diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index ff2364d29..9bcf11b75 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -2405,6 +2405,89 @@ def preset_set_priority(
     console.print("\n[dim]Lower priority = higher precedence in template resolution[/dim]")
 
 
+@preset_app.command("enable")
+def preset_enable(
+    pack_id: str = typer.Argument(help="Preset ID to enable"),
+):
+    """Enable a disabled preset."""
+    from .presets import PresetManager
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    manager = PresetManager(project_root)
+
+    # Check if preset is installed
+    if not manager.registry.is_installed(pack_id):
+        console.print(f"[red]Error:[/red] Preset '{pack_id}' is not installed")
+        raise typer.Exit(1)
+
+    # Get current metadata
+    metadata = manager.registry.get(pack_id)
+    if metadata is None or not isinstance(metadata, dict):
+        console.print(f"[red]Error:[/red] Preset '{pack_id}' not found in registry (corrupted state)")
+        raise typer.Exit(1)
+
+    if metadata.get("enabled", True):
+        console.print(f"[yellow]Preset '{pack_id}' is already enabled[/yellow]")
+        raise typer.Exit(0)
+
+    # Enable the preset
+    manager.registry.update(pack_id, {"enabled": True})
+
+    console.print(f"[green]✓[/green] Preset '{pack_id}' enabled")
+    console.print("\nTemplates from this preset will now be included in resolution.")
+    console.print("[dim]Note: Previously registered commands/skills remain active.[/dim]")
+
+
+@preset_app.command("disable")
+def preset_disable(
+    pack_id: str = typer.Argument(help="Preset ID to disable"),
+):
+    """Disable a preset without removing it."""
+    from .presets import PresetManager
+
+    project_root = Path.cwd()
+
+    # Check if we're in a spec-kit project
+    specify_dir = project_root / ".specify"
+    if not specify_dir.exists():
+        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
+        console.print("Run this command from a spec-kit project root")
+        raise typer.Exit(1)
+
+    manager = PresetManager(project_root)
+
+    # Check if preset is installed
+    if not manager.registry.is_installed(pack_id):
+        console.print(f"[red]Error:[/red] Preset '{pack_id}' is not installed")
+        raise typer.Exit(1)
+
+    # Get current metadata
+    metadata = manager.registry.get(pack_id)
+    if metadata is None or not isinstance(metadata, dict):
+        console.print(f"[red]Error:[/red] Preset '{pack_id}' not found in registry (corrupted state)")
+        raise typer.Exit(1)
+
+    if not metadata.get("enabled", True):
+        console.print(f"[yellow]Preset '{pack_id}' is already disabled[/yellow]")
+        raise typer.Exit(0)
+
+    # Disable the preset
+    manager.registry.update(pack_id, {"enabled": False})
+
+    console.print(f"[green]✓[/green] Preset '{pack_id}' disabled")
+    console.print("\nTemplates from this preset will be skipped during resolution.")
+    console.print("[dim]Note: Previously registered commands/skills remain active until preset removal.[/dim]")
+    console.print(f"To re-enable: specify preset enable {pack_id}")
+
+
 # ===== Preset Catalog Commands =====
 
 
@@ -3841,8 +3924,7 @@ def extension_enable(
         console.print(f"[yellow]Extension '{display_name}' is already enabled[/yellow]")
         raise typer.Exit(0)
 
-    metadata["enabled"] = True
-    manager.registry.update(extension_id, metadata)
+    manager.registry.update(extension_id, {"enabled": True})
 
     # Enable hooks in extensions.yml
     config = hook_executor.get_project_config()
@@ -3889,8 +3971,7 @@ def extension_disable(
         console.print(f"[yellow]Extension '{display_name}' is already disabled[/yellow]")
         raise typer.Exit(0)
 
-    metadata["enabled"] = False
-    manager.registry.update(extension_id, metadata)
+    manager.registry.update(extension_id, {"enabled": False})
 
     # Disable hooks in extensions.yml
     config = hook_executor.get_project_config()
diff --git a/src/specify_cli/extensions.py b/src/specify_cli/extensions.py
index 984ca83d6..0dca39a0c 100644
--- a/src/specify_cli/extensions.py
+++ b/src/specify_cli/extensions.py
@@ -222,7 +222,17 @@ def _load(self) -> dict:
 
         try:
             with open(self.registry_path, 'r') as f:
-                return json.load(f)
+                data = json.load(f)
+            # Validate loaded data is a dict (handles corrupted registry files)
+            if not isinstance(data, dict):
+                return {
+                    "schema_version": self.SCHEMA_VERSION,
+                    "extensions": {}
+                }
+            # Normalize extensions field (handles corrupted extensions value)
+            if not isinstance(data.get("extensions"), dict):
+                data["extensions"] = {}
+            return data
         except (json.JSONDecodeError, FileNotFoundError):
             # Corrupted or missing registry, start fresh
             return {
@@ -244,7 +254,7 @@ def add(self, extension_id: str, metadata: dict):
             metadata: Extension metadata (version, source, etc.)
         """
         self.data["extensions"][extension_id] = {
-            **metadata,
+            **copy.deepcopy(metadata),
             "installed_at": datetime.now(timezone.utc).isoformat()
         }
         self._save()
@@ -267,15 +277,16 @@ def update(self, extension_id: str, metadata: dict):
         Raises:
             KeyError: If extension is not installed
         """
-        if extension_id not in self.data["extensions"]:
+        extensions = self.data.get("extensions")
+        if not isinstance(extensions, dict) or extension_id not in extensions:
             raise KeyError(f"Extension '{extension_id}' is not installed")
         # Merge new metadata with existing, preserving original installed_at
-        existing = self.data["extensions"][extension_id]
+        existing = extensions[extension_id]
         # Handle corrupted registry entries (e.g., string/list instead of dict)
         if not isinstance(existing, dict):
             existing = {}
-        # Merge: existing fields preserved, new fields override
-        merged = {**existing, **metadata}
+        # Merge: existing fields preserved, new fields override (deep copy to prevent caller mutation)
+        merged = {**existing, **copy.deepcopy(metadata)}
         # Always preserve original installed_at based on key existence, not truthiness,
         # to handle cases where the field exists but may be falsy (legacy/corruption)
         if "installed_at" in existing:
@@ -283,7 +294,7 @@ def update(self, extension_id: str, metadata: dict):
         else:
             # If not present in existing, explicitly remove from merged if caller provided it
             merged.pop("installed_at", None)
-        self.data["extensions"][extension_id] = merged
+        extensions[extension_id] = merged
         self._save()
 
     def restore(self, extension_id: str, metadata: dict):
@@ -296,8 +307,16 @@ def restore(self, extension_id: str, metadata: dict):
         Args:
             extension_id: Extension ID
             metadata: Complete extension metadata including installed_at
+
+        Raises:
+            ValueError: If metadata is None or not a dict
         """
-        self.data["extensions"][extension_id] = dict(metadata)
+        if metadata is None or not isinstance(metadata, dict):
+            raise ValueError(f"Cannot restore '{extension_id}': metadata must be a dict")
+        # Ensure extensions dict exists (handle corrupted registry)
+        if not isinstance(self.data.get("extensions"), dict):
+            self.data["extensions"] = {}
+        self.data["extensions"][extension_id] = copy.deepcopy(metadata)
         self._save()
 
     def remove(self, extension_id: str):
@@ -306,8 +325,11 @@ def remove(self, extension_id: str):
         Args:
             extension_id: Extension ID
         """
-        if extension_id in self.data["extensions"]:
-            del self.data["extensions"][extension_id]
+        extensions = self.data.get("extensions")
+        if not isinstance(extensions, dict):
+            return
+        if extension_id in extensions:
+            del extensions[extension_id]
             self._save()
 
     def get(self, extension_id: str) -> Optional[dict]:
@@ -320,21 +342,49 @@ def get(self, extension_id: str) -> Optional[dict]:
             extension_id: Extension ID
 
         Returns:
-            Deep copy of extension metadata, or None if not found
+            Deep copy of extension metadata, or None if not found or corrupted
         """
-        entry = self.data["extensions"].get(extension_id)
-        return copy.deepcopy(entry) if entry is not None else None
+        extensions = self.data.get("extensions")
+        if not isinstance(extensions, dict):
+            return None
+        entry = extensions.get(extension_id)
+        # Return None for missing or corrupted (non-dict) entries
+        if entry is None or not isinstance(entry, dict):
+            return None
+        return copy.deepcopy(entry)
 
     def list(self) -> Dict[str, dict]:
-        """Get all installed extensions.
+        """Get all installed extensions with valid metadata.
+
+        Returns a deep copy of extensions with dict metadata only.
+        Corrupted entries (non-dict values) are filtered out.
+
+        Returns:
+            Dictionary of extension_id -> metadata (deep copies), empty dict if corrupted
+        """
+        extensions = self.data.get("extensions", {}) or {}
+        if not isinstance(extensions, dict):
+            return {}
+        # Filter to only valid dict entries to match type contract
+        return {
+            ext_id: copy.deepcopy(meta)
+            for ext_id, meta in extensions.items()
+            if isinstance(meta, dict)
+        }
+
+    def keys(self) -> set:
+        """Get all extension IDs including corrupted entries.
 
-        Returns a deep copy of the extensions mapping to prevent callers
-        from accidentally mutating nested internal registry state.
+        Lightweight method that returns IDs without deep-copying metadata.
+        Use this when you only need to check which extensions are tracked.
 
         Returns:
-            Dictionary of extension_id -> metadata (deep copies)
+            Set of extension IDs (includes corrupted entries)
         """
-        return copy.deepcopy(self.data["extensions"])
+        extensions = self.data.get("extensions", {}) or {}
+        if not isinstance(extensions, dict):
+            return set()
+        return set(extensions.keys())
 
     def is_installed(self, extension_id: str) -> bool:
         """Check if extension is installed.
@@ -343,17 +393,23 @@ def is_installed(self, extension_id: str) -> bool:
             extension_id: Extension ID
 
         Returns:
-            True if extension is installed
+            True if extension is installed, False if not or registry corrupted
         """
-        return extension_id in self.data["extensions"]
+        extensions = self.data.get("extensions")
+        if not isinstance(extensions, dict):
+            return False
+        return extension_id in extensions
 
-    def list_by_priority(self) -> List[tuple]:
+    def list_by_priority(self, include_disabled: bool = False) -> List[tuple]:
         """Get all installed extensions sorted by priority.
 
         Lower priority number = higher precedence (checked first).
         Extensions with equal priority are sorted alphabetically by ID
         for deterministic ordering.
 
+        Args:
+            include_disabled: If True, include disabled extensions. Default False.
+
         Returns:
             List of (extension_id, metadata_copy) tuples sorted by priority.
             Metadata is deep-copied to prevent accidental mutation.
@@ -365,6 +421,9 @@ def list_by_priority(self) -> List[tuple]:
         for ext_id, meta in extensions.items():
             if not isinstance(meta, dict):
                 continue
+            # Skip disabled extensions unless explicitly requested
+            if not include_disabled and not meta.get("enabled", True):
+                continue
             metadata_copy = copy.deepcopy(meta)
             metadata_copy["priority"] = normalize_priority(metadata_copy.get("priority", 10))
             sortable_extensions.append((ext_id, metadata_copy))
@@ -633,7 +692,7 @@ def remove(self, extension_id: str, keep_config: bool = False) -> bool:
 
         # Get registered commands before removal
         metadata = self.registry.get(extension_id)
-        registered_commands = metadata.get("registered_commands", {})
+        registered_commands = metadata.get("registered_commands", {}) if metadata else {}
 
         extension_dir = self.extensions_dir / extension_id
 
diff --git a/src/specify_cli/presets.py b/src/specify_cli/presets.py
index 121d59617..aaa6e52e5 100644
--- a/src/specify_cli/presets.py
+++ b/src/specify_cli/presets.py
@@ -238,7 +238,17 @@ def _load(self) -> dict:
 
         try:
             with open(self.registry_path, 'r') as f:
-                return json.load(f)
+                data = json.load(f)
+            # Validate loaded data is a dict (handles corrupted registry files)
+            if not isinstance(data, dict):
+                return {
+                    "schema_version": self.SCHEMA_VERSION,
+                    "presets": {}
+                }
+            # Normalize presets field (handles corrupted presets value)
+            if not isinstance(data.get("presets"), dict):
+                data["presets"] = {}
+            return data
         except (json.JSONDecodeError, FileNotFoundError):
             return {
                 "schema_version": self.SCHEMA_VERSION,
@@ -259,7 +269,7 @@ def add(self, pack_id: str, metadata: dict):
             metadata: Pack metadata (version, source, etc.)
         """
         self.data["presets"][pack_id] = {
-            **metadata,
+            **copy.deepcopy(metadata),
             "installed_at": datetime.now(timezone.utc).isoformat()
         }
         self._save()
@@ -270,8 +280,11 @@ def remove(self, pack_id: str):
         Args:
             pack_id: Preset ID
         """
-        if pack_id in self.data["presets"]:
-            del self.data["presets"][pack_id]
+        packs = self.data.get("presets")
+        if not isinstance(packs, dict):
+            return
+        if pack_id in packs:
+            del packs[pack_id]
             self._save()
 
     def update(self, pack_id: str, updates: dict):
@@ -288,14 +301,15 @@ def update(self, pack_id: str, updates: dict):
         Raises:
             KeyError: If preset is not installed
         """
-        if pack_id not in self.data["presets"]:
+        packs = self.data.get("presets")
+        if not isinstance(packs, dict) or pack_id not in packs:
             raise KeyError(f"Preset '{pack_id}' not found in registry")
-        existing = self.data["presets"][pack_id]
+        existing = packs[pack_id]
         # Handle corrupted registry entries (e.g., string/list instead of dict)
         if not isinstance(existing, dict):
             existing = {}
-        # Merge: existing fields preserved, new fields override
-        merged = {**existing, **updates}
+        # Merge: existing fields preserved, new fields override (deep copy to prevent caller mutation)
+        merged = {**existing, **copy.deepcopy(updates)}
         # Always preserve original installed_at based on key existence, not truthiness,
         # to handle cases where the field exists but may be falsy (legacy/corruption)
         if "installed_at" in existing:
@@ -303,35 +317,95 @@ def update(self, pack_id: str, updates: dict):
         else:
             # If not present in existing, explicitly remove from merged if caller provided it
             merged.pop("installed_at", None)
-        self.data["presets"][pack_id] = merged
+        packs[pack_id] = merged
+        self._save()
+
+    def restore(self, pack_id: str, metadata: dict):
+        """Restore preset metadata to registry without modifying timestamps.
+
+        Use this method for rollback scenarios where you have a complete backup
+        of the registry entry (including installed_at) and want to restore it
+        exactly as it was.
+
+        Args:
+            pack_id: Preset ID
+            metadata: Complete preset metadata including installed_at
+
+        Raises:
+            ValueError: If metadata is None or not a dict
+        """
+        if metadata is None or not isinstance(metadata, dict):
+            raise ValueError(f"Cannot restore '{pack_id}': metadata must be a dict")
+        # Ensure presets dict exists (handle corrupted registry)
+        if not isinstance(self.data.get("presets"), dict):
+            self.data["presets"] = {}
+        self.data["presets"][pack_id] = copy.deepcopy(metadata)
         self._save()
 
     def get(self, pack_id: str) -> Optional[dict]:
         """Get preset metadata from registry.
 
+        Returns a deep copy to prevent callers from accidentally mutating
+        nested internal registry state without going through the write path.
+
         Args:
             pack_id: Preset ID
 
         Returns:
-            Pack metadata or None if not found
+            Deep copy of preset metadata, or None if not found or corrupted
         """
-        return self.data["presets"].get(pack_id)
+        packs = self.data.get("presets")
+        if not isinstance(packs, dict):
+            return None
+        entry = packs.get(pack_id)
+        # Return None for missing or corrupted (non-dict) entries
+        if entry is None or not isinstance(entry, dict):
+            return None
+        return copy.deepcopy(entry)
 
     def list(self) -> Dict[str, dict]:
-        """Get all installed presets.
+        """Get all installed presets with valid metadata.
+
+        Returns a deep copy of presets with dict metadata only.
+        Corrupted entries (non-dict values) are filtered out.
 
         Returns:
-            Dictionary of pack_id -> metadata
+            Dictionary of pack_id -> metadata (deep copies), empty dict if corrupted
         """
-        return self.data["presets"]
+        packs = self.data.get("presets", {}) or {}
+        if not isinstance(packs, dict):
+            return {}
+        # Filter to only valid dict entries to match type contract
+        return {
+            pack_id: copy.deepcopy(meta)
+            for pack_id, meta in packs.items()
+            if isinstance(meta, dict)
+        }
+
+    def keys(self) -> set:
+        """Get all preset IDs including corrupted entries.
+
+        Lightweight method that returns IDs without deep-copying metadata.
+        Use this when you only need to check which presets are tracked.
+
+        Returns:
+            Set of preset IDs (includes corrupted entries)
+        """
+        packs = self.data.get("presets", {}) or {}
+        if not isinstance(packs, dict):
+            return set()
+        return set(packs.keys())
 
-    def list_by_priority(self) -> List[tuple]:
+    def list_by_priority(self, include_disabled: bool = False) -> List[tuple]:
         """Get all installed presets sorted by priority.
 
         Lower priority number = higher precedence (checked first).
         Presets with equal priority are sorted alphabetically by ID
         for deterministic ordering.
 
+        Args:
+            include_disabled: If True, include disabled presets. Default False.
+
         Returns:
             List of (pack_id, metadata_copy) tuples sorted by priority.
             Metadata is deep-copied to prevent accidental mutation.
@@ -343,6 +417,9 @@ def list_by_priority(self) -> List[tuple]:
         for pack_id, meta in packs.items():
             if not isinstance(meta, dict):
                 continue
+            # Skip disabled presets unless explicitly requested
+            if not include_disabled and not meta.get("enabled", True):
+                continue
             metadata_copy = copy.deepcopy(meta)
             metadata_copy["priority"] = normalize_priority(metadata_copy.get("priority", 10))
             sortable_packs.append((pack_id, metadata_copy))
@@ -358,9 +435,12 @@ def is_installed(self, pack_id: str) -> bool:
             pack_id: Preset ID
 
         Returns:
-            True if pack is installed
+            True if pack is installed, False if not or registry corrupted
         """
-        return pack_id in self.data["presets"]
+        packs = self.data.get("presets")
+        if not isinstance(packs, dict):
+            return False
+        return pack_id in packs
 
 
 class PresetManager:
@@ -1466,12 +1546,20 @@ def _get_all_extensions_by_priority(self) -> list[tuple[int, str, dict | None]]:
             return []
 
         registry = ExtensionRegistry(self.extensions_dir)
-        registered_extensions = registry.list_by_priority()
-        registered_extension_ids = {ext_id for ext_id, _ in registered_extensions}
+        # Use keys() to track ALL extensions (including corrupted entries) without deep copy
+        # This prevents corrupted entries from being picked up as "unregistered" dirs
+        registered_extension_ids = registry.keys()
+
+        # Get all registered extensions including disabled; we filter disabled manually below
+        all_registered = registry.list_by_priority(include_disabled=True)
 
         all_extensions: list[tuple[int, str, dict | None]] = []
 
-        for ext_id, metadata in registered_extensions:
+        # Only include enabled extensions in the result
+        for ext_id, metadata in all_registered:
+            # Skip disabled extensions
+            if not metadata.get("enabled", True):
+                continue
             priority = normalize_priority(metadata.get("priority") if metadata else None)
             all_extensions.append((priority, ext_id, metadata))
 
diff --git a/tests/test_extensions.py b/tests/test_extensions.py
index c87ba5b53..d99295ea8 100644
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -420,6 +420,48 @@ def test_restore_can_recreate_removed_entry(self, temp_dir):
         assert registry.is_installed("test-ext")
         assert registry.get("test-ext")["version"] == "1.0.0"
 
+    def test_restore_rejects_none_metadata(self, temp_dir):
+        """Test restore() raises ValueError for None metadata."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+        registry = ExtensionRegistry(extensions_dir)
+
+        with pytest.raises(ValueError, match="metadata must be a dict"):
+            registry.restore("test-ext", None)
+
+    def test_restore_rejects_non_dict_metadata(self, temp_dir):
+        """Test restore() raises ValueError for non-dict metadata."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+        registry = ExtensionRegistry(extensions_dir)
+
+        with pytest.raises(ValueError, match="metadata must be a dict"):
+            registry.restore("test-ext", "not-a-dict")
+
+        with pytest.raises(ValueError, match="metadata must be a dict"):
+            registry.restore("test-ext", ["list", "not", "dict"])
+
+    def test_restore_uses_deep_copy(self, temp_dir):
+        """Test restore() deep copies metadata to prevent mutation."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+        registry = ExtensionRegistry(extensions_dir)
+
+        original_metadata = {
+            "version": "1.0.0",
+            "nested": {"key": "original"},
+        }
+        registry.restore("test-ext", original_metadata)
+
+        # Mutate the original metadata after restore
+        original_metadata["version"] = "MUTATED"
+        original_metadata["nested"]["key"] = "MUTATED"
+
+        # Registry should have the original values
+        stored = registry.get("test-ext")
+        assert stored["version"] == "1.0.0"
+        assert stored["nested"]["key"] == "original"
+
     def test_get_returns_deep_copy(self, temp_dir):
         """Test that get() returns deep copies for nested structures."""
         extensions_dir = temp_dir / "extensions"
@@ -439,6 +481,26 @@ def test_get_returns_deep_copy(self, temp_dir):
         internal = registry.data["extensions"]["test-ext"]
         assert internal["registered_commands"] == {"claude": ["cmd1"]}
 
+    def test_get_returns_none_for_corrupted_entry(self, temp_dir):
+        """Test that get() returns None for corrupted (non-dict) entries."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+
+        # Directly corrupt the registry with non-dict entries
+        registry.data["extensions"]["corrupted-string"] = "not a dict"
+        registry.data["extensions"]["corrupted-list"] = ["not", "a", "dict"]
+        registry.data["extensions"]["corrupted-int"] = 42
+        registry._save()
+
+        # All corrupted entries should return None
+        assert registry.get("corrupted-string") is None
+        assert registry.get("corrupted-list") is None
+        assert registry.get("corrupted-int") is None
+        # Non-existent should also return None
+        assert registry.get("nonexistent") is None
+
     def test_list_returns_deep_copy(self, temp_dir):
         """Test that list() returns deep copies for nested structures."""
         extensions_dir = temp_dir / "extensions"
@@ -458,6 +520,20 @@ def test_list_returns_deep_copy(self, temp_dir):
         internal = registry.data["extensions"]["test-ext"]
         assert internal["registered_commands"] == {"claude": ["cmd1"]}
 
+    def test_list_returns_empty_dict_for_corrupted_registry(self, temp_dir):
+        """Test that list() returns empty dict when extensions is not a dict."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+        registry = ExtensionRegistry(extensions_dir)
+
+        # Corrupt the registry - extensions is a list instead of dict
+        registry.data["extensions"] = ["not", "a", "dict"]
+        registry._save()
+
+        # list() should return empty dict, not crash
+        result = registry.list()
+        assert result == {}
+
 
 # ===== ExtensionManager Tests =====
 
@@ -2500,6 +2576,40 @@ def test_list_by_priority_invalid_priority_defaults(self, temp_dir):
         assert [item[0] for item in result] == ["ext-high", "ext-invalid"]
         assert result[1][1]["priority"] == 10
 
+    def test_list_by_priority_excludes_disabled(self, temp_dir):
+        """Test that list_by_priority excludes disabled extensions by default."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        registry.add("ext-enabled", {"version": "1.0.0", "enabled": True, "priority": 5})
+        registry.add("ext-disabled", {"version": "1.0.0", "enabled": False, "priority": 1})
+        registry.add("ext-default", {"version": "1.0.0", "priority": 10})  # no enabled field = True
+
+        # Default: exclude disabled
+        by_priority = registry.list_by_priority()
+        ext_ids = [p[0] for p in by_priority]
+        assert "ext-enabled" in ext_ids
+        assert "ext-default" in ext_ids
+        assert "ext-disabled" not in ext_ids
+
+    def test_list_by_priority_includes_disabled_when_requested(self, temp_dir):
+        """Test that list_by_priority includes disabled extensions when requested."""
+        extensions_dir = temp_dir / "extensions"
+        extensions_dir.mkdir()
+
+        registry = ExtensionRegistry(extensions_dir)
+        registry.add("ext-enabled", {"version": "1.0.0", "enabled": True, "priority": 5})
+        registry.add("ext-disabled", {"version": "1.0.0", "enabled": False, "priority": 1})
+
+        # Include disabled
+        by_priority = registry.list_by_priority(include_disabled=True)
+        ext_ids = [p[0] for p in by_priority]
+        assert "ext-enabled" in ext_ids
+        assert "ext-disabled" in ext_ids
+        # Disabled ext has lower priority number, so it comes first when included
+        assert ext_ids[0] == "ext-disabled"
+
     def test_install_with_priority(self, extension_dir, project_dir):
         """Test that install_from_directory stores priority."""
         manager = ExtensionManager(project_dir)
@@ -2541,8 +2651,8 @@ def test_priority_preserved_on_update(self, temp_dir):
         assert updated["priority"] == 5  # Preserved
         assert updated["enabled"] is False  # Updated
 
-    def test_resolve_uses_unregistered_extension_dirs_when_registry_partially_corrupted(self, project_dir):
-        """Resolution scans unregistered extension dirs after valid registry entries."""
+    def test_corrupted_extension_entry_not_picked_up_as_unregistered(self, project_dir):
+        """Corrupted registry entries are still tracked and NOT picked up as unregistered."""
         extensions_dir = project_dir / ".specify" / "extensions"
 
         valid_dir = extensions_dir / "valid-ext" / "templates"
@@ -2555,20 +2665,21 @@ def test_resolve_uses_unregistered_extension_dirs_when_registry_partially_corrup
 
         registry = ExtensionRegistry(extensions_dir)
         registry.add("valid-ext", {"version": "1.0.0", "priority": 10})
+        # Corrupt the entry - should still be tracked, not picked up as unregistered
         registry.data["extensions"]["broken-ext"] = "corrupted"
         registry._save()
 
         from specify_cli.presets import PresetResolver
 
         resolver = PresetResolver(project_dir)
+        # Corrupted extension templates should NOT be resolved
         resolved = resolver.resolve("target-template")
-        sourced = resolver.resolve_with_source("target-template")
+        assert resolved is None
 
-        assert resolved is not None
-        assert resolved.name == "target-template.md"
-        assert "Broken Target" in resolved.read_text()
-        assert sourced is not None
-        assert sourced["source"] == "extension:broken-ext (unregistered)"
+        # Valid extension template should still resolve
+        valid_resolved = resolver.resolve("other-template")
+        assert valid_resolved is not None
+        assert "Valid" in valid_resolved.read_text()
 
 
 class TestExtensionPriorityCLI:
diff --git a/tests/test_presets.py b/tests/test_presets.py
index b6fe81d5b..2716b73dc 100644
--- a/tests/test_presets.py
+++ b/tests/test_presets.py
@@ -369,6 +369,172 @@ def test_get_nonexistent(self, temp_dir):
         registry = PresetRegistry(packs_dir)
         assert registry.get("nonexistent") is None
 
+    def test_restore(self, temp_dir):
+        """Test restore() preserves timestamps exactly."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        # Create original entry with a specific timestamp
+        original_metadata = {
+            "version": "1.0.0",
+            "source": "local",
+            "installed_at": "2025-01-15T10:30:00+00:00",
+            "enabled": True,
+        }
+        registry.restore("test-pack", original_metadata)
+
+        # Verify exact restoration
+        restored = registry.get("test-pack")
+        assert restored["installed_at"] == "2025-01-15T10:30:00+00:00"
+        assert restored["version"] == "1.0.0"
+        assert restored["enabled"] is True
+
+    def test_restore_rejects_none_metadata(self, temp_dir):
+        """Test restore() raises ValueError for None metadata."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        with pytest.raises(ValueError, match="metadata must be a dict"):
+            registry.restore("test-pack", None)
+
+    def test_restore_rejects_non_dict_metadata(self, temp_dir):
+        """Test restore() raises ValueError for non-dict metadata."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        with pytest.raises(ValueError, match="metadata must be a dict"):
+            registry.restore("test-pack", "not-a-dict")
+
+        with pytest.raises(ValueError, match="metadata must be a dict"):
+            registry.restore("test-pack", ["list", "not", "dict"])
+
+    def test_restore_uses_deep_copy(self, temp_dir):
+        """Test restore() deep copies metadata to prevent mutation."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        original_metadata = {
+            "version": "1.0.0",
+            "nested": {"key": "original"},
+        }
+        registry.restore("test-pack", original_metadata)
+
+        # Mutate the original metadata after restore
+        original_metadata["version"] = "MUTATED"
+        original_metadata["nested"]["key"] = "MUTATED"
+
+        # Registry should have the original values
+        stored = registry.get("test-pack")
+        assert stored["version"] == "1.0.0"
+        assert stored["nested"]["key"] == "original"
+
+    def test_get_returns_deep_copy(self, temp_dir):
+        """Test that get() returns a deep copy to prevent mutation."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        registry.add("test-pack", {"version": "1.0.0", "nested": {"key": "original"}})
+
+        # Get and mutate the returned copy
+        metadata = registry.get("test-pack")
+        metadata["version"] = "MUTATED"
+        metadata["nested"]["key"] = "MUTATED"
+
+        # Original should be unchanged
+        fresh = registry.get("test-pack")
+        assert fresh["version"] == "1.0.0"
+        assert fresh["nested"]["key"] == "original"
+
+    def test_get_returns_none_for_corrupted_entry(self, temp_dir):
+        """Test that get() returns None for corrupted (non-dict) entries."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        # Directly corrupt the registry with non-dict entries
+        registry.data["presets"]["corrupted-string"] = "not a dict"
+        registry.data["presets"]["corrupted-list"] = ["not", "a", "dict"]
+        registry.data["presets"]["corrupted-int"] = 42
+        registry._save()
+
+        # All corrupted entries should return None
+        assert registry.get("corrupted-string") is None
+        assert registry.get("corrupted-list") is None
+        assert registry.get("corrupted-int") is None
+        # Non-existent should also return None
+        assert registry.get("nonexistent") is None
+
+    def test_list_returns_deep_copy(self, temp_dir):
+        """Test that list() returns deep copies to prevent mutation."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        registry.add("test-pack", {"version": "1.0.0", "nested": {"key": "original"}})
+
+        # Get list and mutate
+        all_packs = registry.list()
+        all_packs["test-pack"]["version"] = "MUTATED"
+        all_packs["test-pack"]["nested"]["key"] = "MUTATED"
+
+        # Original should be unchanged
+        fresh = registry.get("test-pack")
+        assert fresh["version"] == "1.0.0"
+        assert fresh["nested"]["key"] == "original"
+
+    def test_list_returns_empty_dict_for_corrupted_registry(self, temp_dir):
+        """Test that list() returns empty dict when presets is not a dict."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        # Corrupt the registry - presets is a list instead of dict
+        registry.data["presets"] = ["not", "a", "dict"]
+        registry._save()
+
+        # list() should return empty dict, not crash
+        result = registry.list()
+        assert result == {}
+
+    def test_list_by_priority_excludes_disabled(self, temp_dir):
+        """Test that list_by_priority excludes disabled presets by default."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        registry.add("pack-enabled", {"version": "1.0.0", "enabled": True, "priority": 5})
+        registry.add("pack-disabled", {"version": "1.0.0", "enabled": False, "priority": 1})
+        registry.add("pack-default", {"version": "1.0.0", "priority": 10})  # no enabled field = True
+
+        # Default: exclude disabled
+        by_priority = registry.list_by_priority()
+        pack_ids = [p[0] for p in by_priority]
+        assert "pack-enabled" in pack_ids
+        assert "pack-default" in pack_ids
+        assert "pack-disabled" not in pack_ids
+
+    def test_list_by_priority_includes_disabled_when_requested(self, temp_dir):
+        """Test that list_by_priority includes disabled presets when requested."""
+        packs_dir = temp_dir / "packs"
+        packs_dir.mkdir()
+        registry = PresetRegistry(packs_dir)
+
+        registry.add("pack-enabled", {"version": "1.0.0", "enabled": True, "priority": 5})
+        registry.add("pack-disabled", {"version": "1.0.0", "enabled": False, "priority": 1})
+
+        # Include disabled
+        by_priority = registry.list_by_priority(include_disabled=True)
+        pack_ids = [p[0] for p in by_priority]
+        assert "pack-enabled" in pack_ids
+        assert "pack-disabled" in pack_ids
+        # Disabled pack has lower priority number, so it comes first when included
+        assert pack_ids[0] == "pack-disabled"
+
 
 # ===== PresetManager Tests =====
 
@@ -707,6 +873,44 @@ def test_resolve_extension_provided_templates(self, project_dir):
         assert result is not None
         assert "Extension Custom Template" in result.read_text()
 
+    def test_resolve_disabled_extension_templates_skipped(self, project_dir):
+        """Test that disabled extension templates are not resolved."""
+        # Create extension with templates
+        ext_dir = project_dir / ".specify" / "extensions" / "disabled-ext"
+        ext_templates_dir = ext_dir / "templates"
+        ext_templates_dir.mkdir(parents=True)
+        ext_template = ext_templates_dir / "disabled-template.md"
+        ext_template.write_text("# Disabled Extension Template\n")
+
+        # Register extension as disabled
+        extensions_dir = project_dir / ".specify" / "extensions"
+        ext_registry = ExtensionRegistry(extensions_dir)
+        ext_registry.add("disabled-ext", {"version": "1.0.0", "priority": 1, "enabled": False})
+
+        # Template should NOT be resolved because extension is disabled
+        resolver = PresetResolver(project_dir)
+        result = resolver.resolve("disabled-template")
+        assert result is None, "Disabled extension template should not be resolved"
+
+    def test_resolve_disabled_extension_not_picked_up_as_unregistered(self, project_dir):
+        """Test that disabled extensions are not picked up via unregistered dir scan."""
+        # Create extension directory with templates
+        ext_dir = project_dir / ".specify" / "extensions" / "test-disabled-ext"
+        ext_templates_dir = ext_dir / "templates"
+        ext_templates_dir.mkdir(parents=True)
+        ext_template = ext_templates_dir / "unique-disabled-template.md"
+        ext_template.write_text("# Should Not Resolve\n")
+
+        # Register the extension but disable it
+        extensions_dir = project_dir / ".specify" / "extensions"
+        ext_registry = ExtensionRegistry(extensions_dir)
+        ext_registry.add("test-disabled-ext", {"version": "1.0.0", "enabled": False})
+
+        # Verify the template is NOT resolved (even though the directory exists)
+        resolver = PresetResolver(project_dir)
+        result = resolver.resolve("unique-disabled-template")
+        assert result is None, "Disabled extension should not be picked up as unregistered"
+
     def test_resolve_pack_over_extension(self, project_dir, pack_dir, temp_dir, valid_pack_data):
         """Test that pack templates take priority over extension templates."""
         # Create extension with templates
@@ -2001,3 +2205,189 @@ def test_mixed_legacy_and_new_presets_ordering(self, temp_dir):
             "legacy-pack",
             "low-priority-pack",
         ]
+
+
+class TestPresetEnableDisable:
+    """Test preset enable/disable CLI commands."""
+
+    def test_disable_preset(self, project_dir, pack_dir):
+        """Test disable command sets enabled=False."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install preset
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(pack_dir, "0.1.5")
+
+        # Verify initially enabled
+        assert manager.registry.get("test-pack").get("enabled", True) is True
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["preset", "disable", "test-pack"])
+
+        assert result.exit_code == 0, result.output
+        assert "disabled" in result.output.lower()
+
+        # Reload registry to see updated value
+        manager2 = PresetManager(project_dir)
+        assert manager2.registry.get("test-pack")["enabled"] is False
+
+    def test_enable_preset(self, project_dir, pack_dir):
+        """Test enable command sets enabled=True."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install preset and disable it
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(pack_dir, "0.1.5")
+        manager.registry.update("test-pack", {"enabled": False})
+
+        # Verify disabled
+        assert manager.registry.get("test-pack")["enabled"] is False
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["preset", "enable", "test-pack"])
+
+        assert result.exit_code == 0, result.output
+        assert "enabled" in result.output.lower()
+
+        # Reload registry to see updated value
+        manager2 = PresetManager(project_dir)
+        assert manager2.registry.get("test-pack")["enabled"] is True
+
+    def test_disable_already_disabled(self, project_dir, pack_dir):
+        """Test disable on already disabled preset shows warning."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install preset and disable it
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(pack_dir, "0.1.5")
+        manager.registry.update("test-pack", {"enabled": False})
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["preset", "disable", "test-pack"])
+
+        assert result.exit_code == 0, result.output
+        assert "already disabled" in result.output.lower()
+
+    def test_enable_already_enabled(self, project_dir, pack_dir):
+        """Test enable on already enabled preset shows warning."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install preset (enabled by default)
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(pack_dir, "0.1.5")
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["preset", "enable", "test-pack"])
+
+        assert result.exit_code == 0, result.output
+        assert "already enabled" in result.output.lower()
+
+    def test_disable_not_installed(self, project_dir):
+        """Test disable fails for non-installed preset."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["preset", "disable", "nonexistent"])
+
+        assert result.exit_code == 1, result.output
+        assert "not installed" in result.output.lower()
+
+    def test_enable_not_installed(self, project_dir):
+        """Test enable fails for non-installed preset."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["preset", "enable", "nonexistent"])
+
+        assert result.exit_code == 1, result.output
+        assert "not installed" in result.output.lower()
+
+    def test_disabled_preset_excluded_from_resolution(self, project_dir, pack_dir):
+        """Test that disabled presets are excluded from template resolution."""
+        # Install preset with a template
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(pack_dir, "0.1.5")
+
+        # Create a template in the preset directory
+        preset_template = project_dir / ".specify" / "presets" / "test-pack" / "templates" / "test-template.md"
+        preset_template.parent.mkdir(parents=True, exist_ok=True)
+        preset_template.write_text("# Template from test-pack")
+
+        resolver = PresetResolver(project_dir)
+
+        # Template should be found when enabled
+        result = resolver.resolve("test-template", "template")
+        assert result is not None
+        assert "test-pack" in str(result)
+
+        # Disable the preset
+        manager.registry.update("test-pack", {"enabled": False})
+
+        # Template should NOT be found when disabled
+        resolver2 = PresetResolver(project_dir)
+        result2 = resolver2.resolve("test-template", "template")
+        assert result2 is None
+
+    def test_enable_corrupted_registry_entry(self, project_dir, pack_dir):
+        """Test enable fails gracefully for corrupted registry entry."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install preset then corrupt the registry entry
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(pack_dir, "0.1.5")
+        manager.registry.data["presets"]["test-pack"] = "corrupted-string"
+        manager.registry._save()
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["preset", "enable", "test-pack"])
+
+        assert result.exit_code == 1
+        assert "corrupted state" in result.output.lower()
+
+    def test_disable_corrupted_registry_entry(self, project_dir, pack_dir):
+        """Test disable fails gracefully for corrupted registry entry."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        # Install preset then corrupt the registry entry
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(pack_dir, "0.1.5")
+        manager.registry.data["presets"]["test-pack"] = "corrupted-string"
+        manager.registry._save()
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["preset", "disable", "test-pack"])
+
+        assert result.exit_code == 1
+        assert "corrupted state" in result.output.lower()