIFF_MAX_RESULTS
+    partial = False
+
+    # Build added list
+    added = []
+    for node_id in sorted(added_ids):
+        if len(added) >= limit:
+            partial = True
+            break
+        node = target_hierarchy[node_id]
+        added.append({
+            "node_id": node_id,
+            "type": node.get("type"),
+            "title": node.get("title"),
+        })
+
+    # Build removed list
+    removed = []
+    for node_id in sorted(removed_ids):
+        if len(removed) >= limit:
+            partial = True
+            break
+        node = source_hierarchy[node_id]
+        removed.append({
+            "node_id": node_id,
+            "type": node.get("type"),
+            "title": node.get("title"),
+        })
+
+    # Build modified list
+    modified = []
+    for node_id in sorted(common_ids):
+        if len(modified) >= limit:
+            partial = True
+            break
+        old_node = source_hierarchy[node_id]
+        new_node = target_hierarchy[node_id]
+        diff = _diff_node(old_node, new_node, node_id)
+        if diff:
+            modified.append(diff)
+
+    # Calculate actual counts (may exceed displayed if partial)
+    total_added = len(added_ids)
+    total_removed = len(removed_ids)
+    total_modified = sum(
+        1 for nid in common_ids
+        if _diff_node(source_hierarchy[nid], target_hierarchy[nid], nid)
+    ) if not partial else len(modified)  # Only count all if not already partial
+
+    return {
+        "summary": {
+            "added_count": total_added,
+            "removed_count": total_removed,
+            "modified_count": total_modified if not partial else len(modified),
+            "total_changes": total_added + total_removed + (total_modified if not partial else len(modified)),
+        },
+        "changes": {
+            "added": added,
+            "removed": removed,
+            "modified": modified,
+        },
+        "partial": partial,
+        "source_spec_id": source_spec.get("spec_id"),
+        "target_spec_id": target_spec.get("spec_id"),
+    }
+
+
+def rollback_spec(
+    spec_id: str,
+    timestamp: str,
+    specs_dir: Optional[Path] = None,
+    dry_run: bool = False,
+    create_backup: bool = True,
+) -> Dict[str, Any]:
+    """
+    Restore a spec from a specific backup timestamp.
+
+    Creates a safety backup of the current state before rollback (by default),
+    then replaces the spec file with the contents from the specified backup.
+
+    Args:
+        spec_id: Specification ID to rollback
+        timestamp: Backup timestamp to restore (e.g., "2025-12-26T18-20-13.456789")
+        specs_dir: Base specs directory (auto-detected if None)
+        dry_run: If True, validate and return what would happen without changes
+        create_backup: If True (default), create safety backup before rollback
+
+    Returns:
+        Dict with structure:
+            {
+                "success": bool,
+                "spec_id": str,
+                "timestamp": str,
+                "dry_run": bool,
+                "backup_created": Optional[str],  # Safety backup path
+                "restored_from": str,              # Source backup path
+                "error": Optional[str]             # Error if failed
+            }
+    """
+    # Resolve specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
+
+    result: Dict[str, Any] = {
+        "success": False,
+        "spec_id": spec_id,
+        "timestamp": timestamp,
+        "dry_run": dry_run,
+        "backup_created": None,
+        "restored_from": None,
+        "error": None,
+    }
+
+    if not specs_dir:
+        result["error"] = "Could not find specs directory"
+        return result
+
+    # Find current spec file
+    spec_file = find_spec_file(spec_id, specs_dir)
+    if not spec_file:
+        result["error"] = f"Spec '{spec_id}' not found"
+        return result
+
+    # Locate backup directory
+    backups_dir = specs_dir / ".backups" / spec_id
+    if not backups_dir.is_dir():
+        result["error"] = f"No backups directory for spec '{spec_id}'"
+        return result
+
+    # Find the backup file matching the timestamp
+    backup_file = backups_dir / f"{timestamp}.json"
+    if not backup_file.is_file():
+        result["error"] = f"Backup not found for timestamp '{timestamp}'"
+        return result
+
+    result["restored_from"] = str(backup_file)
+
+    # Validate backup is valid JSON
+    try:
+        with open(backup_file, "r") as f:
+            backup_data = json.load(f)
+        if not isinstance(backup_data, dict):
+            result["error"] = "Backup file is not a valid spec (not a JSON object)"
+            return result
+    except json.JSONDecodeError as e:
+        result["error"] = f"Backup file is not valid JSON: {e}"
+        return result
+    except IOError as e:
+        result["error"] = f"Could not read backup file: {e}"
+        return result
+
+    # dry_run - return success without making changes
+    if dry_run:
+        result["success"] = True
+        if create_backup:
+            result["backup_created"] = "(would be created)"
+        return result
+
+    # Create safety backup of current state before rollback
+    if create_backup:
+        safety_backup = backup_spec(spec_id, specs_dir)
+        if safety_backup:
+            result["backup_created"] = str(safety_backup)
+
+    # Perform rollback - copy backup to spec location
+    try:
+        shutil.copy2(backup_file, spec_file)
+        result["success"] = True
+    except (IOError, OSError) as e:
+        result["error"] = f"Failed to restore backup: {e}"
+        return result
+
+    return result
+
+
 def _validate_spec_structure(spec_data: Dict[str, Any]) -> bool:
     """
     Validate basic JSON spec file structure.
@@ -297,6 +931,7 @@ def _validate_spec_structure(spec_data: Dict[str, Any]) -> bool:
             "in_progress",
             "completed",
             "blocked",
+            "failed",
         ]:
             return False
 
@@ -684,73 +1319,444 @@ def add_phase(
     }, None
 
 
-def _collect_descendants(hierarchy: Dict[str, Any], node_id: str) -> List[str]:
+def add_phase_bulk(
+    spec_id: str,
+    phase_title: str,
+    tasks: List[Dict[str, Any]],
+    phase_description: Optional[str] = None,
+    phase_purpose: Optional[str] = None,
+    phase_estimated_hours: Optional[float] = None,
+    metadata_defaults: Optional[Dict[str, Any]] = None,
+    position: Optional[int] = None,
+    link_previous: bool = True,
+    specs_dir: Optional[Path] = None,
+) -> Tuple[Optional[Dict[str, Any]], Optional[str]]:
     """
-    Recursively collect all descendant node IDs for a given node.
+    Add a new phase with pre-defined tasks in a single atomic operation.
+
+    Creates a phase and all specified tasks/verify nodes without auto-generating
+    verification scaffolding. This enables creating complete phase structures
+    in one operation.
 
     Args:
-        hierarchy: The spec hierarchy dict
-        node_id: Starting node ID
+        spec_id: Specification ID to mutate.
+        phase_title: Phase title.
+        tasks: List of task definitions, each containing:
+            - type: "task" or "verify" (required)
+            - title: Task title (required)
+            - description: Optional description
+            - acceptance_criteria: Optional list of acceptance criteria
+            - task_category: Optional task category
+            - file_path: Optional associated file path
+            - estimated_hours: Optional time estimate
+            - verification_type: Optional verification type for verify tasks
+        phase_description: Optional phase description.
+        phase_purpose: Optional purpose/goal metadata string.
+        phase_estimated_hours: Optional estimated hours for the phase.
+        metadata_defaults: Optional defaults applied to tasks missing explicit values.
+            Supported keys: task_category, category, acceptance_criteria, estimated_hours
+        position: Optional zero-based insertion index in spec-root children.
+        link_previous: Whether to automatically block on the previous phase.
+        specs_dir: Specs directory override.
 
     Returns:
-        List of all descendant node IDs (not including the starting node)
+        Tuple of (result_dict, error_message).
+        On success: ({"phase_id": ..., "tasks_created": [...], ...}, None)
+        On failure: (None, "error message")
     """
-    descendants: List[str] = []
-    node = hierarchy.get(node_id)
-    if not node:
-        return descendants
+    # Validate required parameters
+    if not spec_id or not spec_id.strip():
+        return None, "Specification ID is required"
 
-    children = node.get("children", [])
-    if not isinstance(children, list):
-        return descendants
+    if not phase_title or not phase_title.strip():
+        return None, "Phase title is required"
 
-    for child_id in children:
-        descendants.append(child_id)
-        descendants.extend(_collect_descendants(hierarchy, child_id))
+    if not tasks or not isinstance(tasks, list) or len(tasks) == 0:
+        return None, "At least one task definition is required"
+
+    if phase_estimated_hours is not None and phase_estimated_hours < 0:
+        return None, "phase_estimated_hours must be non-negative"
+
+    phase_title = phase_title.strip()
+    defaults = metadata_defaults or {}
+
+    # Validate metadata_defaults values
+    if defaults:
+        default_est_hours = defaults.get("estimated_hours")
+        if default_est_hours is not None:
+            if not isinstance(default_est_hours, (int, float)) or default_est_hours < 0:
+                return None, "metadata_defaults.estimated_hours must be a non-negative number"
+        default_category = defaults.get("task_category")
+        if default_category is None:
+            default_category = defaults.get("category")
+        if default_category is not None and not isinstance(default_category, str):
+            return None, "metadata_defaults.task_category must be a string"
+        default_acceptance = defaults.get("acceptance_criteria")
+        if default_acceptance is not None and not isinstance(
+            default_acceptance, (list, str)
+        ):
+            return None, "metadata_defaults.acceptance_criteria must be a list of strings"
+        if isinstance(default_acceptance, list) and any(
+            not isinstance(item, str) for item in default_acceptance
+        ):
+            return None, "metadata_defaults.acceptance_criteria must be a list of strings"
+
+    # Validate each task definition
+    valid_task_types = {"task", "verify"}
+    for idx, task_def in enumerate(tasks):
+        if not isinstance(task_def, dict):
+            return None, f"Task at index {idx} must be a dictionary"
+
+        task_type = task_def.get("type")
+        if not task_type or task_type not in valid_task_types:
+            return None, f"Task at index {idx} must have type 'task' or 'verify'"
+
+        task_title = task_def.get("title")
+        if not task_title or not isinstance(task_title, str) or not task_title.strip():
+            return None, f"Task at index {idx} must have a non-empty title"
+
+        est_hours = task_def.get("estimated_hours")
+        if est_hours is not None:
+            if not isinstance(est_hours, (int, float)) or est_hours < 0:
+                return None, f"Task at index {idx} has invalid estimated_hours"
+
+        task_category = task_def.get("task_category")
+        if task_category is not None and not isinstance(task_category, str):
+            return None, f"Task at index {idx} has invalid task_category"
+
+        legacy_category = task_def.get("category")
+        if legacy_category is not None and not isinstance(legacy_category, str):
+            return None, f"Task at index {idx} has invalid category"
+
+        acceptance_criteria = task_def.get("acceptance_criteria")
+        if acceptance_criteria is not None and not isinstance(
+            acceptance_criteria, (list, str)
+        ):
+            return None, f"Task at index {idx} has invalid acceptance_criteria"
+        if isinstance(acceptance_criteria, list) and any(
+            not isinstance(item, str) for item in acceptance_criteria
+        ):
+            return None, f"Task at index {idx} acceptance_criteria must be a list of strings"
 
-    return descendants
+    # Find specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
 
+    if specs_dir is None:
+        return (
+            None,
+            "No specs directory found. Use specs_dir parameter or set SDD_SPECS_DIR.",
+        )
 
-def _count_tasks_in_subtree(
-    hierarchy: Dict[str, Any], node_ids: List[str]
-) -> Tuple[int, int]:
-    """
-    Count total and completed tasks in a list of nodes.
+    spec_path = find_spec_file(spec_id, specs_dir)
+    if spec_path is None:
+        return None, f"Specification '{spec_id}' not found"
 
-    Args:
-        hierarchy: The spec hierarchy dict
-        node_ids: List of node IDs to count
+    spec_data = load_spec(spec_id, specs_dir)
+    if spec_data is None:
+        return None, f"Failed to load specification '{spec_id}'"
 
-    Returns:
-        Tuple of (total_count, completed_count)
-    """
-    total = 0
-    completed = 0
+    requires_rich_tasks = _requires_rich_task_fields(spec_data)
 
-    for node_id in node_ids:
-        node = hierarchy.get(node_id)
-        if not node:
-            continue
-        node_type = node.get("type")
-        if node_type in ("task", "subtask", "verify"):
-            total += 1
-            if node.get("status") == "completed":
-                completed += 1
+    hierarchy = spec_data.get("hierarchy", {})
+    spec_root = hierarchy.get("spec-root")
 
-    return total, completed
+    if spec_root is None:
+        return None, "Specification root node 'spec-root' not found"
 
+    if spec_root.get("type") not in {"spec", "root"}:
+        return None, "Specification root node has invalid type"
 
-def _remove_dependency_references(
-    hierarchy: Dict[str, Any], removed_ids: List[str]
-) -> None:
-    """
-    Remove references to deleted nodes from all dependency lists.
+    children = spec_root.get("children", []) or []
+    if not isinstance(children, list):
+        children = []
 
-    Args:
-        hierarchy: The spec hierarchy dict
-        removed_ids: List of node IDs being removed
-    """
-    removed_set = set(removed_ids)
+    insert_index = len(children)
+    if position is not None and position >= 0:
+        insert_index = min(position, len(children))
+
+    # Generate phase ID
+    phase_id, phase_num = _generate_phase_id(hierarchy)
+
+    # Build phase metadata
+    phase_metadata: Dict[str, Any] = {
+        "purpose": (phase_purpose.strip() if phase_purpose else ""),
+    }
+    if phase_description:
+        phase_metadata["description"] = phase_description.strip()
+    if phase_estimated_hours is not None:
+        phase_metadata["estimated_hours"] = phase_estimated_hours
+
+    # Create phase node (without children initially)
+    phase_node = {
+        "type": "phase",
+        "title": phase_title,
+        "status": "pending",
+        "parent": "spec-root",
+        "children": [],
+        "total_tasks": 0,
+        "completed_tasks": 0,
+        "metadata": phase_metadata,
+        "dependencies": {
+            "blocks": [],
+            "blocked_by": [],
+            "depends": [],
+        },
+    }
+
+    hierarchy[phase_id] = phase_node
+
+    # Insert phase into spec-root children
+    if insert_index == len(children):
+        children.append(phase_id)
+    else:
+        children.insert(insert_index, phase_id)
+    spec_root["children"] = children
+
+    # Link to previous phase if requested
+    linked_phase_id: Optional[str] = None
+    if link_previous and insert_index > 0 and insert_index == len(children) - 1:
+        candidate = children[insert_index - 1]
+        previous = hierarchy.get(candidate)
+        if previous and previous.get("type") == "phase":
+            linked_phase_id = candidate
+            prev_deps = previous.setdefault(
+                "dependencies",
+                {"blocks": [], "blocked_by": [], "depends": []},
+            )
+            blocks = prev_deps.setdefault("blocks", [])
+            if phase_id not in blocks:
+                blocks.append(phase_id)
+            phase_node["dependencies"]["blocked_by"].append(candidate)
+
+    def _nonempty_string(value: Any) -> bool:
+        return isinstance(value, str) and bool(value.strip())
+
+    def _extract_description(task_def: Dict[str, Any]) -> tuple[Optional[str], Any]:
+        description = task_def.get("description")
+        if _nonempty_string(description) and isinstance(description, str):
+            return "description", description.strip()
+        details = task_def.get("details")
+        if _nonempty_string(details) and isinstance(details, str):
+            return "details", details.strip()
+        if isinstance(details, list):
+            cleaned = [
+                item.strip()
+                for item in details
+                if isinstance(item, str) and item.strip()
+            ]
+            if cleaned:
+                return "details", cleaned
+        return None, None
+
+    # Create tasks under the phase
+    tasks_created: List[Dict[str, Any]] = []
+    task_counter = 0
+    verify_counter = 0
+
+    for task_def in tasks:
+        task_type = task_def["type"]
+        task_title = task_def["title"].strip()
+
+        # Generate task ID based on type
+        if task_type == "verify":
+            verify_counter += 1
+            task_id = f"verify-{phase_num}-{verify_counter}"
+        else:
+            task_counter += 1
+            task_id = f"task-{phase_num}-{task_counter}"
+
+        # Build task metadata with defaults cascade
+        task_metadata: Dict[str, Any] = {}
+
+        # Apply description/details
+        desc_field, desc_value = _extract_description(task_def)
+        if desc_field and desc_value is not None:
+            task_metadata[desc_field] = desc_value
+        elif requires_rich_tasks and task_type == "task":
+            return None, f"Task '{task_title}' missing description"
+
+        # Apply file_path
+        file_path = task_def.get("file_path")
+        if file_path and isinstance(file_path, str):
+            task_metadata["file_path"] = file_path.strip()
+
+        # Apply estimated_hours (task-level overrides defaults)
+        est_hours = task_def.get("estimated_hours")
+        if est_hours is not None:
+            task_metadata["estimated_hours"] = float(est_hours)
+        elif defaults.get("estimated_hours") is not None:
+            task_metadata["estimated_hours"] = float(defaults["estimated_hours"])
+
+        normalized_category = None
+        if task_type == "task":
+            # Apply acceptance_criteria
+            raw_acceptance = task_def.get("acceptance_criteria")
+            if raw_acceptance is None:
+                raw_acceptance = defaults.get("acceptance_criteria")
+            acceptance_criteria = _normalize_acceptance_criteria(raw_acceptance)
+            if acceptance_criteria is not None:
+                task_metadata["acceptance_criteria"] = acceptance_criteria
+            if requires_rich_tasks:
+                if raw_acceptance is None:
+                    return None, f"Task '{task_title}' missing acceptance_criteria"
+                if not acceptance_criteria:
+                    return (
+                        None,
+                        f"Task '{task_title}' acceptance_criteria must include at least one entry",
+                    )
+
+            # Apply task_category from defaults if not specified
+            category = task_def.get("task_category") or task_def.get("category")
+            if category is None:
+                category = defaults.get("task_category") or defaults.get("category")
+            if category and isinstance(category, str):
+                normalized_category = category.strip().lower()
+                if normalized_category not in CATEGORIES:
+                    return (
+                        None,
+                        f"Task '{task_title}' has invalid task_category '{category}'",
+                    )
+                task_metadata["task_category"] = normalized_category
+            if requires_rich_tasks and normalized_category is None:
+                return None, f"Task '{task_title}' missing task_category"
+
+            if normalized_category in {"implementation", "refactoring"}:
+                if not _nonempty_string(task_metadata.get("file_path")):
+                    return (
+                        None,
+                        f"Task '{task_title}' missing file_path for category '{normalized_category}'",
+                    )
+
+        # Apply verification_type for verify tasks
+        if task_type == "verify":
+            verify_type = task_def.get("verification_type")
+            if verify_type and verify_type in VERIFICATION_TYPES:
+                task_metadata["verification_type"] = verify_type
+
+        # Create task node
+        task_node = {
+            "type": task_type,
+            "title": task_title,
+            "status": "pending",
+            "parent": phase_id,
+            "children": [],
+            "total_tasks": 1,
+            "completed_tasks": 0,
+            "metadata": task_metadata,
+            "dependencies": {
+                "blocks": [],
+                "blocked_by": [],
+                "depends": [],
+            },
+        }
+
+        hierarchy[task_id] = task_node
+        phase_node["children"].append(task_id)
+        phase_node["total_tasks"] += 1
+
+        tasks_created.append({
+            "task_id": task_id,
+            "title": task_title,
+            "type": task_type,
+        })
+
+    # Update spec-root total_tasks
+    total_tasks = spec_root.get("total_tasks", 0)
+    spec_root["total_tasks"] = total_tasks + phase_node["total_tasks"]
+
+    # Update spec-level estimated hours if provided
+    if phase_estimated_hours is not None:
+        spec_metadata = spec_data.setdefault("metadata", {})
+        current_hours = spec_metadata.get("estimated_hours")
+        if isinstance(current_hours, (int, float)):
+            spec_metadata["estimated_hours"] = current_hours + phase_estimated_hours
+        else:
+            spec_metadata["estimated_hours"] = phase_estimated_hours
+
+    # Save spec atomically
+    saved = save_spec(spec_id, spec_data, specs_dir)
+    if not saved:
+        return None, "Failed to save specification"
+
+    return {
+        "spec_id": spec_id,
+        "phase_id": phase_id,
+        "title": phase_title,
+        "position": insert_index,
+        "linked_previous": linked_phase_id,
+        "tasks_created": tasks_created,
+        "total_tasks": len(tasks_created),
+    }, None
+
+
+def _collect_descendants(hierarchy: Dict[str, Any], node_id: str) -> List[str]:
+    """
+    Recursively collect all descendant node IDs for a given node.
+
+    Args:
+        hierarchy: The spec hierarchy dict
+        node_id: Starting node ID
+
+    Returns:
+        List of all descendant node IDs (not including the starting node)
+    """
+    descendants: List[str] = []
+    node = hierarchy.get(node_id)
+    if not node:
+        return descendants
+
+    children = node.get("children", [])
+    if not isinstance(children, list):
+        return descendants
+
+    for child_id in children:
+        descendants.append(child_id)
+        descendants.extend(_collect_descendants(hierarchy, child_id))
+
+    return descendants
+
+
+def _count_tasks_in_subtree(
+    hierarchy: Dict[str, Any], node_ids: List[str]
+) -> Tuple[int, int]:
+    """
+    Count total and completed tasks in a list of nodes.
+
+    Args:
+        hierarchy: The spec hierarchy dict
+        node_ids: List of node IDs to count
+
+    Returns:
+        Tuple of (total_count, completed_count)
+    """
+    total = 0
+    completed = 0
+
+    for node_id in node_ids:
+        node = hierarchy.get(node_id)
+        if not node:
+            continue
+        node_type = node.get("type")
+        if node_type in ("task", "subtask", "verify"):
+            total += 1
+            if node.get("status") == "completed":
+                completed += 1
+
+    return total, completed
+
+
+def _remove_dependency_references(
+    hierarchy: Dict[str, Any], removed_ids: List[str]
+) -> None:
+    """
+    Remove references to deleted nodes from all dependency lists.
+
+    Args:
+        hierarchy: The spec hierarchy dict
+        removed_ids: List of node IDs being removed
+    """
+    removed_set = set(removed_ids)
 
     for node_id, node in hierarchy.items():
         deps = node.get("dependencies")
@@ -971,26 +1977,519 @@ def remove_phase(
     return result, None
 
 
+def move_phase(
+    spec_id: str,
+    phase_id: str,
+    position: int,
+    link_previous: bool = True,
+    dry_run: bool = False,
+    specs_dir: Optional[Path] = None,
+) -> Tuple[Optional[Dict[str, Any]], Optional[str]]:
+    """
+    Move a phase to a new position within spec-root's children.
+
+    Supports reordering phases and optionally re-linking phase dependencies
+    according to the link_previous pattern (each phase blocked by its predecessor).
+
+    Args:
+        spec_id: Specification ID containing the phase.
+        phase_id: Phase ID to move (e.g., "phase-2").
+        position: Target position (1-based index) in spec-root children.
+        link_previous: If True, update dependencies to maintain the sequential
+                       blocking pattern. If False, preserve existing dependencies.
+        dry_run: If True, validate and return preview without saving changes.
+        specs_dir: Path to specs directory (auto-detected if not provided).
+
+    Returns:
+        Tuple of (result_dict, error_message).
+        On success: ({"spec_id": ..., "phase_id": ..., "old_position": ..., "new_position": ..., ...}, None)
+        On failure: (None, "error message")
+    """
+    # Validate inputs
+    if not spec_id or not spec_id.strip():
+        return None, "Specification ID is required"
+
+    if not phase_id or not phase_id.strip():
+        return None, "Phase ID is required"
+
+    if not isinstance(position, int) or position < 1:
+        return None, "Position must be a positive integer (1-based)"
+
+    # Find specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
+
+    if specs_dir is None:
+        return (
+            None,
+            "No specs directory found. Use specs_dir parameter or set SDD_SPECS_DIR.",
+        )
+
+    # Find and load the spec
+    spec_path = find_spec_file(spec_id, specs_dir)
+    if spec_path is None:
+        return None, f"Specification '{spec_id}' not found"
+
+    spec_data = load_spec(spec_id, specs_dir)
+    if spec_data is None:
+        return None, f"Failed to load specification '{spec_id}'"
+
+    hierarchy = spec_data.get("hierarchy", {})
+
+    # Validate phase exists
+    phase = hierarchy.get(phase_id)
+    if phase is None:
+        return None, f"Phase '{phase_id}' not found"
+
+    # Validate node type is phase
+    node_type = phase.get("type")
+    if node_type != "phase":
+        return None, f"Node '{phase_id}' is not a phase (type: {node_type})"
+
+    # Get spec-root
+    spec_root = hierarchy.get("spec-root")
+    if spec_root is None:
+        return None, "Specification root node 'spec-root' not found"
+
+    children = spec_root.get("children", [])
+    if not isinstance(children, list):
+        children = []
+
+    # Find current position
+    try:
+        old_index = children.index(phase_id)
+    except ValueError:
+        return None, f"Phase '{phase_id}' not found in spec-root children"
+
+    # Convert to 0-based index for internal use
+    new_index = position - 1
+
+    # Validate position is within bounds
+    if new_index < 0 or new_index >= len(children):
+        return None, f"Invalid position {position}. Must be 1-{len(children)}"
+
+    # No change needed if same position
+    if old_index == new_index:
+        return {
+            "spec_id": spec_id,
+            "phase_id": phase_id,
+            "phase_title": phase.get("title", ""),
+            "old_position": old_index + 1,
+            "new_position": new_index + 1,
+            "moved": False,
+            "dry_run": dry_run,
+            "message": "Phase is already at the specified position",
+        }, None
+
+    # Identify old neighbors for dependency cleanup
+    old_prev_id: Optional[str] = None
+    old_next_id: Optional[str] = None
+
+    if old_index > 0:
+        candidate = children[old_index - 1]
+        if hierarchy.get(candidate, {}).get("type") == "phase":
+            old_prev_id = candidate
+
+    if old_index < len(children) - 1:
+        candidate = children[old_index + 1]
+        if hierarchy.get(candidate, {}).get("type") == "phase":
+            old_next_id = candidate
+
+    # Perform the move in children list
+    children.remove(phase_id)
+    # After removal, adjust target index if moving forward
+    insert_index = new_index if new_index <= old_index else new_index
+    if insert_index >= len(children):
+        children.append(phase_id)
+    else:
+        children.insert(insert_index, phase_id)
+
+    # Identify new neighbors
+    actual_new_index = children.index(phase_id)
+    new_prev_id: Optional[str] = None
+    new_next_id: Optional[str] = None
+
+    if actual_new_index > 0:
+        candidate = children[actual_new_index - 1]
+        if hierarchy.get(candidate, {}).get("type") == "phase":
+            new_prev_id = candidate
+
+    if actual_new_index < len(children) - 1:
+        candidate = children[actual_new_index + 1]
+        if hierarchy.get(candidate, {}).get("type") == "phase":
+            new_next_id = candidate
+
+    # Track dependency changes
+    dependencies_updated: List[Dict[str, Any]] = []
+
+    if link_previous:
+        # Remove old dependency links
+        phase_deps = phase.setdefault(
+            "dependencies", {"blocks": [], "blocked_by": [], "depends": []}
+        )
+
+        # 1. Remove this phase from old_prev's blocks list
+        if old_prev_id:
+            old_prev = hierarchy.get(old_prev_id)
+            if old_prev:
+                old_prev_deps = old_prev.get("dependencies", {})
+                old_prev_blocks = old_prev_deps.get("blocks", [])
+                if phase_id in old_prev_blocks:
+                    old_prev_blocks.remove(phase_id)
+                    dependencies_updated.append({
+                        "action": "removed",
+                        "from": old_prev_id,
+                        "relationship": "blocks",
+                        "target": phase_id,
+                    })
+
+        # 2. Remove old_prev from this phase's blocked_by
+        phase_blocked_by = phase_deps.setdefault("blocked_by", [])
+        if old_prev_id and old_prev_id in phase_blocked_by:
+            phase_blocked_by.remove(old_prev_id)
+            dependencies_updated.append({
+                "action": "removed",
+                "from": phase_id,
+                "relationship": "blocked_by",
+                "target": old_prev_id,
+            })
+
+        # 3. Remove this phase from old_next's blocked_by
+        if old_next_id:
+            old_next = hierarchy.get(old_next_id)
+            if old_next:
+                old_next_deps = old_next.get("dependencies", {})
+                old_next_blocked_by = old_next_deps.get("blocked_by", [])
+                if phase_id in old_next_blocked_by:
+                    old_next_blocked_by.remove(phase_id)
+                    dependencies_updated.append({
+                        "action": "removed",
+                        "from": old_next_id,
+                        "relationship": "blocked_by",
+                        "target": phase_id,
+                    })
+
+        # 4. Remove old_next from this phase's blocks
+        phase_blocks = phase_deps.setdefault("blocks", [])
+        if old_next_id and old_next_id in phase_blocks:
+            phase_blocks.remove(old_next_id)
+            dependencies_updated.append({
+                "action": "removed",
+                "from": phase_id,
+                "relationship": "blocks",
+                "target": old_next_id,
+            })
+
+        # 5. Link old neighbors to each other (if they were adjacent via this phase)
+        if old_prev_id and old_next_id:
+            old_prev = hierarchy.get(old_prev_id)
+            old_next = hierarchy.get(old_next_id)
+            if old_prev and old_next:
+                old_prev_deps = old_prev.setdefault(
+                    "dependencies", {"blocks": [], "blocked_by": [], "depends": []}
+                )
+                old_prev_blocks = old_prev_deps.setdefault("blocks", [])
+                if old_next_id not in old_prev_blocks:
+                    old_prev_blocks.append(old_next_id)
+                    dependencies_updated.append({
+                        "action": "added",
+                        "from": old_prev_id,
+                        "relationship": "blocks",
+                        "target": old_next_id,
+                    })
+
+                old_next_deps = old_next.setdefault(
+                    "dependencies", {"blocks": [], "blocked_by": [], "depends": []}
+                )
+                old_next_blocked_by = old_next_deps.setdefault("blocked_by", [])
+                if old_prev_id not in old_next_blocked_by:
+                    old_next_blocked_by.append(old_prev_id)
+                    dependencies_updated.append({
+                        "action": "added",
+                        "from": old_next_id,
+                        "relationship": "blocked_by",
+                        "target": old_prev_id,
+                    })
+
+        # Add new dependency links
+        # 6. New prev blocks this phase
+        if new_prev_id:
+            new_prev = hierarchy.get(new_prev_id)
+            if new_prev:
+                new_prev_deps = new_prev.setdefault(
+                    "dependencies", {"blocks": [], "blocked_by": [], "depends": []}
+                )
+                new_prev_blocks = new_prev_deps.setdefault("blocks", [])
+                if phase_id not in new_prev_blocks:
+                    new_prev_blocks.append(phase_id)
+                    dependencies_updated.append({
+                        "action": "added",
+                        "from": new_prev_id,
+                        "relationship": "blocks",
+                        "target": phase_id,
+                    })
+
+                # This phase is blocked by new prev
+                if new_prev_id not in phase_blocked_by:
+                    phase_blocked_by.append(new_prev_id)
+                    dependencies_updated.append({
+                        "action": "added",
+                        "from": phase_id,
+                        "relationship": "blocked_by",
+                        "target": new_prev_id,
+                    })
+
+        # 7. This phase blocks new next
+        if new_next_id:
+            new_next = hierarchy.get(new_next_id)
+            if new_next:
+                if new_next_id not in phase_blocks:
+                    phase_blocks.append(new_next_id)
+                    dependencies_updated.append({
+                        "action": "added",
+                        "from": phase_id,
+                        "relationship": "blocks",
+                        "target": new_next_id,
+                    })
+
+                new_next_deps = new_next.setdefault(
+                    "dependencies", {"blocks": [], "blocked_by": [], "depends": []}
+                )
+                new_next_blocked_by = new_next_deps.setdefault("blocked_by", [])
+                if phase_id not in new_next_blocked_by:
+                    new_next_blocked_by.append(phase_id)
+                    dependencies_updated.append({
+                        "action": "added",
+                        "from": new_next_id,
+                        "relationship": "blocked_by",
+                        "target": phase_id,
+                    })
+
+                # Remove old link from new prev to new next (now goes through this phase)
+                if new_prev_id:
+                    new_prev = hierarchy.get(new_prev_id)
+                    if new_prev:
+                        new_prev_deps = new_prev.get("dependencies", {})
+                        new_prev_blocks = new_prev_deps.get("blocks", [])
+                        if new_next_id in new_prev_blocks:
+                            new_prev_blocks.remove(new_next_id)
+                            dependencies_updated.append({
+                                "action": "removed",
+                                "from": new_prev_id,
+                                "relationship": "blocks",
+                                "target": new_next_id,
+                            })
+
+                    if new_prev_id in new_next_blocked_by:
+                        new_next_blocked_by.remove(new_prev_id)
+                        dependencies_updated.append({
+                            "action": "removed",
+                            "from": new_next_id,
+                            "relationship": "blocked_by",
+                            "target": new_prev_id,
+                        })
+
+    # Update spec-root children
+    spec_root["children"] = children
+
+    # Build result
+    result: Dict[str, Any] = {
+        "spec_id": spec_id,
+        "phase_id": phase_id,
+        "phase_title": phase.get("title", ""),
+        "old_position": old_index + 1,
+        "new_position": actual_new_index + 1,
+        "moved": True,
+        "link_previous": link_previous,
+        "dry_run": dry_run,
+    }
+
+    if dependencies_updated:
+        result["dependencies_updated"] = dependencies_updated
+
+    if dry_run:
+        result["message"] = "Dry run - changes not saved"
+        return result, None
+
+    # Save the spec
+    saved = save_spec(spec_id, spec_data, specs_dir)
+    if not saved:
+        return None, "Failed to save specification"
+
+    return result, None
+
+
+def update_phase_metadata(
+    spec_id: str,
+    phase_id: str,
+    *,
+    estimated_hours: Optional[float] = None,
+    description: Optional[str] = None,
+    purpose: Optional[str] = None,
+    dry_run: bool = False,
+    specs_dir: Optional[Path] = None,
+) -> Tuple[Optional[Dict[str, Any]], Optional[str]]:
+    """
+    Update metadata fields of a phase in a specification.
+
+    Allows updating phase-level metadata such as estimated_hours, description,
+    and purpose. Tracks previous values for audit purposes.
+
+    Args:
+        spec_id: Specification ID containing the phase.
+        phase_id: Phase ID to update (e.g., "phase-1").
+        estimated_hours: New estimated hours value (must be >= 0 if provided).
+        description: New description text for the phase.
+        purpose: New purpose text for the phase.
+        dry_run: If True, validate and return preview without saving changes.
+        specs_dir: Path to specs directory (auto-detected if not provided).
+
+    Returns:
+        Tuple of (result_dict, error_message).
+        On success: ({"spec_id": ..., "phase_id": ..., "updates": [...], ...}, None)
+        On failure: (None, "error message")
+    """
+    # Validate spec_id
+    if not spec_id or not spec_id.strip():
+        return None, "Specification ID is required"
+
+    # Validate phase_id
+    if not phase_id or not phase_id.strip():
+        return None, "Phase ID is required"
+
+    # Validate estimated_hours if provided
+    if estimated_hours is not None:
+        if not isinstance(estimated_hours, (int, float)):
+            return None, "estimated_hours must be a number"
+        if estimated_hours < 0:
+            return None, "estimated_hours must be >= 0"
+
+    # Check that at least one field is being updated
+    has_update = any(
+        v is not None for v in [estimated_hours, description, purpose]
+    )
+    if not has_update:
+        return None, "At least one field (estimated_hours, description, purpose) must be provided"
+
+    # Find specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
+
+    if specs_dir is None:
+        return (
+            None,
+            "No specs directory found. Use specs_dir parameter or set SDD_SPECS_DIR.",
+        )
+
+    # Find and load the spec
+    spec_path = find_spec_file(spec_id, specs_dir)
+    if spec_path is None:
+        return None, f"Specification '{spec_id}' not found"
+
+    spec_data = load_spec(spec_id, specs_dir)
+    if spec_data is None:
+        return None, f"Failed to load specification '{spec_id}'"
+
+    hierarchy = spec_data.get("hierarchy", {})
+
+    # Validate phase exists
+    phase = hierarchy.get(phase_id)
+    if phase is None:
+        return None, f"Phase '{phase_id}' not found"
+
+    # Validate node type is phase
+    node_type = phase.get("type")
+    if node_type != "phase":
+        return None, f"Node '{phase_id}' is not a phase (type: {node_type})"
+
+    # Ensure metadata exists on phase
+    if "metadata" not in phase:
+        phase["metadata"] = {}
+
+    phase_metadata = phase["metadata"]
+
+    # Track updates with previous values
+    updates: List[Dict[str, Any]] = []
+
+    if estimated_hours is not None:
+        previous = phase_metadata.get("estimated_hours")
+        phase_metadata["estimated_hours"] = estimated_hours
+        updates.append({
+            "field": "estimated_hours",
+            "previous_value": previous,
+            "new_value": estimated_hours,
+        })
+
+    if description is not None:
+        description = description.strip() if description else description
+        previous = phase_metadata.get("description")
+        phase_metadata["description"] = description
+        updates.append({
+            "field": "description",
+            "previous_value": previous,
+            "new_value": description,
+        })
+
+    if purpose is not None:
+        purpose = purpose.strip() if purpose else purpose
+        previous = phase_metadata.get("purpose")
+        phase_metadata["purpose"] = purpose
+        updates.append({
+            "field": "purpose",
+            "previous_value": previous,
+            "new_value": purpose,
+        })
+
+    # Build result
+    result: Dict[str, Any] = {
+        "spec_id": spec_id,
+        "phase_id": phase_id,
+        "phase_title": phase.get("title", ""),
+        "updates": updates,
+        "dry_run": dry_run,
+    }
+
+    if dry_run:
+        result["message"] = "Dry run - changes not saved"
+        return result, None
+
+    # Save the spec
+    saved = save_spec(spec_id, spec_data, specs_dir)
+    if not saved:
+        return None, "Failed to save specification"
+
+    return result, None
+
+
 def get_template_structure(template: str, category: str) -> Dict[str, Any]:
     """
     Get the hierarchical structure for a spec template.
 
-    All templates include per-phase verification (auto + fidelity) for each phase.
+    Only the 'empty' template is supported. Use phase templates to add structure.
 
     Args:
-        template: Template type (simple, medium, complex, security).
+        template: Template type (only 'empty' is valid).
         category: Default task category.
 
     Returns:
         Hierarchy dict for the spec.
+
+    Raises:
+        ValueError: If template is not 'empty'.
     """
-    base_hierarchy = {
+    if template != "empty":
+        raise ValueError(
+            f"Invalid template '{template}'. Only 'empty' template is supported. "
+            f"Use phase templates (phase-add-bulk or phase-template apply) to add structure."
+        )
+
+    return {
         "spec-root": {
             "type": "spec",
             "title": "",  # Filled in later
             "status": "pending",
             "parent": None,
-            "children": ["phase-1"],
+            "children": [],
             "total_tasks": 0,
             "completed_tasks": 0,
             "metadata": {
@@ -1003,201 +2502,300 @@ def get_template_structure(template: str, category: str) -> Dict[str, Any]:
                 "depends": [],
             },
         },
-        "phase-1": {
-            "type": "phase",
-            "title": "Planning & Discovery",
-            "status": "pending",
-            "parent": "spec-root",
-            "children": ["task-1-1"],
-            "total_tasks": 1,
-            "completed_tasks": 0,
-            "metadata": {
-                "purpose": "Initial planning and requirements gathering",
-                "estimated_hours": 2,
-            },
-            "dependencies": {
-                "blocks": [],
-                "blocked_by": [],
-                "depends": [],
-            },
-        },
-        "task-1-1": {
-            "type": "task",
-            "title": "Define requirements",
-            "status": "pending",
-            "parent": "phase-1",
-            "children": [],
-            "total_tasks": 1,
-            "completed_tasks": 0,
-            "metadata": {
-                "details": "Document the requirements and acceptance criteria",
-                "category": category,
-                "estimated_hours": 1,
-            },
-            "dependencies": {
-                "blocks": [],
-                "blocked_by": [],
-                "depends": [],
-            },
-        },
     }
 
-    # Add verification to phase-1 (all templates)
-    _add_phase_verification(base_hierarchy, 1, "phase-1")
-    base_hierarchy["spec-root"]["total_tasks"] = 3  # task + 2 verify
 
-    if template == "simple":
-        return base_hierarchy
+def get_phase_template_structure(
+    template: str, category: str = "implementation"
+) -> Dict[str, Any]:
+    """
+    Get the structure definition for a phase template.
+
+    Phase templates define reusable phase structures with pre-configured tasks.
+    Each template includes automatic verification scaffolding (run-tests + fidelity).
+
+    Args:
+        template: Phase template type (planning, implementation, testing, security, documentation).
+        category: Default task category for tasks in this phase.
 
-    # Medium/complex/security: add implementation phase
-    if template in ("medium", "complex", "security"):
-        base_hierarchy["spec-root"]["children"].append("phase-2")
-        base_hierarchy["phase-1"]["dependencies"]["blocks"].append("phase-2")
-        base_hierarchy["phase-2"] = {
-            "type": "phase",
+    Returns:
+        Dict with phase structure including:
+        - title: Phase title
+        - description: Phase description
+        - purpose: Phase purpose for metadata
+        - estimated_hours: Total estimated hours
+        - tasks: List of task definitions (title, description, category, estimated_hours)
+        - includes_verification: Always True (verification auto-added)
+    """
+    templates: Dict[str, Dict[str, Any]] = {
+        "planning": {
+            "title": "Planning & Discovery",
+            "description": "Requirements gathering, analysis, and initial planning",
+            "purpose": "Define scope, requirements, and acceptance criteria",
+            "estimated_hours": 4,
+            "tasks": [
+                {
+                    "title": "Define requirements",
+                    "description": "Document functional and non-functional requirements",
+                    "task_category": "investigation",
+                    "acceptance_criteria": [
+                        "Requirements are documented and reviewed",
+                    ],
+                    "estimated_hours": 2,
+                },
+                {
+                    "title": "Design solution approach",
+                    "description": "Outline the technical approach and architecture decisions",
+                    "task_category": "investigation",
+                    "acceptance_criteria": [
+                        "Solution approach and key decisions are documented",
+                    ],
+                    "estimated_hours": 2,
+                },
+            ],
+        },
+        "implementation": {
             "title": "Implementation",
-            "status": "pending",
-            "parent": "spec-root",
-            "children": ["task-2-1"],
-            "total_tasks": 1,
-            "completed_tasks": 0,
-            "metadata": {
-                "purpose": "Core implementation work",
-                "estimated_hours": 8,
-            },
-            "dependencies": {
-                "blocks": [],
-                "blocked_by": ["phase-1"],
-                "depends": [],
-            },
-        }
-        base_hierarchy["task-2-1"] = {
-            "type": "task",
-            "title": "Implement core functionality",
-            "status": "pending",
-            "parent": "phase-2",
-            "children": [],
-            "total_tasks": 1,
-            "completed_tasks": 0,
-            "metadata": {
-                "details": "Implement the main features",
-                "category": category,
-                "estimated_hours": 4,
-            },
-            "dependencies": {
-                "blocks": [],
-                "blocked_by": [],
-                "depends": [],
-            },
-        }
-        # Add verification to phase-2
-        _add_phase_verification(base_hierarchy, 2, "phase-2")
-        base_hierarchy["spec-root"]["total_tasks"] = 6  # 2 tasks + 4 verify
-
-    # Security: add security review phase
-    if template == "security":
-        base_hierarchy["spec-root"]["children"].append("phase-3")
-        base_hierarchy["phase-2"]["dependencies"]["blocks"].append("phase-3")
-        base_hierarchy["phase-3"] = {
-            "type": "phase",
-            "title": "Security Review",
-            "status": "pending",
-            "parent": "spec-root",
-            "children": ["task-3-1"],
-            "total_tasks": 1,
-            "completed_tasks": 0,
-            "metadata": {
-                "purpose": "Security audit and hardening",
-                "estimated_hours": 4,
-            },
-            "dependencies": {
-                "blocks": [],
-                "blocked_by": ["phase-2"],
-                "depends": [],
-            },
-        }
-        base_hierarchy["task-3-1"] = {
-            "type": "task",
-            "title": "Security audit",
-            "status": "pending",
-            "parent": "phase-3",
-            "children": [],
-            "total_tasks": 1,
-            "completed_tasks": 0,
-            "metadata": {
-                "details": "Review for security vulnerabilities",
-                "category": "investigation",
-                "estimated_hours": 2,
-            },
-            "dependencies": {
-                "blocks": [],
-                "blocked_by": [],
-                "depends": [],
-            },
-        }
-        # Add verification to phase-3
-        _add_phase_verification(base_hierarchy, 3, "phase-3")
-        base_hierarchy["spec-root"]["total_tasks"] = 9  # 3 tasks + 6 verify
+            "description": "Core development and feature implementation",
+            "purpose": "Build the primary functionality",
+            "estimated_hours": 8,
+            "tasks": [
+                {
+                    "title": "Implement core functionality",
+                    "description": "Build the main features and business logic",
+                    "task_category": "investigation",
+                    "acceptance_criteria": [
+                        "Core functionality is implemented and verified",
+                    ],
+                    "estimated_hours": 6,
+                },
+                {
+                    "title": "Add error handling",
+                    "description": "Implement error handling and edge cases",
+                    "task_category": "investigation",
+                    "acceptance_criteria": [
+                        "Error handling covers expected edge cases",
+                    ],
+                    "estimated_hours": 2,
+                },
+            ],
+        },
+        "testing": {
+            "title": "Testing & Validation",
+            "description": "Comprehensive testing and quality assurance",
+            "purpose": "Ensure code quality and correctness",
+            "estimated_hours": 6,
+            "tasks": [
+                {
+                    "title": "Write unit tests",
+                    "description": "Create unit tests for individual components",
+                    "task_category": "investigation",
+                    "acceptance_criteria": [
+                        "Unit tests cover primary logic paths",
+                    ],
+                    "estimated_hours": 3,
+                },
+                {
+                    "title": "Write integration tests",
+                    "description": "Create integration tests for component interactions",
+                    "task_category": "investigation",
+                    "acceptance_criteria": [
+                        "Integration tests cover critical workflows",
+                    ],
+                    "estimated_hours": 3,
+                },
+            ],
+        },
+        "security": {
+            "title": "Security Review",
+            "description": "Security audit, vulnerability assessment, and hardening",
+            "purpose": "Identify and remediate security vulnerabilities",
+            "estimated_hours": 6,
+            "tasks": [
+                {
+                    "title": "Security audit",
+                    "description": "Review code for security vulnerabilities (OWASP Top 10)",
+                    "task_category": "investigation",
+                    "acceptance_criteria": [
+                        "Security findings are documented with severity",
+                    ],
+                    "estimated_hours": 3,
+                },
+                {
+                    "title": "Security remediation",
+                    "description": "Fix identified vulnerabilities and harden implementation",
+                    "task_category": "investigation",
+                    "acceptance_criteria": [
+                        "Security findings are addressed or tracked",
+                    ],
+                    "estimated_hours": 3,
+                },
+            ],
+        },
+        "documentation": {
+            "title": "Documentation",
+            "description": "Technical documentation and knowledge capture",
+            "purpose": "Document the implementation for maintainability",
+            "estimated_hours": 4,
+            "tasks": [
+                {
+                    "title": "Write API documentation",
+                    "description": "Document public APIs, parameters, and return values",
+                    "task_category": "research",
+                    "acceptance_criteria": [
+                        "API documentation is updated with current behavior",
+                    ],
+                    "estimated_hours": 2,
+                },
+                {
+                    "title": "Write user guide",
+                    "description": "Create usage examples and integration guide",
+                    "task_category": "research",
+                    "acceptance_criteria": [
+                        "User guide includes usage examples",
+                    ],
+                    "estimated_hours": 2,
+                },
+            ],
+        },
+    }
 
-    return base_hierarchy
+    if template not in templates:
+        raise ValueError(
+            f"Invalid phase template '{template}'. Must be one of: {', '.join(PHASE_TEMPLATES)}"
+        )
 
+    result = templates[template].copy()
+    result["includes_verification"] = True
+    result["template_name"] = template
+    return result
 
-def create_spec(
-    name: str,
-    template: str = "medium",
-    category: str = "implementation",
+
+def apply_phase_template(
+    spec_id: str,
+    template: str,
     specs_dir: Optional[Path] = None,
+    category: str = "implementation",
+    position: Optional[int] = None,
+    link_previous: bool = True,
 ) -> Tuple[Optional[Dict[str, Any]], Optional[str]]:
     """
-    Create a new specification file from a template.
+    Apply a phase template to an existing spec.
+
+    Creates a new phase with pre-configured tasks based on the template.
+    Automatically includes verification scaffolding (run-tests + fidelity).
 
     Args:
-        name: Human-readable name for the specification.
-        template: Template type (simple, medium, complex, security). Default: medium.
-        category: Default task category. Default: implementation.
+        spec_id: ID of the spec to add the phase to.
+        template: Phase template name (planning, implementation, testing, security, documentation).
         specs_dir: Path to specs directory (auto-detected if not provided).
+        category: Default task category for tasks (can be overridden by template).
+        position: Position to insert phase (None = append at end).
+        link_previous: Whether to link this phase to the previous one with dependencies.
 
     Returns:
         Tuple of (result_dict, error_message).
-        On success: ({"spec_id": ..., "spec_path": ..., ...}, None)
+        On success: ({"phase_id": ..., "tasks_created": [...], ...}, None)
         On failure: (None, "error message")
     """
     # Validate template
-    if template not in TEMPLATES:
+    if template not in PHASE_TEMPLATES:
         return (
             None,
-            f"Invalid template '{template}'. Must be one of: {', '.join(TEMPLATES)}",
+            f"Invalid phase template '{template}'. Must be one of: {', '.join(PHASE_TEMPLATES)}",
         )
 
-    # Validate category
-    if category not in CATEGORIES:
+    # Get template structure
+    template_struct = get_phase_template_structure(template, category)
+
+    # Build tasks list for add_phase_bulk
+    tasks = []
+    for task_def in template_struct["tasks"]:
+        tasks.append({
+            "type": "task",
+            "title": task_def["title"],
+            "description": task_def.get("description", ""),
+            "task_category": task_def.get("task_category", task_def.get("category", category)),
+            "acceptance_criteria": task_def.get("acceptance_criteria"),
+            "estimated_hours": task_def.get("estimated_hours", 1),
+        })
+
+    # Append verification scaffolding (run-tests + fidelity-review)
+    tasks.append({
+        "type": "verify",
+        "title": "Run tests",
+        "verification_type": "run-tests",
+    })
+    tasks.append({
+        "type": "verify",
+        "title": "Fidelity review",
+        "verification_type": "fidelity",
+    })
+
+    # Use add_phase_bulk to create the phase atomically
+    result, error = add_phase_bulk(
+        spec_id=spec_id,
+        phase_title=template_struct["title"],
+        tasks=tasks,
+        specs_dir=specs_dir,
+        phase_description=template_struct.get("description"),
+        phase_purpose=template_struct.get("purpose"),
+        phase_estimated_hours=template_struct.get("estimated_hours"),
+        position=position,
+        link_previous=link_previous,
+    )
+
+    if error:
+        return None, error
+
+    # Enhance result with template info
+    if result:
+        result["template_applied"] = template
+        result["template_title"] = template_struct["title"]
+
+    return result, None
+
+
+def generate_spec_data(
+    name: str,
+    template: str = "empty",
+    category: str = "implementation",
+    mission: Optional[str] = None,
+) -> Tuple[Optional[Dict[str, Any]], Optional[str]]:
+    """
+    Generate spec data structure without writing to disk.
+
+    Used for preflight validation (dry_run) and by create_spec.
+
+    Args:
+        name: Human-readable name for the specification.
+        template: Template type (only 'empty' is valid).
+        category: Default task category.
+        mission: Optional mission statement for the spec.
+
+    Returns:
+        Tuple of (spec_data, error_message).
+        On success: (dict, None)
+        On failure: (None, "error message")
+    """
+    # Validate template - only 'empty' is supported
+    if template not in TEMPLATES:
         return (
             None,
-            f"Invalid category '{category}'. Must be one of: {', '.join(CATEGORIES)}",
+            f"Invalid template '{template}'. Only 'empty' template is supported. "
+            f"Use phase templates to add structure.",
         )
 
-    # Find specs directory
-    if specs_dir is None:
-        specs_dir = find_specs_directory()
-
-    if specs_dir is None:
+    # Validate category
+    if category not in CATEGORIES:
         return (
             None,
-            "No specs directory found. Use specs_dir parameter or set SDD_SPECS_DIR.",
+            f"Invalid category '{category}'. Must be one of: {', '.join(CATEGORIES)}",
         )
 
-    # Ensure pending directory exists
-    pending_dir = specs_dir / "pending"
-    pending_dir.mkdir(parents=True, exist_ok=True)
-
     # Generate spec ID
     spec_id = generate_spec_id(name)
 
-    # Check if spec already exists
-    spec_path = pending_dir / f"{spec_id}.json"
-    if spec_path.exists():
-        return None, f"Specification already exists: {spec_id}"
-
     # Generate spec structure
     now = datetime.now(timezone.utc).isoformat().replace("+00:00", "Z")
     hierarchy = get_template_structure(template, category)
@@ -1219,24 +2817,77 @@ def create_spec(
         "last_updated": now,
         "metadata": {
             "description": "",
+            "mission": mission.strip() if isinstance(mission, str) else "",
             "objectives": [],
-            "complexity": "medium" if template in ("medium", "complex") else "low",
+            "complexity": "low",  # Complexity set via explicit metadata, not template
             "estimated_hours": estimated_hours,
             "assumptions": [],
-            "status": "pending",
             "owner": "",
-            "progress_percentage": 0,
-            "current_phase": "phase-1",
             "category": category,
             "template": template,
         },
         "progress_percentage": 0,
         "status": "pending",
-        "current_phase": "phase-1",
+        "current_phase": None,  # Empty template has no phases
         "hierarchy": hierarchy,
         "journal": [],
     }
 
+    return spec_data, None
+
+
+def create_spec(
+    name: str,
+    template: str = "empty",
+    category: str = "implementation",
+    mission: Optional[str] = None,
+    specs_dir: Optional[Path] = None,
+) -> Tuple[Optional[Dict[str, Any]], Optional[str]]:
+    """
+    Create a new specification file from a template.
+
+    Args:
+        name: Human-readable name for the specification.
+        template: Template type (only 'empty' is valid). Use phase templates to add structure.
+        category: Default task category. Default: implementation.
+        mission: Optional mission statement for the spec.
+        specs_dir: Path to specs directory (auto-detected if not provided).
+
+    Returns:
+        Tuple of (result_dict, error_message).
+        On success: ({"spec_id": ..., "spec_path": ..., ...}, None)
+        On failure: (None, "error message")
+    """
+    # Generate spec data (handles validation)
+    spec_data, error = generate_spec_data(
+        name=name,
+        template=template,
+        category=category,
+        mission=mission,
+    )
+    if error or spec_data is None:
+        return None, error or "Failed to generate spec data"
+
+    # Find specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
+
+    if specs_dir is None:
+        return (
+            None,
+            "No specs directory found. Use specs_dir parameter or set SDD_SPECS_DIR.",
+        )
+
+    # Ensure pending directory exists
+    pending_dir = specs_dir / "pending"
+    pending_dir.mkdir(parents=True, exist_ok=True)
+
+    # Check if spec already exists
+    spec_id = spec_data["spec_id"]
+    spec_path = pending_dir / f"{spec_id}.json"
+    if spec_path.exists():
+        return None, f"Specification already exists: {spec_id}"
+
     # Write the spec file
     try:
         with open(spec_path, "w") as f:
@@ -1245,6 +2896,7 @@ def create_spec(
         return None, f"Failed to write spec file: {e}"
 
     # Count tasks and phases
+    hierarchy = spec_data["hierarchy"]
     task_count = sum(
         1
         for node in hierarchy.values()
@@ -1543,6 +3195,7 @@ def list_assumptions(
 FRONTMATTER_KEYS = (
     "title",
     "description",
+    "mission",
     "objectives",
     "complexity",
     "estimated_hours",
@@ -1618,20 +3271,27 @@ def update_frontmatter(
     if "metadata" not in spec_data:
         spec_data["metadata"] = {}
 
-    # Get previous value for result
-    previous_value = spec_data["metadata"].get(key)
+    # Get previous value for result (check appropriate location)
+    if key in ("status", "progress_percentage", "current_phase"):
+        previous_value = spec_data.get(key)
+    else:
+        previous_value = spec_data["metadata"].get(key)
 
     # Process value based on type
     if isinstance(value, str):
         value = value.strip() if value else value
 
-    # Update the metadata field
-    spec_data["metadata"][key] = value
-
-    # Also update top-level fields if they exist (for backward compatibility)
-    # Some fields like title, status, progress_percentage exist at both levels
-    if key in ("title", "status", "progress_percentage", "current_phase"):
+    # Computed fields (status, progress_percentage, current_phase) are now
+    # stored only at top-level. Title is kept in metadata for descriptive purposes.
+    if key in ("status", "progress_percentage", "current_phase"):
+        # Update top-level only (canonical location for computed fields)
         spec_data[key] = value
+    else:
+        # Regular metadata field
+        spec_data["metadata"][key] = value
+        # Also sync title to top-level if updating it
+        if key == "title":
+            spec_data[key] = value
 
     # Update last_updated
     now = datetime.now(timezone.utc).isoformat().replace("+00:00", "Z")
@@ -1648,3 +3308,546 @@ def update_frontmatter(
         "value": value,
         "previous_value": previous_value,
     }, None
+
+
+# Safety constraints for find/replace operations
+_FR_MAX_PATTERN_LENGTH = 256
+_FR_DEFAULT_MAX_REPLACEMENTS = 1000
+_FR_VALID_SCOPES = {"all", "titles", "descriptions"}
+_FR_MAX_SAMPLE_DIFFS = 10
+
+
+def find_replace_in_spec(
+    spec_id: str,
+    find: str,
+    replace: str,
+    *,
+    scope: str = "all",
+    use_regex: bool = False,
+    case_sensitive: bool = True,
+    dry_run: bool = False,
+    max_replacements: int = _FR_DEFAULT_MAX_REPLACEMENTS,
+    specs_dir: Optional[Path] = None,
+) -> Tuple[Optional[Dict[str, Any]], Optional[str]]:
+    """
+    Find and replace text across spec hierarchy nodes.
+
+    Performs literal or regex find/replace across titles and/or descriptions
+    in a specification's hierarchy nodes.
+
+    Args:
+        spec_id: Specification ID to modify.
+        find: Text or regex pattern to find.
+        replace: Replacement text (supports backreferences if use_regex=True).
+        scope: Where to search - "all", "titles", or "descriptions".
+        use_regex: If True, treat `find` as a regex pattern.
+        case_sensitive: If False, perform case-insensitive matching.
+        dry_run: If True, preview changes without modifying the spec.
+        max_replacements: Maximum number of replacements (safety limit).
+        specs_dir: Path to specs directory (auto-detected if not provided).
+
+    Returns:
+        Tuple of (result_dict, error_message).
+        On success: ({"spec_id": ..., "total_replacements": ..., ...}, None)
+        On failure: (None, "error message")
+    """
+    # Validate find pattern
+    if not find or not isinstance(find, str):
+        return None, "find must be a non-empty string"
+    # Don't strip the pattern - use exactly what user provides (whitespace may be intentional)
+    if not find.strip():
+        return None, "find must be a non-empty string"
+    if len(find) > _FR_MAX_PATTERN_LENGTH:
+        return None, f"find pattern exceeds maximum length of {_FR_MAX_PATTERN_LENGTH} characters"
+
+    # Validate replace
+    if replace is None:
+        return None, "replace must be provided (use empty string to delete matches)"
+    if not isinstance(replace, str):
+        return None, "replace must be a string"
+
+    # Validate scope
+    if scope not in _FR_VALID_SCOPES:
+        return None, f"scope must be one of: {sorted(_FR_VALID_SCOPES)}"
+
+    # Validate max_replacements
+    if not isinstance(max_replacements, int) or max_replacements <= 0:
+        return None, "max_replacements must be a positive integer"
+
+    # Compile regex if needed
+    compiled_pattern = None
+    if use_regex:
+        try:
+            flags = 0 if case_sensitive else re.IGNORECASE
+            compiled_pattern = re.compile(find, flags)
+        except re.error as e:
+            return None, f"Invalid regex pattern: {e}"
+    else:
+        # For literal search, prepare flags
+        if not case_sensitive:
+            # Create case-insensitive literal pattern
+            compiled_pattern = re.compile(re.escape(find), re.IGNORECASE)
+
+    # Find specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
+    if specs_dir is None:
+        return None, "No specs directory found"
+
+    # Load spec
+    spec_path = find_spec_file(spec_id, specs_dir)
+    if not spec_path:
+        return None, f"Specification '{spec_id}' not found"
+    spec_data = load_spec(spec_id, specs_dir)
+    if not spec_data:
+        return None, f"Failed to load specification '{spec_id}'"
+
+    hierarchy = spec_data.get("hierarchy", {})
+    if not hierarchy:
+        return {
+            "spec_id": spec_id,
+            "total_replacements": 0,
+            "nodes_affected": 0,
+            "changes": [],
+            "dry_run": dry_run,
+            "message": "No hierarchy nodes to process",
+        }, None
+
+    # Track changes
+    changes: List[Dict[str, Any]] = []
+    total_replacements = 0
+    nodes_affected = set()
+    warnings: List[str] = []
+    limit_reached = False
+
+    # Helper to perform replacement
+    def do_replace(text: str) -> Tuple[str, int]:
+        if compiled_pattern:
+            new_text, count = compiled_pattern.subn(replace, text)
+            return new_text, count
+        else:
+            # Case-sensitive literal replace
+            count = text.count(find)
+            new_text = text.replace(find, replace)
+            return new_text, count
+
+    # Process hierarchy nodes
+    for node_id, node_data in hierarchy.items():
+        if node_id == "spec-root":
+            continue
+        if limit_reached:
+            break
+
+        # Process title if in scope
+        if scope in ("all", "titles"):
+            title = node_data.get("title", "")
+            if title and isinstance(title, str):
+                new_title, count = do_replace(title)
+                if count > 0:
+                    if total_replacements + count > max_replacements:
+                        count = max_replacements - total_replacements
+                        # Partial replacement not supported, skip this field
+                        warnings.append(
+                            f"max_replacements limit ({max_replacements}) reached"
+                        )
+                        limit_reached = True
+                    else:
+                        total_replacements += count
+                        nodes_affected.add(node_id)
+                        changes.append({
+                            "node_id": node_id,
+                            "field": "title",
+                            "old": title,
+                            "new": new_title,
+                            "replacement_count": count,
+                        })
+                        if not dry_run:
+                            node_data["title"] = new_title
+
+        # Process description if in scope
+        if scope in ("all", "descriptions") and not limit_reached:
+            metadata = node_data.get("metadata", {})
+            if isinstance(metadata, dict):
+                description = metadata.get("description", "")
+                if description and isinstance(description, str):
+                    new_description, count = do_replace(description)
+                    if count > 0:
+                        if total_replacements + count > max_replacements:
+                            warnings.append(
+                                f"max_replacements limit ({max_replacements}) reached"
+                            )
+                            limit_reached = True
+                        else:
+                            total_replacements += count
+                            nodes_affected.add(node_id)
+                            changes.append({
+                                "node_id": node_id,
+                                "field": "description",
+                                "old": description,
+                                "new": new_description,
+                                "replacement_count": count,
+                            })
+                            if not dry_run:
+                                metadata["description"] = new_description
+
+    # Save if not dry_run and there were changes
+    if not dry_run and total_replacements > 0:
+        if not save_spec(spec_id, spec_data, specs_dir):
+            return None, "Failed to save specification after replacements"
+
+    # Build result
+    result: Dict[str, Any] = {
+        "spec_id": spec_id,
+        "total_replacements": total_replacements,
+        "nodes_affected": len(nodes_affected),
+        "dry_run": dry_run,
+        "scope": scope,
+        "find": find,
+        "replace": replace,
+        "use_regex": use_regex,
+        "case_sensitive": case_sensitive,
+    }
+
+    # Include sample diffs (limited)
+    if changes:
+        result["changes"] = changes[:_FR_MAX_SAMPLE_DIFFS]
+        if len(changes) > _FR_MAX_SAMPLE_DIFFS:
+            result["changes_truncated"] = True
+            result["total_changes"] = len(changes)
+
+    if warnings:
+        result["warnings"] = warnings
+
+    if total_replacements == 0:
+        result["message"] = "No matches found"
+
+    return result, None
+
+
+# Completeness check constants
+_CC_WEIGHT_TITLES = 0.20
+_CC_WEIGHT_DESCRIPTIONS = 0.30
+_CC_WEIGHT_FILE_PATHS = 0.25
+_CC_WEIGHT_ESTIMATES = 0.25
+
+
+def check_spec_completeness(
+    spec_id: str,
+    *,
+    specs_dir: Optional[Path] = None,
+) -> Tuple[Optional[Dict[str, Any]], Optional[str]]:
+    """
+    Check spec completeness and calculate a score (0-100).
+
+    Evaluates spec quality by checking for:
+    - Empty titles
+    - Missing task descriptions
+    - Missing file_path for implementation/refactoring tasks
+    - Missing estimated_hours
+
+    Args:
+        spec_id: Specification ID to check.
+        specs_dir: Path to specs directory (auto-detected if not provided).
+
+    Returns:
+        Tuple of (result_dict, error_message).
+        On success: ({"spec_id": ..., "completeness_score": ..., ...}, None)
+        On failure: (None, "error message")
+    """
+    # Find specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
+    if specs_dir is None:
+        return None, "No specs directory found"
+
+    # Load spec
+    spec_path = find_spec_file(spec_id, specs_dir)
+    if not spec_path:
+        return None, f"Specification '{spec_id}' not found"
+    spec_data = load_spec(spec_id, specs_dir)
+    if not spec_data:
+        return None, f"Failed to load specification '{spec_id}'"
+
+    hierarchy = spec_data.get("hierarchy", {})
+    if not hierarchy:
+        return {
+            "spec_id": spec_id,
+            "completeness_score": 100,
+            "categories": {},
+            "issues": [],
+            "message": "No hierarchy nodes to check",
+        }, None
+
+    # Helper functions
+    def _nonempty_string(value: Any) -> bool:
+        return isinstance(value, str) and bool(value.strip())
+
+    def _has_description(metadata: Dict[str, Any]) -> bool:
+        if _nonempty_string(metadata.get("description")):
+            return True
+        details = metadata.get("details")
+        if _nonempty_string(details):
+            return True
+        if isinstance(details, list):
+            return any(_nonempty_string(item) for item in details)
+        return False
+
+    # Tracking
+    issues: List[Dict[str, Any]] = []
+    categories: Dict[str, Dict[str, Any]] = {
+        "titles": {"complete": 0, "total": 0, "score": 0.0},
+        "descriptions": {"complete": 0, "total": 0, "score": 0.0},
+        "file_paths": {"complete": 0, "total": 0, "score": 0.0},
+        "estimates": {"complete": 0, "total": 0, "score": 0.0},
+    }
+
+    # Check each node
+    for node_id, node in hierarchy.items():
+        if node_id == "spec-root":
+            continue
+        if not isinstance(node, dict):
+            continue
+
+        node_type = node.get("type", "")
+        title = node.get("title", "")
+        metadata = node.get("metadata", {})
+        if not isinstance(metadata, dict):
+            metadata = {}
+
+        # Check title (all nodes)
+        categories["titles"]["total"] += 1
+        if _nonempty_string(title):
+            categories["titles"]["complete"] += 1
+        else:
+            issues.append({
+                "node_id": node_id,
+                "category": "titles",
+                "message": "Empty or missing title",
+            })
+
+        # Check description (tasks and verify nodes only)
+        if node_type in ("task", "verify"):
+            categories["descriptions"]["total"] += 1
+            if _has_description(metadata):
+                categories["descriptions"]["complete"] += 1
+            else:
+                issues.append({
+                    "node_id": node_id,
+                    "category": "descriptions",
+                    "message": "Missing description",
+                })
+
+            # Check file_path (implementation/refactoring tasks only)
+            task_category = metadata.get("task_category", "")
+            if task_category in ("implementation", "refactoring"):
+                categories["file_paths"]["total"] += 1
+                if _nonempty_string(metadata.get("file_path")):
+                    categories["file_paths"]["complete"] += 1
+                else:
+                    issues.append({
+                        "node_id": node_id,
+                        "category": "file_paths",
+                        "message": "Missing file_path for implementation task",
+                    })
+
+            # Check estimated_hours (tasks only)
+            if node_type == "task":
+                categories["estimates"]["total"] += 1
+                est = metadata.get("estimated_hours")
+                if isinstance(est, (int, float)) and est > 0:
+                    categories["estimates"]["complete"] += 1
+                else:
+                    issues.append({
+                        "node_id": node_id,
+                        "category": "estimates",
+                        "message": "Missing or invalid estimated_hours",
+                    })
+
+    # Calculate category scores
+    for cat_data in categories.values():
+        if cat_data["total"] > 0:
+            cat_data["score"] = round(cat_data["complete"] / cat_data["total"], 2)
+        else:
+            cat_data["score"] = 1.0  # No items to check = complete
+
+    # Calculate weighted completeness score
+    weighted_score = 0.0
+    total_weight = 0.0
+
+    if categories["titles"]["total"] > 0:
+        weighted_score += categories["titles"]["score"] * _CC_WEIGHT_TITLES
+        total_weight += _CC_WEIGHT_TITLES
+
+    if categories["descriptions"]["total"] > 0:
+        weighted_score += categories["descriptions"]["score"] * _CC_WEIGHT_DESCRIPTIONS
+        total_weight += _CC_WEIGHT_DESCRIPTIONS
+
+    if categories["file_paths"]["total"] > 0:
+        weighted_score += categories["file_paths"]["score"] * _CC_WEIGHT_FILE_PATHS
+        total_weight += _CC_WEIGHT_FILE_PATHS
+
+    if categories["estimates"]["total"] > 0:
+        weighted_score += categories["estimates"]["score"] * _CC_WEIGHT_ESTIMATES
+        total_weight += _CC_WEIGHT_ESTIMATES
+
+    # Normalize score
+    if total_weight > 0:
+        completeness_score = int(round((weighted_score / total_weight) * 100))
+    else:
+        completeness_score = 100  # Nothing to check
+
+    return {
+        "spec_id": spec_id,
+        "completeness_score": completeness_score,
+        "categories": categories,
+        "issues": issues,
+        "issue_count": len(issues),
+    }, None
+
+
+# Duplicate detection constants
+_DD_DEFAULT_THRESHOLD = 0.8
+_DD_MAX_PAIRS = 100
+_DD_VALID_SCOPES = {"titles", "descriptions", "both"}
+
+
+def detect_duplicate_tasks(
+    spec_id: str,
+    *,
+    scope: str = "titles",
+    threshold: float = _DD_DEFAULT_THRESHOLD,
+    max_pairs: int = _DD_MAX_PAIRS,
+    specs_dir: Optional[Path] = None,
+) -> Tuple[Optional[Dict[str, Any]], Optional[str]]:
+    """
+    Detect duplicate or near-duplicate tasks in a spec.
+
+    Uses text similarity to find tasks with similar titles or descriptions.
+
+    Args:
+        spec_id: Specification ID to check.
+        scope: What to compare - "titles", "descriptions", or "both".
+        threshold: Similarity threshold (0.0-1.0). Default 0.8.
+        max_pairs: Maximum duplicate pairs to return. Default 100.
+        specs_dir: Path to specs directory (auto-detected if not provided).
+
+    Returns:
+        Tuple of (result_dict, error_message).
+        On success: ({"spec_id": ..., "duplicates": [...], ...}, None)
+        On failure: (None, "error message")
+    """
+    from difflib import SequenceMatcher
+
+    # Validate scope
+    if scope not in _DD_VALID_SCOPES:
+        return None, f"scope must be one of: {sorted(_DD_VALID_SCOPES)}"
+
+    # Validate threshold
+    if not isinstance(threshold, (int, float)) or not 0.0 <= threshold <= 1.0:
+        return None, "threshold must be a number between 0.0 and 1.0"
+
+    # Validate max_pairs
+    if not isinstance(max_pairs, int) or max_pairs <= 0:
+        return None, "max_pairs must be a positive integer"
+
+    # Find specs directory
+    if specs_dir is None:
+        specs_dir = find_specs_directory()
+    if specs_dir is None:
+        return None, "No specs directory found"
+
+    # Load spec
+    spec_path = find_spec_file(spec_id, specs_dir)
+    if not spec_path:
+        return None, f"Specification '{spec_id}' not found"
+    spec_data = load_spec(spec_id, specs_dir)
+    if not spec_data:
+        return None, f"Failed to load specification '{spec_id}'"
+
+    hierarchy = spec_data.get("hierarchy", {})
+    if not hierarchy:
+        return {
+            "spec_id": spec_id,
+            "duplicates": [],
+            "duplicate_count": 0,
+            "scope": scope,
+            "threshold": threshold,
+            "message": "No hierarchy nodes to check",
+        }, None
+
+    # Collect tasks/verify nodes with their text
+    nodes: List[Dict[str, Any]] = []
+    for node_id, node in hierarchy.items():
+        if node_id == "spec-root":
+            continue
+        if not isinstance(node, dict):
+            continue
+        node_type = node.get("type", "")
+        if node_type not in ("task", "verify"):
+            continue
+
+        title = node.get("title", "") or ""
+        metadata = node.get("metadata", {})
+        if not isinstance(metadata, dict):
+            metadata = {}
+        description = metadata.get("description", "") or ""
+
+        nodes.append({
+            "id": node_id,
+            "title": title.strip().lower(),
+            "description": description.strip().lower(),
+        })
+
+    # Compare pairs
+    duplicates: List[Dict[str, Any]] = []
+    truncated = False
+    total_compared = 0
+
+    def similarity(a: str, b: str) -> float:
+        if not a or not b:
+            return 0.0
+        return SequenceMatcher(None, a, b).ratio()
+
+    for i, node_a in enumerate(nodes):
+        if len(duplicates) >= max_pairs:
+            truncated = True
+            break
+        for node_b in nodes[i + 1:]:
+            total_compared += 1
+            if len(duplicates) >= max_pairs:
+                truncated = True
+                break
+
+            # Calculate similarity based on scope
+            if scope == "titles":
+                sim = similarity(node_a["title"], node_b["title"])
+            elif scope == "descriptions":
+                sim = similarity(node_a["description"], node_b["description"])
+            else:  # both
+                title_sim = similarity(node_a["title"], node_b["title"])
+                desc_sim = similarity(node_a["description"], node_b["description"])
+                sim = max(title_sim, desc_sim)
+
+            if sim >= threshold:
+                duplicates.append({
+                    "node_a": node_a["id"],
+                    "node_b": node_b["id"],
+                    "similarity": round(sim, 2),
+                    "scope": scope,
+                })
+
+    result: Dict[str, Any] = {
+        "spec_id": spec_id,
+        "duplicates": duplicates,
+        "duplicate_count": len(duplicates),
+        "scope": scope,
+        "threshold": threshold,
+        "nodes_checked": len(nodes),
+        "pairs_compared": total_compared,
+    }
+
+    if truncated:
+        result["truncated"] = True
+        result["warnings"] = [f"Results limited to {max_pairs} pairs"]
+
+    return result, None