unity-agentic-tools 0.4.1 → 0.4.3

package/dist/cli.js

@@ -2299,7 +2299,7 @@ var require_package = __commonJS((exports2, module2) => {
   module2.exports = {
     name: "unity-agentic-tools",
     packageManager: "bun@latest",
-    version: "0.4.1",
+    version: "0.4.3",
     description: "Fast, token-efficient Unity YAML parser for AI agents",
     exports: {
       ".": {
@@ -2595,8 +2595,8 @@ function removeDirectoryRecursive(dir) {
 }
 
 // src/cmd-create.ts
-var import_fs17 = require("fs");
-var import_path7 = require("path");
+var import_fs18 = require("fs");
+var import_path10 = require("path");
 var import_crypto2 = require("crypto");
 
 // src/utils.ts
@@ -2619,6 +2619,9 @@ function find_unity_project_root(startDir) {
   }
   return null;
 }
+function resolve_project_path(project_path) {
+  return import_path4.resolve(project_path || process.cwd());
+}
 function ensure_parent_dir(file_path) {
   const dir = import_path4.dirname(file_path);
   if (dir && dir !== "." && !import_fs4.existsSync(dir)) {
@@ -2806,6 +2809,19 @@ function build_guid_cache(project_path, raw) {
         }
       }
       return substringMatch;
+    },
+    find_all_by_name_exact(name, extension) {
+      const nameLower = name.toLowerCase().replace(/\.[^.]+$/, "");
+      const matches = [];
+      for (const [guid, assetPath] of Object.entries(raw)) {
+        if (extension && !assetPath.endsWith(extension))
+          continue;
+        const fileName = import_path5.basename(assetPath, import_path5.extname(assetPath)).toLowerCase();
+        if (fileName === nameLower) {
+          matches.push({ guid, path: assetPath });
+        }
+      }
+      return matches;
     }
   };
 }
@@ -2904,15 +2920,14 @@ var UNITY_CLASS_IDS = {
   114: "MonoBehaviour",
   115: "MonoScript",
   117: "Texture3D",
-  119: "NewAnimationTrack",
-  120: "Projector",
-  121: "LineRenderer",
-  122: "Flare",
-  123: "Halo",
-  124: "LensFlare",
-  125: "FlareLayer",
-  126: "HaloLayer",
-  127: "NavMeshProjectSettings",
+  118: "NewAnimationTrack",
+  119: "Projector",
+  120: "LineRenderer",
+  121: "Flare",
+  122: "Halo",
+  123: "LensFlare",
+  124: "FlareLayer",
+  126: "NavMeshProjectSettings",
   128: "Font",
   129: "PlayerSettings",
   130: "NamedObject",
@@ -2939,6 +2954,7 @@ var UNITY_CLASS_IDS = {
   164: "AudioReverbFilter",
   165: "AudioHighPassFilter",
   166: "AudioChorusFilter",
+  1660057539: "SceneRoots",
   167: "AudioReverbZone",
   168: "AudioEchoFilter",
   169: "AudioLowPassFilter",
@@ -3009,29 +3025,41 @@ var UNITY_CLASS_IDS = {
   257: "TargetJoint2D",
   258: "LightProbes",
   259: "LightProbeProxyVolume",
-  260: "SampleClip",
-  261: "AudioMixerSnapshot",
-  262: "AudioMixerGroup",
+  260: "SampleClipLegacy",
+  261: "AudioMixerSnapshotLegacy",
+  262: "AudioMixerGroupLegacy",
   265: "NScreenBridge",
-  271: "AssetBundleManifest",
+  271: "SampleClip",
   272: "UnityAdsManager",
-  273: "RuntimeInitializeOnLoadManager",
-  280: "UnityConnectSettings",
-  281: "AvatarMask",
-  290: "PlayableDirector",
-  292: "VideoPlayer",
-  293: "VideoClip",
-  294: "ParticleSystemForceField",
-  298: "SpriteMask",
+  273: "AudioMixerGroup",
+  280: "UnityConnectSettingsLegacy",
+  281: "AvatarMaskLegacy",
+  290: "AssetBundleManifest",
+  292: "VideoPlayerLegacy",
+  293: "VideoClipLegacy",
+  294: "ParticleSystemForceFieldLegacy",
+  298: "SpriteMaskLegacy",
   300: "WorldAnchor",
-  301: "OcclusionCullingData",
-  310: "PrefabInstance",
-  319: "TextureImporter",
-  363: "Preset",
+  301: "OcclusionCullingDataLegacy",
+  310: "UnityConnectSettings",
+  1001: "PrefabInstance",
+  319: "AvatarMask",
+  320: "PlayableDirector",
+  328: "VideoPlayer",
+  329: "VideoClip",
+  330: "ParticleSystemForceField",
+  331: "SpriteMask",
+  363: "OcclusionCullingData",
+  1006: "TextureImporter",
+  181963792: "Preset",
   687078895: "SpriteAtlas",
+  156049354: "Grid",
+  1742807556: "GridLayout",
   1839735485: "Tilemap",
-  1839735486: "TilemapCollider2D",
-  1839735487: "TilemapRenderer"
+  19719996: "TilemapCollider2D",
+  483693784: "TilemapRenderer",
+  1839735486: "TilemapCollider2DLegacy",
+  1839735487: "TilemapRendererLegacy"
 };
 var UNITY_CLASS_NAMES = Object.fromEntries(Object.entries(UNITY_CLASS_IDS).map(([id, name]) => [name, parseInt(id, 10)]));
 function get_class_id_name(class_id) {
@@ -3097,8 +3125,12 @@ function resolve_source_prefab(doc, file_path, project_path) {
     prefab_instance_block: pi_block
   };
 }
-function resolveScriptGuid(script, projectPath) {
+function resolveScriptGuid(script, projectPath, options) {
+  const strictExactName = options?.strict_exact_name === true;
   if (/^[a-f0-9]{32}$/i.test(script)) {
+    if (/^0{32}$/i.test(script)) {
+      throw new Error(`Invalid script GUID "${script}": all-zero GUID is not allowed. Provide a real script GUID from a .meta file.`);
+    }
     return { guid: script.toLowerCase(), path: null };
   }
   if (script.endsWith(".cs")) {
@@ -3123,9 +3155,20 @@ function resolveScriptGuid(script, projectPath) {
   if (projectPath) {
     const guidCache = load_guid_cache(projectPath);
     if (guidCache) {
-      const result = guidCache.find_by_name(script, ".cs");
-      if (result)
-        return result;
+      if (strictExactName) {
+        const exactMatches = guidCache.find_all_by_name_exact(script, ".cs");
+        if (exactMatches.length === 1) {
+          return exactMatches[0];
+        }
+        if (exactMatches.length > 1) {
+          const paths = exactMatches.map((m) => m.path).join(", ");
+          throw new Error(`Ambiguous type "${script}": found ${exactMatches.length} exact script name matches (${paths}). ` + 'Use a qualified name (e.g., "Namespace.TypeName") or provide the full script path.');
+        }
+      } else {
+        const result = guidCache.find_by_name(script, ".cs");
+        if (result)
+          return result;
+      }
     }
     const registryPath = path.join(projectPath, ".unity-agentic", "type-registry.json");
     if (import_fs6.existsSync(registryPath)) {
@@ -3276,16 +3319,49 @@ function resolveScriptGuid(script, projectPath) {
         continue;
       try {
         const cache = JSON.parse(import_fs6.readFileSync(cachePath, "utf-8"));
+        const exactMatches = [];
         for (const [guid, assetPath] of Object.entries(cache)) {
           if (!assetPath.endsWith(".cs"))
             continue;
           const fileName = path.basename(assetPath, ".cs").toLowerCase();
           if (fileName === scriptNameLower || classNameOnly && fileName === classNameOnly) {
-            return { guid, path: assetPath };
+            exactMatches.push({ guid, path: assetPath });
           }
         }
-      } catch {}
+        if (exactMatches.length === 1) {
+          return exactMatches[0];
+        }
+        if (exactMatches.length > 1) {
+          const paths = exactMatches.map((m) => m.path).join(", ");
+          throw new Error(`Ambiguous type "${script}": found ${exactMatches.length} exact script name matches (${paths}). ` + 'Use a qualified name (e.g., "Namespace.TypeName") or provide the full script path.');
+        }
+      } catch (err) {
+        if (err instanceof Error && err.message.startsWith("Ambiguous type")) {
+          throw err;
+        }
+      }
     }
+    if (strictExactName) {
+      return null;
+    }
+    try {
+      const assetsDir = path.join(projectPath, "Assets");
+      if (import_fs6.existsSync(assetsDir)) {
+        const entries = import_fs6.readdirSync(assetsDir, { recursive: true, withFileTypes: false });
+        for (const entry of entries) {
+          if (!entry.endsWith(".cs"))
+            continue;
+          const fileName = path.basename(entry, ".cs").toLowerCase();
+          if (fileName === scriptNameLower || classNameOnly && fileName === classNameOnly) {
+            const fullPath = path.join(assetsDir, entry);
+            const guid = extractGuidFromMeta(fullPath + ".meta");
+            if (guid) {
+              return { guid, path: path.join("Assets", entry) };
+            }
+          }
+        }
+      }
+    } catch {}
   }
   return null;
 }
@@ -3337,19 +3413,38 @@ function resolveAssetPathToPPtr(value, file_path, project_path) {
     return null;
   return `{fileID: ${mapping.fileID}, guid: ${guid}, type: ${mapping.type}}`;
 }
-function resolve_script_with_fields(script, project_path) {
-  const resolved = resolveScriptGuid(script, project_path);
+function detect_abstract_class_in_source(file_path, class_name) {
+  try {
+    const source = import_fs6.readFileSync(file_path, "utf-8");
+    const escaped_name = class_name.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+    const pattern = new RegExp(`(^|[^\\w])abstract\\s+class\\s+${escaped_name}(?=$|[^\\w])`, "m");
+    return pattern.test(source);
+  } catch {
+    return false;
+  }
+}
+function resolve_script_with_fields(script, project_path, options) {
+  const resolved = resolveScriptGuid(script, project_path, options);
   if (!resolved)
     return null;
   const result = {
     guid: resolved.guid,
     path: resolved.path
   };
+  if (resolved.path && resolved.path.endsWith(".cs")) {
+    const full_path = path.isAbsolute(resolved.path) ? resolved.path : project_path ? path.join(project_path, resolved.path) : resolved.path;
+    if (import_fs6.existsSync(full_path)) {
+      const class_name = script.includes(".") ? script.split(".").pop() : script;
+      if (class_name.length > 0) {
+        result.is_abstract = detect_abstract_class_in_source(full_path, class_name);
+      }
+    }
+  }
   if (!project_path)
     return result;
   if (resolved.path) {
     try {
-      const full_path = resolved.path.startsWith("/") ? resolved.path : path.join(project_path, resolved.path);
+      const full_path = path.isAbsolute(resolved.path) ? resolved.path : path.join(project_path, resolved.path);
       if (!import_fs6.existsSync(full_path)) {
         result.extraction_error = `Script file not found at resolved path: ${full_path}`;
       } else if (resolved.path.endsWith(".cs")) {
@@ -3363,6 +3458,10 @@ function resolve_script_with_fields(script, project_path) {
             result.fields = chosen.fields;
             result.base_class = chosen.baseClass ?? undefined;
             result.kind = chosen.kind;
+            result.class_name = chosen.name;
+            if (chosen.name) {
+              result.is_abstract = detect_abstract_class_in_source(full_path, chosen.name);
+            }
           }
         } else {
           result.extraction_error = "Native extractSerializedFields function not available";
@@ -3440,8 +3539,8 @@ function build_type_lookup(project_path) {
   const assetsDir = path.join(project_path, "Assets");
   const csIndex = new Map;
   try {
-    const { readdirSync: readdirSync3 } = require("fs");
-    const entries = readdirSync3(assetsDir, { recursive: true, withFileTypes: false });
+    const { readdirSync: readdirSync4 } = require("fs");
+    const entries = readdirSync4(assetsDir, { recursive: true, withFileTypes: false });
     for (const entry of entries) {
       if (typeof entry === "string" && entry.endsWith(".cs")) {
         const basename3 = entry.substring(entry.lastIndexOf("/") + 1).replace(/\.cs$/, "");
@@ -4462,7 +4561,21 @@ class UnityDocument {
         }
       }
     }
-    return transform_ids;
+    const escaped = name.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+    const name_pattern = new RegExp(`propertyPath: m_Name\\s*\\n\\s*value:\\s*${escaped}\\s*$`, "m");
+    for (const block of this._blocks) {
+      if ((block.class_id === 1001 || block.class_id === 310) && name_pattern.test(block.raw)) {
+        const pi_id = block.file_id;
+        const pi_ref_pattern = new RegExp(`m_PrefabInstance:[ \\t]*\\{fileID:[ \\t]*${pi_id}\\}`);
+        const stripped_transform = this._blocks.find((b) => (b.class_id === 4 || b.class_id === 224) && b.is_stripped && pi_ref_pattern.test(b.raw));
+        if (stripped_transform) {
+          transform_ids.push(stripped_transform.file_id);
+        } else {
+          transform_ids.push(pi_id);
+        }
+      }
+    }
+    return Array.from(new Set(transform_ids));
   }
   require_unique_game_object(name_or_id) {
     if (/^-?\d+$/.test(name_or_id)) {
@@ -4491,10 +4604,7 @@ class UnityDocument {
       if (!block) {
         return { error: `Block with fileID ${name_or_id} not found` };
       }
-      if (block.class_id === 4) {
-        return block;
-      }
-      if (block.class_id === 224) {
+      if (block.class_id === 4 || block.class_id === 224 || block.class_id === 1001 || block.class_id === 310) {
         return block;
       }
       if (block.class_id === 1) {
@@ -4507,15 +4617,40 @@ class UnityDocument {
         }
         return { error: `Transform for GameObject fileID ${name_or_id} not found` };
       }
-      return { error: `fileID ${name_or_id} is not a GameObject or Transform (class ${block.class_id})` };
+      return { error: `fileID ${name_or_id} is not a GameObject, Transform, or PrefabInstance (class ${block.class_id})` };
     }
     const transform_ids = this.find_transforms_by_name(name_or_id);
     if (transform_ids.length === 0) {
-      return { error: `GameObject "${name_or_id}" not found` };
+      return { error: `Object "${name_or_id}" not found` };
     }
     if (transform_ids.length > 1) {
-      const go_ids = this.find_game_objects_by_name(name_or_id).map((b) => b.file_id).join(", ");
-      return { error: `Multiple GameObjects named "${name_or_id}" found (fileIDs: ${go_ids}). Use numeric fileID to specify which one.` };
+      const entity_ids = [];
+      for (const tid of transform_ids) {
+        const block = this.find_by_file_id(tid);
+        if (block) {
+          if (block.class_id === 4 || block.class_id === 224) {
+            const go_match = block.raw.match(/m_GameObject:\s*\{fileID:\s*(-?\d+)\}/);
+            if (go_match) {
+              entity_ids.push(go_match[1]);
+            } else {
+              entity_ids.push(tid);
+            }
+          } else if (block.class_id === 1001 || block.class_id === 310) {
+            entity_ids.push(tid);
+          } else if (block.is_stripped) {
+            const pi_match = block.raw.match(/m_PrefabInstance:\s*\{fileID:\s*(-?\d+)\}/);
+            if (pi_match) {
+              entity_ids.push(pi_match[1]);
+            } else {
+              entity_ids.push(tid);
+            }
+          } else {
+            entity_ids.push(tid);
+          }
+        }
+      }
+      const ids_str = Array.from(new Set(entity_ids)).join(", ");
+      return { error: `Multiple GameObjects/PrefabInstances named "${name_or_id}" found (fileIDs: ${ids_str}). Use numeric fileID to specify which one.` };
     }
     const transform = this.find_by_file_id(transform_ids[0]);
     if (!transform) {
@@ -4543,7 +4678,7 @@ class UnityDocument {
           if (t_block.class_id === 4 && t_block.is_stripped) {
             let name = "Variant";
             for (const pi_block of this._blocks) {
-              if (pi_block.class_id === 1001) {
+              if (pi_block.class_id === 1001 || pi_block.class_id === 310) {
                 const name_mod = pi_block.raw.match(/propertyPath: m_Name\s*\n\s*value:\s*(.+)/);
                 if (name_mod) {
                   name = name_mod[1].trim();
@@ -4696,7 +4831,7 @@ class UnityDocument {
   }
   add_child_to_parent(parent_id, child_id) {
     const parent = this.find_by_file_id(parent_id);
-    if (!parent || parent.class_id !== 4)
+    if (!parent || parent.class_id !== 4 && parent.class_id !== 224)
       return false;
     let raw = parent.raw;
     const inline_empty = /m_Children:\s*\[\]/;
@@ -4732,7 +4867,7 @@ class UnityDocument {
   }
   remove_child_from_parent(parent_id, child_id) {
     const parent = this.find_by_file_id(parent_id);
-    if (!parent || parent.class_id !== 4)
+    if (!parent || parent.class_id !== 4 && parent.class_id !== 224)
       return false;
     let raw = parent.raw;
     const child_line = new RegExp(`\\n[ \\t]*- \\{fileID: ${child_id}\\}`);
@@ -4753,7 +4888,49 @@ class UnityDocument {
   }
   _collect_hierarchy_recursive(transform_id, result) {
     const transform = this.find_by_file_id(transform_id);
-    if (!transform || transform.class_id !== 4)
+    if (!transform)
+      return;
+    if (transform.class_id === 1001 || transform.class_id === 310) {
+      const pi_id = transform.file_id;
+      const pi_ref_pattern = new RegExp(`m_PrefabInstance:[ \\t]*\\{fileID:[ \\t]*${pi_id}\\}`);
+      for (const block of this._blocks) {
+        if (block.is_stripped && pi_ref_pattern.test(block.raw)) {
+          result.add(block.file_id);
+          if (block.class_id === 4 || block.class_id === 224) {
+            this._collect_hierarchy_recursive(block.file_id, result);
+          }
+        }
+      }
+      const added_go_matches = transform.raw.matchAll(/addedObject:[ \t]*\{[^}]*fileID:[ \t]*(-?\d+)\}/g);
+      for (const match of added_go_matches) {
+        const added_id = match[1];
+        if (added_id !== "0" && !result.has(added_id)) {
+          result.add(added_id);
+          const added_block = this.find_by_file_id(added_id);
+          if (added_block && added_block.class_id === 1) {
+            const comp_matches = added_block.raw.matchAll(/component:[ \t]*\{fileID:[ \t]*(-?\d+)\}/g);
+            for (const cm of comp_matches) {
+              const comp_block = this.find_by_file_id(cm[1]);
+              if (comp_block && (comp_block.class_id === 4 || comp_block.class_id === 224)) {
+                if (!result.has(cm[1])) {
+                  result.add(cm[1]);
+                  this._collect_hierarchy_recursive(cm[1], result);
+                }
+                break;
+              }
+            }
+          }
+        }
+      }
+      const added_comp_matches = transform.raw.matchAll(/addedObject:[ \t]*\{[^}]*fileID:[ \t]*(-?\d+)\}/g);
+      for (const match of added_comp_matches) {
+        const added_id = match[1];
+        if (added_id !== "0")
+          result.add(added_id);
+      }
+      return;
+    }
+    if (transform.class_id !== 4 && transform.class_id !== 224)
       return;
     const children_section = transform.raw.match(/m_Children:[\s\S]*?(?=\s*m_Father:)/);
     if (!children_section)
@@ -4788,14 +4965,21 @@ class UnityDocument {
     if (parent_id === "0") {
       let count = 0;
       for (const block of this._blocks) {
-        if (block.class_id === 4 && /m_Father:\s*\{fileID:\s*0\}/.test(block.raw)) {
+        if ((block.class_id === 4 || block.class_id === 224) && /m_Father:\s*\{fileID:\s*0\}/.test(block.raw)) {
           count++;
+        } else if ((block.class_id === 1001 || block.class_id === 310) && /m_TransformParent:\s*\{fileID:\s*0\}/.test(block.raw)) {
+          const pi_id = block.file_id;
+          const pi_ref_pattern = new RegExp(`m_PrefabInstance:[ \\t]*\\{fileID:[ \\t]*${pi_id}\\}`);
+          const has_stripped = this._blocks.some((b) => (b.class_id === 4 || b.class_id === 224) && b.is_stripped && pi_ref_pattern.test(b.raw));
+          if (!has_stripped) {
+            count++;
+          }
         }
       }
       return count;
     }
     const parent = this.find_by_file_id(parent_id);
-    if (!parent || parent.class_id !== 4)
+    if (!parent || parent.class_id !== 4 && parent.class_id !== 224)
       return 0;
     const children_match = parent.raw.match(/m_Children:[\s\S]*?(?=\s*m_Father:)/);
     if (children_match) {
@@ -4828,19 +5012,97 @@ ${new_children}`);
     }
     return false;
   }
+  add_root_to_scene_roots(root_id) {
+    const pi_block = this.find_by_file_id(root_id);
+    if (pi_block && (pi_block.class_id === 1001 || pi_block.class_id === 310)) {
+      const pi_ref_pattern = new RegExp(`m_PrefabInstance:[ \\t]*\\{fileID:[ \\t]*${root_id}\\}`);
+      const stripped_root = this._blocks.find((b) => (b.class_id === 4 || b.class_id === 224) && b.is_stripped && pi_ref_pattern.test(b.raw) && /m_Father:\s*\{fileID:\s*0\}/.test(b.raw));
+      if (stripped_root) {
+        root_id = stripped_root.file_id;
+      }
+    }
+    const sr_blocks = [...this.find_by_class_id(166), ...this.find_by_class_id(1660057539)];
+    if (sr_blocks.length === 0)
+      return false;
+    const sr_block = sr_blocks[0];
+    let raw = sr_block.raw;
+    const roots_pattern = /(m_Roots:\s*\n(?:\s*-\s*\{fileID:\s*-?\d+\}\s*\n)*)/;
+    if (roots_pattern.test(raw)) {
+      raw = raw.replace(roots_pattern, `$1  - {fileID: ${root_id}}
+`);
+      sr_block.replace_raw(raw);
+      return true;
+    }
+    const empty_roots = /m_Roots:\s*\[\]/;
+    if (empty_roots.test(raw)) {
+      raw = raw.replace(empty_roots, `m_Roots:
+  - {fileID: ${root_id}}`);
+      sr_block.replace_raw(raw);
+      return true;
+    }
+    return false;
+  }
+  remove_root_from_scene_roots(root_id) {
+    const pi_block = this.find_by_file_id(root_id);
+    if (pi_block && (pi_block.class_id === 1001 || pi_block.class_id === 310)) {
+      const pi_ref_pattern = new RegExp(`m_PrefabInstance:[ \\t]*\\{fileID:[ \\t]*${root_id}\\}`);
+      const stripped_root = this._blocks.find((b) => (b.class_id === 4 || b.class_id === 224) && b.is_stripped && pi_ref_pattern.test(b.raw));
+      if (stripped_root) {
+        this._remove_id_from_scene_roots(stripped_root.file_id);
+      }
+    }
+    return this._remove_id_from_scene_roots(root_id);
+  }
+  _remove_id_from_scene_roots(id) {
+    const sr_blocks = [...this.find_by_class_id(166), ...this.find_by_class_id(1660057539)];
+    if (sr_blocks.length === 0)
+      return false;
+    const sr_block = sr_blocks[0];
+    let raw = sr_block.raw;
+    const root_line = new RegExp(`\\n[ \\t]*- \\{fileID: ${id}\\}`);
+    if (!root_line.test(raw))
+      return false;
+    raw = raw.replace(root_line, "");
+    sr_block.replace_raw(raw);
+    return true;
+  }
   reorder_entities(ordered_transform_ids) {
     const entity_groups = [];
     for (const transform_id of ordered_transform_ids) {
-      const transform = this.find_by_file_id(transform_id);
-      if (!transform)
+      const block = this.find_by_file_id(transform_id);
+      if (!block)
+        continue;
+      let pi_block = null;
+      if (block.class_id === 1001 || block.class_id === 310) {
+        pi_block = block;
+      } else if (block.is_stripped) {
+        const pi_match = block.raw.match(/m_PrefabInstance:\s*\{fileID:\s*(-?\d+)\}/);
+        if (pi_match) {
+          const found = this.find_by_file_id(pi_match[1]);
+          if (found && (found.class_id === 1001 || found.class_id === 310)) {
+            pi_block = found;
+          }
+        }
+      }
+      if (pi_block) {
+        const group = [pi_block.file_id];
+        const hierarchy = this.collect_hierarchy(pi_block.file_id);
+        for (const id of hierarchy)
+          group.push(id);
+        entity_groups.push(group);
         continue;
-      const go_match = transform.raw.match(/m_GameObject:\s*\{fileID:\s*(-?\d+)\}/);
-      if (!go_match)
+      }
+      const go_match = block.raw.match(/m_GameObject:\s*\{fileID:\s*(-?\d+)\}/);
+      if (!go_match) {
+        entity_groups.push([transform_id]);
         continue;
+      }
       const go_id = go_match[1];
       const go = this.find_by_file_id(go_id);
-      if (!go)
+      if (!go) {
+        entity_groups.push([transform_id]);
         continue;
+      }
       const comp_ids = [];
       const comp_matches = go.raw.matchAll(/component:\s*\{fileID:\s*(-?\d+)\}/g);
       for (const m of comp_matches) {
@@ -5223,48 +5485,320 @@ function find_game_object_in_variant(doc, name, file_path, project_path) {
   }
   return null;
 }
-function appendToAddedGameObjects(doc, piId, targetSourceRef, newGoId) {
-  const piBlock = doc.find_by_file_id(piId);
-  if (!piBlock)
-    return;
-  const entry = `
-    - targetCorrespondingSourceObject: ${targetSourceRef}
-      insertIndex: -1
-      addedObject: {fileID: ${newGoId}}`;
-  let raw = piBlock.raw;
-  const emptyPattern = /m_AddedGameObjects:[ \t]*\[\]/;
-  if (emptyPattern.test(raw)) {
-    raw = raw.replace(emptyPattern, `m_AddedGameObjects:${entry}`);
-    piBlock.replace_raw(raw);
-    return;
+function parsePrefabRef(refText) {
+  const fileIdMatch = refText.match(/fileID:[ \t]*(-?\d+)/i);
+  if (!fileIdMatch)
+    return null;
+  const guidMatch = refText.match(/guid:[ \t]*([a-f0-9]{32})/i);
+  const typeMatch = refText.match(/type:[ \t]*(-?\d+)/i);
+  return {
+    file_id: fileIdMatch[1],
+    guid: guidMatch ? guidMatch[1].toLowerCase() : undefined,
+    type: typeMatch ? typeMatch[1] : undefined
+  };
+}
+function extractPrefabSourceGuid(prefabInstanceRaw) {
+  const sourceMatch = prefabInstanceRaw.match(/m_SourcePrefab:[ \t]*\{[^}]*guid:[ \t]*([a-f0-9]{32})/i);
+  return sourceMatch ? sourceMatch[1].toLowerCase() : null;
+}
+function normalizePrefabRef(refText, sourceGuid) {
+  const parsed = parsePrefabRef(refText);
+  if (!parsed) {
+    return { error: `Invalid reference "${refText}". Expected format: {fileID: N, guid: ..., type: T}` };
+  }
+  const guid = parsed.guid ?? sourceGuid;
+  if (!guid) {
+    return { error: `Reference "${refText}" is missing guid and source prefab guid could not be inferred.` };
   }
-  const existingPattern = /(m_AddedGameObjects:[ \t]*\n(?:[ \t]+-[\s\S]*?(?=\n[ \t]+m_|$))*)/;
-  if (existingPattern.test(raw)) {
-    raw = raw.replace(existingPattern, `$1${entry}`);
-    piBlock.replace_raw(raw);
+  if (!/^[a-f0-9]{32}$/i.test(guid)) {
+    return { error: `Invalid guid in reference "${refText}". Expected 32-character hex GUID.` };
   }
+  const type = parsed.type ?? "3";
+  if (!/^-?\d+$/.test(type)) {
+    return { error: `Invalid type in reference "${refText}". Expected an integer type value.` };
+  }
+  return {
+    ref: {
+      file_id: parsed.file_id,
+      guid,
+      type
+    }
+  };
 }
-function appendToAddedComponents(doc, piId, targetSourceRef, newComponentId) {
-  const piBlock = doc.find_by_file_id(piId);
-  if (!piBlock)
-    return;
-  const entry = `
-    - targetCorrespondingSourceObject: ${targetSourceRef}
-      insertIndex: -1
-      addedObject: {fileID: ${newComponentId}}`;
-  let raw = piBlock.raw;
-  const emptyPattern = /m_AddedComponents:[ \t]*\[\]/;
-  if (emptyPattern.test(raw)) {
-    raw = raw.replace(emptyPattern, `m_AddedComponents:${entry}`);
-    piBlock.replace_raw(raw);
-    return;
+function serializePrefabRef(ref) {
+  return `{fileID: ${ref.file_id}, guid: ${ref.guid}, type: ${ref.type}}`;
+}
+function ensurePrefabModificationSerializedVersion(prefabInstanceBlock) {
+  const raw = prefabInstanceBlock.raw;
+  const updated = raw.replace(/(^([ \t]*)m_Modification:[ \t]*\n)(?!\2[ \t]+serializedVersion:[ \t]*\d+)/m, (_match, prefix, indent) => `${prefix}${indent}  serializedVersion: 3
+`);
+  if (updated === raw) {
+    return false;
+  }
+  prefabInstanceBlock.replace_raw(updated);
+  return true;
+}
+function addedOverrideEntryKey(entry) {
+  return `${entry.target.file_id}|${entry.target.guid}|${entry.target.type}|${entry.insert_index}|${entry.added_object_file_id}`;
+}
+function splitPrefabArraySection(rawText, key) {
+  const lines = rawText.split(`
+`);
+  const keyPattern = new RegExp(`^([ 	]*)${key}:[ 	]*(.*)$`);
+  let keyIndex = -1;
+  let indent = "";
+  for (let i = 0;i < lines.length; i++) {
+    const match = lines[i].match(keyPattern);
+    if (match) {
+      keyIndex = i;
+      indent = match[1];
+      break;
+    }
+  }
+  if (keyIndex === -1) {
+    return null;
+  }
+  const keyIndentLen = indent.length;
+  let sectionEnd = keyIndex + 1;
+  for (let i = keyIndex + 1;i < lines.length; i++) {
+    const line = lines[i];
+    const trimmed = line.trim();
+    if (trimmed.length === 0) {
+      sectionEnd = i + 1;
+      continue;
+    }
+    const indentLen = (line.match(/^[ \t]*/) || [""])[0].length;
+    if (indentLen < keyIndentLen) {
+      break;
+    }
+    if (indentLen === keyIndentLen && !trimmed.startsWith("-") && /^[A-Za-z_][A-Za-z0-9_]*:/.test(trimmed)) {
+      break;
+    }
+    sectionEnd = i + 1;
+  }
+  return {
+    lines,
+    key_index: keyIndex,
+    section_end: sectionEnd,
+    indent
+  };
+}
+function collectAddedOverrideEntries(lines, key_index, section_end, sourceGuid) {
+  const sectionLines = lines.slice(key_index + 1, section_end);
+  const dedup = new Map;
+  let i = 0;
+  while (i < sectionLines.length) {
+    const line = sectionLines[i];
+    const trimmed = line.trimStart();
+    if (!trimmed.startsWith("-")) {
+      i++;
+      continue;
+    }
+    const entryIndent = (line.match(/^[ \t]*/) || [""])[0].length;
+    const entryLines = [line];
+    i++;
+    while (i < sectionLines.length) {
+      const nextLine = sectionLines[i];
+      const nextTrimmed = nextLine.trim();
+      const nextIndent = (nextLine.match(/^[ \t]*/) || [""])[0].length;
+      if (nextTrimmed.length > 0 && nextIndent === entryIndent && nextTrimmed.startsWith("-")) {
+        break;
+      }
+      entryLines.push(nextLine);
+      i++;
+    }
+    const entryText = entryLines.join(`
+`);
+    const targetMatch = entryText.match(/targetCorrespondingSourceObject:[ \t]*(\{[^}]+\})/);
+    const insertMatch = entryText.match(/insertIndex:[ \t]*(-?\d+)/);
+    const addedObjectMatch = entryText.match(/addedObject:[ \t]*\{[^}]*fileID:[ \t]*(-?\d+)/);
+    if (!targetMatch || !addedObjectMatch) {
+      continue;
+    }
+    const normalizedTarget = normalizePrefabRef(targetMatch[1], sourceGuid).ref;
+    if (!normalizedTarget) {
+      continue;
+    }
+    const insertIndex = insertMatch ? Number.parseInt(insertMatch[1], 10) : -1;
+    const entry = {
+      target: normalizedTarget,
+      insert_index: Number.isNaN(insertIndex) ? -1 : insertIndex,
+      added_object_file_id: addedObjectMatch[1]
+    };
+    const dedupKey = addedOverrideEntryKey(entry);
+    if (!dedup.has(dedupKey)) {
+      dedup.set(dedupKey, entry);
+    }
   }
-  const existingPattern = /(m_AddedComponents:[ \t]*\n(?:[ \t]+-[\s\S]*?(?=\n[ \t]+m_|$))*)/;
-  if (existingPattern.test(raw)) {
-    raw = raw.replace(existingPattern, `$1${entry}`);
-    piBlock.replace_raw(raw);
+  return [...dedup.values()];
+}
+function appendToAddedOverrideArray(doc, piId, key, targetSourceRef, newObjectId) {
+  const piBlock = doc.find_by_file_id(piId);
+  if (!piBlock) {
+    return { success: false, error: `PrefabInstance with fileID ${piId} not found` };
+  }
+  ensurePrefabModificationSerializedVersion(piBlock);
+  const split = splitPrefabArraySection(piBlock.raw, key);
+  if (!split) {
+    return { success: false, error: `${key} property not found in PrefabInstance ${piId}` };
+  }
+  const sourceGuid = extractPrefabSourceGuid(piBlock.raw);
+  const normalizedTarget = normalizePrefabRef(targetSourceRef, sourceGuid);
+  if (!normalizedTarget.ref) {
+    return { success: false, error: normalizedTarget.error };
+  }
+  const candidate = {
+    target: normalizedTarget.ref,
+    insert_index: -1,
+    added_object_file_id: newObjectId
+  };
+  const candidateKey = addedOverrideEntryKey(candidate);
+  const existing = collectAddedOverrideEntries(split.lines, split.key_index, split.section_end, sourceGuid);
+  if (existing.some((entry) => addedOverrideEntryKey(entry) === candidateKey)) {
+    return { success: true, changed: false };
+  }
+  const entryLines = [
+    `${split.indent}- targetCorrespondingSourceObject: ${serializePrefabRef(candidate.target)}`,
+    `${split.indent}  insertIndex: ${candidate.insert_index}`,
+    `${split.indent}  addedObject: {fileID: ${candidate.added_object_file_id}}`
+  ];
+  const keyLine = split.lines[split.key_index].trim();
+  let insertIndex = split.section_end;
+  while (insertIndex > split.key_index + 1 && split.lines[insertIndex - 1].trim().length === 0) {
+    insertIndex--;
+  }
+  let updatedLines;
+  if (keyLine === `${key}: []`) {
+    const replacement = [`${split.indent}${key}:`, ...entryLines];
+    updatedLines = [
+      ...split.lines.slice(0, split.key_index),
+      ...replacement,
+      ...split.lines.slice(split.section_end)
+    ];
+  } else {
+    updatedLines = [
+      ...split.lines.slice(0, insertIndex),
+      ...entryLines,
+      ...split.lines.slice(insertIndex)
+    ];
   }
+  piBlock.replace_raw(updatedLines.join(`
+`));
+  return { success: true, changed: true };
+}
+function appendToAddedGameObjects(doc, piId, targetSourceRef, newGoId) {
+  return appendToAddedOverrideArray(doc, piId, "m_AddedGameObjects", targetSourceRef, newGoId);
+}
+function appendToAddedComponents(doc, piId, targetSourceRef, newComponentId) {
+  return appendToAddedOverrideArray(doc, piId, "m_AddedComponents", targetSourceRef, newComponentId);
 }
+var COMPONENT_FULL_TEMPLATES = {
+  65: (gameObjectId) => `  m_GameObject: {fileID: ${gameObjectId}}
+  m_Material: {fileID: 0}
+  m_IncludeLayers:
+    serializedVersion: 2
+    m_Bits: 0
+  m_ExcludeLayers:
+    serializedVersion: 2
+    m_Bits: 0
+  m_LayerOverridePriority: 0
+  m_IsTrigger: 0
+  m_ProvidesContacts: 0
+  m_Enabled: 1
+  serializedVersion: 3
+  m_Size: {x: 1, y: 1, z: 1}
+  m_Center: {x: 0, y: 0, z: 0}`,
+  82: (gameObjectId) => `  m_GameObject: {fileID: ${gameObjectId}}
+  m_Enabled: 1
+  serializedVersion: 4
+  OutputAudioMixerGroup: {fileID: 0}
+  m_audioClip: {fileID: 0}
+  m_PlayOnAwake: 1
+  m_Volume: 1
+  m_Pitch: 1
+  Loop: 0
+  Mute: 0
+  Spatialize: 0
+  SpatializePostEffects: 0
+  Priority: 128
+  DopplerLevel: 1
+  MinDistance: 1
+  MaxDistance: 500
+  Pan2D: 0
+  rolloffMode: 0
+  BypassEffects: 0
+  BypassListenerEffects: 0
+  BypassReverbZones: 0
+  rolloffCustomCurve:
+    serializedVersion: 2
+    m_Curve:
+    - serializedVersion: 3
+      time: 0
+      value: 1
+      inSlope: 0
+      outSlope: 0
+      tangentMode: 0
+      weightedMode: 0
+      inWeight: 0.33333334
+      outWeight: 0.33333334
+    - serializedVersion: 3
+      time: 1
+      value: 0
+      inSlope: 0
+      outSlope: 0
+      tangentMode: 0
+      weightedMode: 0
+      inWeight: 0.33333334
+      outWeight: 0.33333334
+    m_PreInfinity: 2
+    m_PostInfinity: 2
+    m_RotationOrder: 4
+  panLevelCustomCurve:
+    serializedVersion: 2
+    m_Curve:
+    - serializedVersion: 3
+      time: 0
+      value: 0
+      inSlope: 0
+      outSlope: 0
+      tangentMode: 0
+      weightedMode: 0
+      inWeight: 0.33333334
+      outWeight: 0.33333334
+    m_PreInfinity: 2
+    m_PostInfinity: 2
+    m_RotationOrder: 4
+  spreadCustomCurve:
+    serializedVersion: 2
+    m_Curve:
+    - serializedVersion: 3
+      time: 0
+      value: 0
+      inSlope: 0
+      outSlope: 0
+      tangentMode: 0
+      weightedMode: 0
+      inWeight: 0.33333334
+      outWeight: 0.33333334
+    m_PreInfinity: 2
+    m_PostInfinity: 2
+    m_RotationOrder: 4
+  reverbZoneMixCustomCurve:
+    serializedVersion: 2
+    m_Curve:
+    - serializedVersion: 3
+      time: 0
+      value: 1
+      inSlope: 0
+      outSlope: 0
+      tangentMode: 0
+      weightedMode: 0
+      inWeight: 0.33333334
+      outWeight: 0.33333334
+    m_PreInfinity: 2
+    m_PostInfinity: 2
+    m_RotationOrder: 4`
+};
 var COMPONENT_DEFAULTS = {
   20: `  serializedVersion: 2
   m_ClearFlags: 1
@@ -5391,6 +5925,17 @@ var COMPONENT_DEFAULTS = {
   m_IgnoreParentGroups: 0`
 };
 function createGenericComponentYAML(componentName, classId, componentId, gameObjectId) {
+  const fullTemplate = COMPONENT_FULL_TEMPLATES[classId];
+  if (fullTemplate) {
+    return `--- !u!${classId} &${componentId}
+${componentName}:
+  m_ObjectHideFlags: 0
+  m_CorrespondingSourceObject: {fileID: 0}
+  m_PrefabInstance: {fileID: 0}
+  m_PrefabAsset: {fileID: 0}
+${fullTemplate(gameObjectId)}
+`;
+  }
   const defaults = COMPONENT_DEFAULTS[classId] ? `
 ` + COMPONENT_DEFAULTS[classId] + `
 ` : "";
@@ -5543,7 +6088,14 @@ function createGameObject(options) {
     doc.add_child_to_parent(parentTransformIdStr, transformIdStr);
   }
   if (variantPiId && strippedSourceRef) {
-    appendToAddedGameObjects(doc, variantPiId, strippedSourceRef, gameObjectIdStr);
+    const appendResult = appendToAddedGameObjects(doc, variantPiId, strippedSourceRef, gameObjectIdStr);
+    if (!appendResult.success) {
+      return {
+        success: false,
+        file_path,
+        error: appendResult.error || `Failed to update m_AddedGameObjects for PrefabInstance ${variantPiId}`
+      };
+    }
   }
   const saveResult = doc.save();
   if (!saveResult.success) {
@@ -6026,6 +6578,7 @@ PrefabInstance:
   m_ObjectHideFlags: 0
   serializedVersion: 2
   m_Modification:
+    serializedVersion: 3
     m_TransformParent: {fileID: 0}
     m_Modifications:
     - target: {fileID: ${rootInfo.game_object.file_id}, guid: ${sourceGuid}, type: 3}
@@ -6172,6 +6725,7 @@ PrefabInstance:
   m_ObjectHideFlags: 0
   serializedVersion: 2
   m_Modification:
+    serializedVersion: 3
     m_TransformParent: {fileID: ${parentTransformIdStr}}
     m_Modifications:
     - target: {fileID: ${rootGoFileId}, guid: ${sourceGuid}, type: 3}
@@ -6276,6 +6830,9 @@ function createScriptableObject(options) {
   if (resolved.kind === "enum" || resolved.kind === "interface") {
     return { success: false, output_path, error: `"${script}" is ${resolved.kind === "enum" ? "an enum" : "an interface"}, not a ScriptableObject.` };
   }
+  if (resolved.is_abstract) {
+    return { success: false, output_path, error: `"${script}" is abstract and cannot be instantiated as a ScriptableObject asset.` };
+  }
   if (resolved.base_class && resolved.base_class !== "ScriptableObject") {
     return { success: false, output_path, error: `"${script}" extends ${resolved.base_class}, not ScriptableObject. Cannot create as a ScriptableObject asset.` };
   }
@@ -6476,6 +7033,8 @@ function is_valid_component_base(base_class, project_path, depth = 0) {
         }
         if (!fullPath.endsWith(".cs") || !import_fs8.existsSync(fullPath)) {
           if (match.kind === "class") {
+            if (fullPath.includes("Assembly-CSharp.dll"))
+              return true;
             return is_likely_component_base_name(base_class);
           }
         }
@@ -6557,6 +7116,13 @@ function addComponent(options) {
   }
   const gameObjectId = gameObjectIdStr;
   const classId = get_class_id(component_type);
+  if (classId === 114 && component_type.toLowerCase() === "monobehaviour") {
+    return {
+      success: false,
+      file_path,
+      error: '"MonoBehaviour" is a base class, not a concrete component script. Provide a script type/path/GUID (for example, "PlayerController", "Assets/Scripts/PlayerController.cs", or a 32-char GUID).'
+    };
+  }
   let duplicateWarning;
   const goBlock = doc.find_by_file_id(gameObjectIdStr);
   if (goBlock && classId !== null) {
@@ -6581,7 +7147,7 @@ function addComponent(options) {
   } else {
     let resolved;
     try {
-      resolved = resolve_script_with_fields(component_type, project_path);
+      resolved = resolve_script_with_fields(component_type, project_path, { strict_exact_name: true });
     } catch (e) {
       return {
         success: false,
@@ -6619,13 +7185,20 @@ function addComponent(options) {
         error: `"${component_type}" is ${resolved.kind === "enum" ? "an enum" : "an interface"}, not a MonoBehaviour. Cannot add as a component.`
       };
     }
-    if (resolved.base_class && !COMPONENT_BASE_CLASSES.has(resolved.base_class) && !is_valid_component_base(resolved.base_class, project_path)) {
+    if (resolved.is_abstract) {
       return {
         success: false,
         file_path,
-        error: `"${component_type}" extends ${resolved.base_class}, which does not inherit from MonoBehaviour. Cannot add as a component. If this is incorrect, ensure the type registry is up to date ("setup" command).`
+        error: `"${component_type}" is abstract and cannot be added as a component.`
       };
     }
+    if (resolved.base_class && !COMPONENT_BASE_CLASSES.has(resolved.base_class) && !is_valid_component_base(resolved.base_class, project_path)) {
+      const warn = `"${component_type}" extends ${resolved.base_class}, which does not inherit from MonoBehaviour. Adding anyway, but ensure the script is a valid component. (Re-run "setup" if the inheritance graph is stale).`;
+      if (!extractionError)
+        extractionError = warn;
+      else
+        extractionError += " " + warn;
+    }
     let version;
     if (project_path) {
       try {
@@ -6640,10 +7213,22 @@ function addComponent(options) {
     componentYAML = createMonoBehaviourYAML(componentId, gameObjectId, resolved.guid, resolved.fields, version, scriptFileId, type_lookup_comp);
     scriptGuid = resolved.guid;
     scriptPath = resolved.path || undefined;
-    extractionError = resolved.extraction_error;
+    if (resolved.extraction_error) {
+      if (!extractionError)
+        extractionError = resolved.extraction_error;
+      else
+        extractionError += " " + resolved.extraction_error;
+    }
   }
   if (variantInfo) {
-    appendToAddedComponents(doc, variantInfo.prefab_instance_id, variantInfo.source_ref, componentIdStr);
+    const appendResult = appendToAddedComponents(doc, variantInfo.prefab_instance_id, variantInfo.source_ref, componentIdStr);
+    if (!appendResult.success) {
+      return {
+        success: false,
+        file_path,
+        error: appendResult.error || `Failed to update m_AddedComponents for PrefabInstance ${variantInfo.prefab_instance_id}`
+      };
+    }
   } else {
     const added = addComponentToGameObject(doc, gameObjectIdStr, componentIdStr);
     if (!added) {
@@ -7439,6 +8024,56 @@ function validate_value_type(current_value, new_value) {
   }
   return null;
 }
+function findStrippedTransformForPrefabInstance(doc, prefabInstanceId) {
+  const piRefPattern = new RegExp(`m_PrefabInstance:[ \\t]*\\{fileID:[ \\t]*${prefabInstanceId}\\}`);
+  for (const block of doc.blocks) {
+    if ((block.class_id === 4 || block.class_id === 224) && block.is_stripped && piRefPattern.test(block.raw)) {
+      return block;
+    }
+  }
+  return null;
+}
+function resolvePrefabRootOrderTarget(prefabInstanceBlock) {
+  const modificationPattern = /- target:\s*(\{[^}]+\})\s*\n\s*propertyPath:\s*('?)([^\n']+)\2/gm;
+  const transformPropertyPattern = /^m_(?:RootOrder|LocalPosition|LocalRotation|LocalScale|ConstrainProportionsScale)(?:\.|$)/;
+  let transformTarget = null;
+  for (const match of prefabInstanceBlock.raw.matchAll(modificationPattern)) {
+    const targetRef = match[1];
+    const propertyPath = match[3].trim();
+    if (propertyPath === "m_RootOrder") {
+      return targetRef;
+    }
+    if (!transformTarget && transformPropertyPattern.test(propertyPath)) {
+      transformTarget = targetRef;
+    }
+  }
+  return transformTarget;
+}
+function upsertPrefabRootOrderOverride(prefabInstanceBlock, newRootOrder) {
+  const existingRootOrderPattern = /(- target:\s*\{[^}]+\}\s*\n\s*propertyPath:\s*'?m_RootOrder'?\s*\n\s*value:\s*)([^\n]*)(\s*\n\s*objectReference:\s*\{[^}]+\})/m;
+  if (existingRootOrderPattern.test(prefabInstanceBlock.raw)) {
+    prefabInstanceBlock.replace_raw(prefabInstanceBlock.raw.replace(existingRootOrderPattern, `$1${newRootOrder}$3`));
+    return true;
+  }
+  const targetRef = resolvePrefabRootOrderTarget(prefabInstanceBlock) ?? "{fileID: 400000}";
+  const rootOrderOverride = `    - target: ${targetRef}
+` + `      propertyPath: m_RootOrder
+` + `      value: ${newRootOrder}
+` + "      objectReference: {fileID: 0}";
+  const removedPattern = /(\n\s*m_RemovedComponents:)/m;
+  if (removedPattern.test(prefabInstanceBlock.raw)) {
+    prefabInstanceBlock.replace_raw(prefabInstanceBlock.raw.replace(removedPattern, `
+${rootOrderOverride}$1`));
+    return true;
+  }
+  const modsPattern = /(m_Modifications:\s*\n)/;
+  if (modsPattern.test(prefabInstanceBlock.raw)) {
+    prefabInstanceBlock.replace_raw(prefabInstanceBlock.raw.replace(modsPattern, `$1${rootOrderOverride}
+`));
+    return true;
+  }
+  return false;
+}
 function isAncestor(doc, childTransformId, candidateAncestorTransformId) {
   let currentId = candidateAncestorTransformId;
   const visited = new Set;
@@ -7449,20 +8084,37 @@ function isAncestor(doc, childTransformId, candidateAncestorTransformId) {
       return false;
     visited.add(currentId);
     const block = doc.find_by_file_id(currentId);
-    if (!block || block.class_id !== 4)
+    if (!block)
+      break;
+    if (block.class_id === 1001 || block.class_id === 310) {
+      const parentMatch = block.raw.match(/m_TransformParent:\s*\{fileID:\s*(-?\d+)\}/);
+      currentId = parentMatch ? parentMatch[1] : "0";
+    } else if (block.class_id === 4 || block.class_id === 224) {
+      const fatherMatch = block.raw.match(/m_Father:\s*\{fileID:\s*(-?\d+)\}/);
+      currentId = fatherMatch ? fatherMatch[1] : "0";
+    } else {
       break;
-    const fatherMatch = block.raw.match(/m_Father:\s*\{fileID:\s*(-?\d+)\}/);
-    currentId = fatherMatch ? fatherMatch[1] : "0";
+    }
   }
   return false;
 }
 function resolveTransformByGameObjectId(doc, gameObjectFileId) {
   const found = doc.find_by_file_id(gameObjectFileId);
-  if (!found || found.class_id !== 1) {
-    return { error: `GameObject with fileID ${gameObjectFileId} not found` };
+  if (!found) {
+    return { error: `Block with fileID ${gameObjectFileId} not found` };
   }
-  const componentMatch = found.raw.match(/m_Component:\s*\n\s*-\s*component:\s*\{fileID:\s*(-?\d+)\}/);
-  if (!componentMatch) {
+  if (found.class_id === 4 || found.class_id === 224) {
+    return { id: gameObjectFileId };
+  }
+  if (found.class_id === 1001 || found.class_id === 310) {
+    const strippedTransform = findStrippedTransformForPrefabInstance(doc, gameObjectFileId);
+    return { id: strippedTransform ? strippedTransform.file_id : gameObjectFileId };
+  }
+  if (found.class_id !== 1) {
+    return { error: `fileID ${gameObjectFileId} is not a GameObject, Transform, or PrefabInstance (class ${found.class_id})` };
+  }
+  const componentMatch = found.raw.match(/m_Component:\s*\n\s*-\s*component:\s*\{fileID:\s*(-?\d+)\}/);
+  if (!componentMatch) {
     return { error: `GameObject fileID ${gameObjectFileId} has no Transform component` };
   }
   const transformId = componentMatch[1];
@@ -7615,7 +8267,7 @@ function editComponentByFileId(options) {
     return {
       success: false,
       file_path,
-      error: `Could not resolve "${new_value}" to asset reference. Ensure GUID cache exists (run "setup <project>" first).`
+      error: `Could not resolve "${new_value}" to asset reference. Ensure GUID cache exists (run "setup" first, or "setup -p <path>").`
     };
   }
   if (resolved !== undefined) {
@@ -7652,7 +8304,7 @@ function editComponentByFileId(options) {
   }
   const targetBlock = doc.find_by_file_id(file_id);
   if (!targetBlock) {
-    const hasPrefabInstance = doc.find_by_class_id(1001).length > 0;
+    const hasPrefabInstance = doc.find_by_class_id(1001).length > 0 || doc.find_by_class_id(310).length > 0;
     if (hasPrefabInstance) {
       return {
         success: false,
@@ -8117,10 +8769,26 @@ function reparentGameObject(options) {
   }
   const childBlock = doc.find_by_file_id(childTransformId);
   if (!childBlock) {
-    return { success: false, file_path, error: `Transform ${childTransformId} not found` };
+    return { success: false, file_path, error: `Transform or PrefabInstance ${childTransformId} not found` };
+  }
+  const childHierarchyTransformId = (() => {
+    if (childBlock.class_id === 4 || childBlock.class_id === 224) {
+      return childBlock.file_id;
+    }
+    if (childBlock.class_id === 1001 || childBlock.class_id === 310) {
+      const stripped = findStrippedTransformForPrefabInstance(doc, childBlock.file_id);
+      return stripped ? stripped.file_id : null;
+    }
+    return null;
+  })();
+  let oldParentTransformId = "0";
+  if (childBlock.class_id === 1001 || childBlock.class_id === 310) {
+    const parentMatch = childBlock.raw.match(/m_TransformParent:\s*\{fileID:\s*(-?\d+)\}/);
+    oldParentTransformId = parentMatch ? parentMatch[1] : "0";
+  } else {
+    const fatherMatch = childBlock.raw.match(/m_Father:\s*\{fileID:\s*(-?\d+)\}/);
+    oldParentTransformId = fatherMatch ? fatherMatch[1] : "0";
   }
-  const fatherMatch = childBlock.raw.match(/m_Father:\s*\{fileID:\s*(-?\d+)\}/);
-  const oldParentTransformId = fatherMatch ? fatherMatch[1] : "0";
   let newParentTransformId = "0";
   if (new_parent.toLowerCase() !== "root") {
     if (by_id || /^-?\d+$/.test(new_parent)) {
@@ -8147,11 +8815,55 @@ function reparentGameObject(options) {
     }
   }
   if (oldParentTransformId !== "0") {
-    doc.remove_child_from_parent(oldParentTransformId, childTransformId);
+    if (childHierarchyTransformId) {
+      doc.remove_child_from_parent(oldParentTransformId, childHierarchyTransformId);
+    } else {
+      doc.remove_child_from_parent(oldParentTransformId, childBlock.file_id);
+    }
+  } else {
+    if (childHierarchyTransformId) {
+      doc.remove_root_from_scene_roots(childHierarchyTransformId);
+    } else {
+      doc.remove_root_from_scene_roots(childBlock.file_id);
+    }
+  }
+  if (childBlock.class_id === 1001 || childBlock.class_id === 310) {
+    const tpPattern = new RegExp(`(m_TransformParent:\\s*)\\{fileID:\\s*(-?\\d+)\\}`);
+    if (tpPattern.test(childBlock.raw)) {
+      let updatedChildRaw = childBlock.raw.replace(tpPattern, `$1{fileID: ${newParentTransformId}}`);
+      childBlock.replace_raw(updatedChildRaw);
+    } else {
+      const modPattern = /(m_Modification:\s*\n)/;
+      const modIndentMatch = childBlock.raw.match(/^([ \t]*)m_Modification:/m);
+      const indent = modIndentMatch ? modIndentMatch[1] : "";
+      let updatedChildRaw = childBlock.raw.replace(modPattern, `$1${indent}  m_TransformParent: {fileID: ${newParentTransformId}}
+`);
+      childBlock.replace_raw(updatedChildRaw);
+    }
+  } else {
+    const fatherPattern = new RegExp(`(m_Father:\\s*)\\{fileID:\\s*\\d+\\}`);
+    if (fatherPattern.test(childBlock.raw)) {
+      let updatedChildRaw = childBlock.raw.replace(fatherPattern, `$1{fileID: ${newParentTransformId}}`);
+      childBlock.replace_raw(updatedChildRaw);
+    } else {
+      const anchorPattern = /^([ \t]*(?:m_GameObject|m_CorrespondingSourceObject|m_PrefabInstance):[ \t]*\{fileID:[ \t]*(-?\d+)[^}]*\}.*)/m;
+      const headerPattern = /(^--- !u!(?:4|224) &-?\d+ stripped\n(?:Rect)?Transform:)/m;
+      if (anchorPattern.test(childBlock.raw)) {
+        let updatedChildRaw = childBlock.raw.replace(anchorPattern, `$1
+  m_Father: {fileID: ${newParentTransformId}}`);
+        childBlock.replace_raw(updatedChildRaw);
+      } else if (headerPattern.test(childBlock.raw)) {
+        let updatedChildRaw = childBlock.raw.replace(headerPattern, `$1
+  m_Father: {fileID: ${newParentTransformId}}`);
+        childBlock.replace_raw(updatedChildRaw);
+      } else {
+        let updatedChildRaw = childBlock.raw.trimEnd() + `
+  m_Father: {fileID: ${newParentTransformId}}
+`;
+        childBlock.replace_raw(updatedChildRaw);
+      }
+    }
   }
-  const fatherPattern = new RegExp(`(m_Father:\\s*)\\{fileID:\\s*\\d+\\}`);
-  let updatedChildRaw = childBlock.raw.replace(fatherPattern, `$1{fileID: ${newParentTransformId}}`);
-  childBlock.replace_raw(updatedChildRaw);
   {
     let newRootOrder;
     if (newParentTransformId === "0") {
@@ -8159,10 +8871,25 @@ function reparentGameObject(options) {
     } else {
       newRootOrder = doc.calculate_root_order(newParentTransformId);
     }
-    childBlock.set_property("m_RootOrder", String(newRootOrder));
+    if (childBlock.class_id === 1001 || childBlock.class_id === 310) {
+      const stripped = doc.blocks.find((b) => (b.class_id === 4 || b.class_id === 224) && b.is_stripped && new RegExp(`m_PrefabInstance:[ \\t]*\\{fileID:[ \\t]*${childTransformId}\\}`).test(b.raw));
+      if (stripped) {
+        stripped.set_property("m_RootOrder", String(newRootOrder));
+      } else {
+        upsertPrefabRootOrderOverride(childBlock, newRootOrder);
+      }
+    } else {
+      childBlock.set_property("m_RootOrder", String(newRootOrder));
+    }
   }
   if (newParentTransformId !== "0") {
-    doc.add_child_to_parent(newParentTransformId, childTransformId);
+    if (childHierarchyTransformId) {
+      doc.add_child_to_parent(newParentTransformId, childHierarchyTransformId);
+    }
+  } else {
+    if (childHierarchyTransformId) {
+      doc.add_root_to_scene_roots(childHierarchyTransformId);
+    }
   }
   if (!doc.validate()) {
     return { success: false, file_path, error: "Validation failed after reparent" };
@@ -8181,9 +8908,9 @@ function reparentGameObject(options) {
 }
 function findPrefabInstanceBlock(doc, identifier) {
   const asId = doc.find_by_file_id(identifier);
-  if (asId && asId.class_id === 1001)
+  if (asId && (asId.class_id === 1001 || asId.class_id === 310))
     return asId;
-  const piBlocks = doc.find_by_class_id(1001);
+  const piBlocks = [...doc.find_by_class_id(1001), ...doc.find_by_class_id(310)];
   const escaped = identifier.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
   const namePattern = new RegExp(`propertyPath:\\s*m_Name\\s+value:\\s*${escaped}\\s`);
   for (const block of piBlocks) {
@@ -8192,6 +8919,193 @@ function findPrefabInstanceBlock(doc, identifier) {
   }
   return null;
 }
+function parsePrefabRef2(refText) {
+  const fileIdMatch = refText.match(/fileID:[ \t]*(-?\d+)/i);
+  if (!fileIdMatch)
+    return null;
+  const guidMatch = refText.match(/guid:[ \t]*([a-f0-9]{32})/i);
+  const typeMatch = refText.match(/type:[ \t]*(-?\d+)/i);
+  return {
+    file_id: fileIdMatch[1],
+    guid: guidMatch ? guidMatch[1].toLowerCase() : undefined,
+    type: typeMatch ? typeMatch[1] : undefined
+  };
+}
+function extractPrefabSourceGuid2(prefabInstanceRaw) {
+  const sourceMatch = prefabInstanceRaw.match(/m_SourcePrefab:[ \t]*\{[^}]*guid:[ \t]*([a-f0-9]{32})/i);
+  return sourceMatch ? sourceMatch[1].toLowerCase() : null;
+}
+function normalizePrefabRef2(refText, sourceGuid) {
+  const parsed = parsePrefabRef2(refText);
+  if (!parsed) {
+    return { error: `Invalid reference "${refText}". Expected format: {fileID: N, guid: ..., type: T}` };
+  }
+  const guid = parsed.guid ?? sourceGuid;
+  if (!guid) {
+    return { error: `Reference "${refText}" is missing guid and source prefab guid could not be inferred.` };
+  }
+  if (!/^[a-f0-9]{32}$/i.test(guid)) {
+    return { error: `Invalid guid in reference "${refText}". Expected 32-character hex GUID.` };
+  }
+  const type = parsed.type ?? "3";
+  if (!/^-?\d+$/.test(type)) {
+    return { error: `Invalid type in reference "${refText}". Expected an integer type value.` };
+  }
+  return {
+    ref: {
+      file_id: parsed.file_id,
+      guid,
+      type
+    }
+  };
+}
+function parsePrefabRefMatcher(refText) {
+  const parsed = parsePrefabRef2(refText);
+  if (!parsed) {
+    return { error: `Invalid reference "${refText}". Expected format: {fileID: N, guid: ..., type: T}` };
+  }
+  if (parsed.guid && !/^[a-f0-9]{32}$/i.test(parsed.guid)) {
+    return { error: `Invalid guid in reference "${refText}". Expected 32-character hex GUID.` };
+  }
+  if (parsed.type && !/^-?\d+$/.test(parsed.type)) {
+    return { error: `Invalid type in reference "${refText}". Expected an integer type value.` };
+  }
+  return { matcher: parsed };
+}
+function prefabRefKey(ref) {
+  return `${ref.file_id}|${ref.guid}|${ref.type}`;
+}
+function serializePrefabRef2(ref) {
+  return `{fileID: ${ref.file_id}, guid: ${ref.guid}, type: ${ref.type}}`;
+}
+function splitPrefabArraySection2(rawText, key) {
+  const lines = rawText.split(`
+`);
+  const keyPattern = new RegExp(`^([ 	]*)${key}:[ 	]*(.*)$`);
+  let keyIndex = -1;
+  let indent = "";
+  for (let i = 0;i < lines.length; i++) {
+    const match = lines[i].match(keyPattern);
+    if (match) {
+      keyIndex = i;
+      indent = match[1];
+      break;
+    }
+  }
+  if (keyIndex === -1) {
+    return null;
+  }
+  const keyIndentLen = indent.length;
+  let sectionEnd = keyIndex + 1;
+  for (let i = keyIndex + 1;i < lines.length; i++) {
+    const line = lines[i];
+    const trimmed = line.trim();
+    if (trimmed.length === 0) {
+      sectionEnd = i + 1;
+      continue;
+    }
+    const indentLen = (line.match(/^[ \t]*/) || [""])[0].length;
+    if (indentLen < keyIndentLen) {
+      break;
+    }
+    if (indentLen === keyIndentLen && !trimmed.startsWith("-") && /^[A-Za-z_][A-Za-z0-9_]*:/.test(trimmed)) {
+      break;
+    }
+    sectionEnd = i + 1;
+  }
+  return {
+    lines,
+    key_index: keyIndex,
+    section_end: sectionEnd,
+    indent
+  };
+}
+function collectNormalizedRefsFromSection(lines, key_index, section_end, sourceGuid) {
+  const sectionText = lines.slice(key_index, section_end).join(`
+`);
+  const refMatches = sectionText.match(/\{[^}]*\}/g) || [];
+  const dedup = new Map;
+  for (const token of refMatches) {
+    const parsed = parsePrefabRef2(token);
+    if (!parsed)
+      continue;
+    const guid = parsed.guid ?? sourceGuid;
+    if (!guid || !/^[a-f0-9]{32}$/i.test(guid))
+      continue;
+    const type = parsed.type ?? "3";
+    if (!/^-?\d+$/.test(type))
+      continue;
+    const normalized = {
+      file_id: parsed.file_id,
+      guid: guid.toLowerCase(),
+      type
+    };
+    const key = prefabRefKey(normalized);
+    if (!dedup.has(key)) {
+      dedup.set(key, normalized);
+    }
+  }
+  return [...dedup.values()];
+}
+function mutatePrefabReferenceList(options) {
+  const { target_block, key, ref_text, action, item_label } = options;
+  const split = splitPrefabArraySection2(target_block.raw, key);
+  if (!split) {
+    return { success: false, error: `${key} property not found in PrefabInstance` };
+  }
+  const sourceGuid = extractPrefabSourceGuid2(target_block.raw);
+  const existing = collectNormalizedRefsFromSection(split.lines, split.key_index, split.section_end, sourceGuid);
+  let next = existing;
+  if (action === "add") {
+    const normalized = normalizePrefabRef2(ref_text, sourceGuid);
+    if (!normalized.ref) {
+      return { success: false, error: normalized.error };
+    }
+    const keyText = prefabRefKey(normalized.ref);
+    if (existing.some((entry) => prefabRefKey(entry) === keyText)) {
+      return { success: true, changed: false };
+    }
+    next = [...existing, normalized.ref];
+  } else {
+    const matcherResult = parsePrefabRefMatcher(ref_text);
+    const matcher = matcherResult.matcher;
+    if (!matcher) {
+      return { success: false, error: matcherResult.error };
+    }
+    next = existing.filter((entry) => {
+      if (entry.file_id !== matcher.file_id)
+        return true;
+      if (matcher.guid && entry.guid !== matcher.guid.toLowerCase())
+        return true;
+      if (matcher.type && entry.type !== matcher.type)
+        return true;
+      return false;
+    });
+    if (next.length === existing.length) {
+      return {
+        success: false,
+        error: `${item_label} reference "${ref_text}" not found in ${key}`
+      };
+    }
+  }
+  const replacement = [];
+  if (next.length === 0) {
+    replacement.push(`${split.indent}${key}: []`);
+  } else {
+    replacement.push(`${split.indent}${key}:`);
+    for (const entry of next) {
+      replacement.push(`${split.indent}- ${serializePrefabRef2(entry)}`);
+    }
+  }
+  const updatedLines = [
+    ...split.lines.slice(0, split.key_index),
+    ...replacement,
+    ...split.lines.slice(split.section_end)
+  ];
+  target_block.replace_raw(updatedLines.join(`
+`));
+  return { success: true, changed: true };
+}
 function editArray(options) {
   const { file_path, file_id, array_property, action, value, index } = options;
   if (!import_fs10.existsSync(file_path)) {
@@ -8402,9 +9316,6 @@ function addRemovedComponent(options) {
   if (!import_fs10.existsSync(file_path)) {
     return { success: false, file_path, error: `File not found: ${file_path}` };
   }
-  if (!/^\{fileID:\s*-?\d+/.test(component_ref)) {
-    return { success: false, file_path, error: `Invalid component reference "${component_ref}". Expected format: {fileID: N, guid: ..., type: T}` };
-  }
   let doc;
   try {
     doc = UnityDocument.from_file(file_path);
@@ -8415,19 +9326,16 @@ function addRemovedComponent(options) {
   if (!targetBlock) {
     return { success: false, file_path, error: `PrefabInstance "${prefab_instance}" not found` };
   }
-  let rawText = targetBlock.raw;
-  if (/m_RemovedComponents:\s*\[\]/.test(rawText)) {
-    rawText = rawText.replace(/m_RemovedComponents:\s*\[\]/, "m_RemovedComponents:");
-  }
-  const removedPattern = /m_RemovedComponents:\s*\n/;
-  if (removedPattern.test(rawText)) {
-    rawText = rawText.replace(removedPattern, `m_RemovedComponents:
-  - ${component_ref}
-`);
-  } else {
-    return { success: false, file_path, error: "m_RemovedComponents property not found in PrefabInstance" };
+  const mutation = mutatePrefabReferenceList({
+    target_block: targetBlock,
+    key: "m_RemovedComponents",
+    ref_text: component_ref,
+    action: "add",
+    item_label: "Component"
+  });
+  if (!mutation.success) {
+    return { success: false, file_path, error: mutation.error };
   }
-  targetBlock.replace_raw(rawText);
   if (!doc.validate()) {
     return { success: false, file_path, error: "Validation failed after adding removed component" };
   }
@@ -8456,13 +9364,16 @@ function removeRemovedComponent(options) {
   if (!targetBlock) {
     return { success: false, file_path, error: `PrefabInstance "${prefab_instance}" not found` };
   }
-  const escapedRef = component_ref.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
-  const refPattern = new RegExp(`\\s*- ${escapedRef}\\n?`, "m");
-  if (!refPattern.test(targetBlock.raw)) {
-    return { success: false, file_path, error: `Component reference "${component_ref}" not found in m_RemovedComponents` };
+  const mutation = mutatePrefabReferenceList({
+    target_block: targetBlock,
+    key: "m_RemovedComponents",
+    ref_text: component_ref,
+    action: "remove",
+    item_label: "Component"
+  });
+  if (!mutation.success) {
+    return { success: false, file_path, error: mutation.error };
   }
-  const updatedRaw = targetBlock.raw.replace(refPattern, "");
-  targetBlock.replace_raw(updatedRaw);
   if (!doc.validate()) {
     return { success: false, file_path, error: "Validation failed after removing component" };
   }
@@ -8481,9 +9392,6 @@ function addRemovedGameObject(options) {
   if (!import_fs10.existsSync(file_path)) {
     return { success: false, file_path, error: `File not found: ${file_path}` };
   }
-  if (!/^\{fileID:\s*-?\d+/.test(component_ref)) {
-    return { success: false, file_path, error: `Invalid GameObject reference "${component_ref}". Expected format: {fileID: N, guid: ..., type: T}` };
-  }
   let doc;
   try {
     doc = UnityDocument.from_file(file_path);
@@ -8494,19 +9402,16 @@ function addRemovedGameObject(options) {
   if (!targetBlock) {
     return { success: false, file_path, error: `PrefabInstance "${prefab_instance}" not found` };
   }
-  let rawText = targetBlock.raw;
-  if (/m_RemovedGameObjects:\s*\[\]/.test(rawText)) {
-    rawText = rawText.replace(/m_RemovedGameObjects:\s*\[\]/, "m_RemovedGameObjects:");
-  }
-  const removedPattern = /m_RemovedGameObjects:\s*\n/;
-  if (removedPattern.test(rawText)) {
-    rawText = rawText.replace(removedPattern, `m_RemovedGameObjects:
-  - ${component_ref}
-`);
-  } else {
-    return { success: false, file_path, error: "m_RemovedGameObjects property not found in PrefabInstance" };
+  const mutation = mutatePrefabReferenceList({
+    target_block: targetBlock,
+    key: "m_RemovedGameObjects",
+    ref_text: component_ref,
+    action: "add",
+    item_label: "GameObject"
+  });
+  if (!mutation.success) {
+    return { success: false, file_path, error: mutation.error };
   }
-  targetBlock.replace_raw(rawText);
   if (!doc.validate()) {
     return { success: false, file_path, error: "Validation failed after adding removed GameObject" };
   }
@@ -8535,13 +9440,16 @@ function removeRemovedGameObject(options) {
   if (!targetBlock) {
     return { success: false, file_path, error: `PrefabInstance "${prefab_instance}" not found` };
   }
-  const escapedRef = component_ref.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
-  const refPattern = new RegExp(`\\s*- ${escapedRef}\\n?`, "m");
-  if (!refPattern.test(targetBlock.raw)) {
-    return { success: false, file_path, error: `GameObject reference "${component_ref}" not found in m_RemovedGameObjects` };
+  const mutation = mutatePrefabReferenceList({
+    target_block: targetBlock,
+    key: "m_RemovedGameObjects",
+    ref_text: component_ref,
+    action: "remove",
+    item_label: "GameObject"
+  });
+  if (!mutation.success) {
+    return { success: false, file_path, error: mutation.error };
   }
-  const updatedRaw = targetBlock.raw.replace(refPattern, "");
-  targetBlock.replace_raw(updatedRaw);
   if (!doc.validate()) {
     return { success: false, file_path, error: "Validation failed after removing GameObject" };
   }
@@ -8804,6 +9712,7 @@ ${fieldIndent}  - rid: ${nextRid}`;
 }
 // src/editor/delete.ts
 var import_fs13 = require("fs");
+var import_path6 = require("path");
 
 // src/project-search.ts
 init_scanner();
@@ -9398,6 +10307,7 @@ function removeComponent(options) {
     return { success: false, file_path, error: "Cannot remove a Transform with remove-component. Use delete to remove the entire GameObject." };
   }
   const resolved_file_id = found.file_id;
+  let removed_added_component_overrides = 0;
   const goMatch = found.raw.match(/m_GameObject:[ \t]*\{fileID:[ \t]*(-?\d+)\}/);
   if (goMatch) {
     const parentGoId = goMatch[1];
@@ -9408,6 +10318,19 @@ function removeComponent(options) {
       const modifiedRaw = goBlock.raw.replace(compLinePattern, "");
       if (modifiedRaw === goBlock.raw) {}
       goBlock.replace_raw(modifiedRaw);
+      if (goBlock.is_stripped) {
+        const piMatch = goBlock.raw.match(/m_PrefabInstance:[ \t]*\{fileID:[ \t]*(-?\d+)\}/);
+        if (piMatch) {
+          const piBlock = doc.find_by_file_id(piMatch[1]);
+          if (piBlock && piBlock.class_id === 1001) {
+            const updated = removeAddedComponentOverrideEntries(piBlock.raw, resolved_file_id);
+            if (updated.removed_count > 0) {
+              piBlock.replace_raw(updated.updated_raw);
+              removed_added_component_overrides += updated.removed_count;
+            }
+          }
+        }
+      }
     }
   }
   const dangling = [];
@@ -9431,7 +10354,7 @@ function removeComponent(options) {
     file_path,
     removed_file_id: resolved_file_id,
     removed_class_id: found.class_id,
-    warning: dangling.length > 0 ? `Dangling references to deleted component found in blocks: ${dangling.join(", ")}` : undefined
+    warning: dangling.length > 0 ? `Dangling references to deleted component found in blocks: ${dangling.join(", ")}${removed_added_component_overrides > 0 ? ` (removed ${removed_added_component_overrides} m_AddedComponents override entr${removed_added_component_overrides === 1 ? "y" : "ies"})` : ""}` : undefined
   };
 }
 function removeComponentBatch(options) {
@@ -9549,6 +10472,124 @@ function findPrefabInstanceBlock2(doc, identifier) {
   }
   return null;
 }
+function splitPrefabArraySection3(rawText, key) {
+  const lines = rawText.split(`
+`);
+  const keyPattern = new RegExp(`^[ 	]*${key}:[ 	]*(.*)$`);
+  let keyIndex = -1;
+  let keyIndentLen = 0;
+  for (let i = 0;i < lines.length; i++) {
+    const match = lines[i].match(keyPattern);
+    if (match) {
+      keyIndex = i;
+      keyIndentLen = (lines[i].match(/^[ \t]*/) || [""])[0].length;
+      break;
+    }
+  }
+  if (keyIndex === -1) {
+    return null;
+  }
+  let sectionEnd = keyIndex + 1;
+  for (let i = keyIndex + 1;i < lines.length; i++) {
+    const line = lines[i];
+    const trimmed = line.trim();
+    if (trimmed.length === 0) {
+      sectionEnd = i + 1;
+      continue;
+    }
+    const indentLen = (line.match(/^[ \t]*/) || [""])[0].length;
+    if (indentLen < keyIndentLen) {
+      break;
+    }
+    if (indentLen === keyIndentLen && !trimmed.startsWith("-") && /^[A-Za-z_][A-Za-z0-9_]*:/.test(trimmed)) {
+      break;
+    }
+    sectionEnd = i + 1;
+  }
+  return {
+    lines,
+    key_index: keyIndex,
+    section_end: sectionEnd
+  };
+}
+function collectAddedObjectFileIdsFromArray(rawText, key) {
+  const section = splitPrefabArraySection3(rawText, key);
+  if (!section)
+    return [];
+  const keyLine = section.lines[section.key_index].trim();
+  if (new RegExp(`^${key}:[ 	]*[]$`).test(keyLine)) {
+    return [];
+  }
+  const sectionText = section.lines.slice(section.key_index, section.section_end).join(`
+`);
+  const fileIds = new Set;
+  const addedObjectPattern = /addedObject:[ \t]*\{[^}]*fileID:[ \t]*(-?\d+)/g;
+  let match;
+  while ((match = addedObjectPattern.exec(sectionText)) !== null) {
+    fileIds.add(match[1]);
+  }
+  if (fileIds.size === 0) {
+    const inlineEntryPattern = /^[ \t]*-[ \t]*\{[^}]*fileID:[ \t]*(-?\d+)/gm;
+    while ((match = inlineEntryPattern.exec(sectionText)) !== null) {
+      fileIds.add(match[1]);
+    }
+  }
+  return [...fileIds];
+}
+function removeAddedComponentOverrideEntries(rawText, componentId) {
+  const section = splitPrefabArraySection3(rawText, "m_AddedComponents");
+  if (!section)
+    return { updated_raw: rawText, removed_count: 0 };
+  const keyLine = section.lines[section.key_index].trim();
+  if (/^m_AddedComponents:[ \t]*\[\]$/.test(keyLine)) {
+    return { updated_raw: rawText, removed_count: 0 };
+  }
+  const bodyLines = section.lines.slice(section.key_index + 1, section.section_end);
+  const keptEntries = [];
+  let removed = 0;
+  let i = 0;
+  while (i < bodyLines.length) {
+    const line = bodyLines[i];
+    const trimmed = line.trimStart();
+    if (!trimmed.startsWith("-")) {
+      i++;
+      continue;
+    }
+    const entryIndent = (line.match(/^[ \t]*/) || [""])[0].length;
+    const entryLines = [line];
+    i++;
+    while (i < bodyLines.length) {
+      const nextLine = bodyLines[i];
+      const nextTrimmed = nextLine.trim();
+      const nextIndent = (nextLine.match(/^[ \t]*/) || [""])[0].length;
+      if (nextTrimmed.length > 0 && nextIndent === entryIndent && nextTrimmed.startsWith("-")) {
+        break;
+      }
+      entryLines.push(nextLine);
+      i++;
+    }
+    const entryText = entryLines.join(`
+`);
+    const addedObjectMatch = entryText.match(/addedObject:[ \t]*\{[^}]*fileID:[ \t]*(-?\d+)/);
+    if (addedObjectMatch && addedObjectMatch[1] === componentId) {
+      removed++;
+      continue;
+    }
+    keptEntries.push(entryLines);
+  }
+  if (removed === 0) {
+    return { updated_raw: rawText, removed_count: 0 };
+  }
+  const keyIndent = (section.lines[section.key_index].match(/^[ \t]*/) || [""])[0];
+  const replacement = keptEntries.length === 0 ? [`${keyIndent}m_AddedComponents: []`] : [`${keyIndent}m_AddedComponents:`, ...keptEntries.flat()];
+  const updatedLines = [
+    ...section.lines.slice(0, section.key_index),
+    ...replacement,
+    ...section.lines.slice(section.section_end)
+  ];
+  return { updated_raw: updatedLines.join(`
+`), removed_count: removed };
+}
 function deletePrefabInstance(options) {
   const { file_path, prefab_instance } = options;
   const pathError = validate_file_path(file_path, "write");
@@ -9576,36 +10617,23 @@ function deletePrefabInstance(options) {
       allToRemove.add(block.file_id);
     }
   }
-  const addedGOPattern = /m_AddedGameObjects:\s*\n((?:\s*- \{fileID: \d+\}\n)*)/m;
-  const addedGOMatch = piBlock.raw.match(addedGOPattern);
-  if (addedGOMatch) {
-    const addedGOSection = addedGOMatch[1];
-    const goMatches = addedGOSection.matchAll(/fileID:[ \t]*(\d+)/g);
-    for (const match of goMatches) {
-      const goId = match[1];
-      allToRemove.add(goId);
-      const goBlock = doc.find_by_file_id(goId);
-      if (goBlock) {
-        const compMatch = goBlock.raw.match(/component:[ \t]*\{fileID:[ \t]*(\d+)\}/);
-        if (compMatch) {
-          const transformId = compMatch[1];
-          allToRemove.add(transformId);
-          const descendants = doc.collect_hierarchy(transformId);
-          for (const id of descendants) {
-            allToRemove.add(id);
-          }
+  for (const goId of collectAddedObjectFileIdsFromArray(piBlock.raw, "m_AddedGameObjects")) {
+    allToRemove.add(goId);
+    const goBlock = doc.find_by_file_id(goId);
+    if (goBlock) {
+      const compMatch = goBlock.raw.match(/component:[ \t]*\{fileID:[ \t]*(\d+)\}/);
+      if (compMatch) {
+        const transformId = compMatch[1];
+        allToRemove.add(transformId);
+        const descendants = doc.collect_hierarchy(transformId);
+        for (const id of descendants) {
+          allToRemove.add(id);
         }
       }
     }
   }
-  const addedCompPattern = /m_AddedComponents:\s*\n((?:\s*- \{fileID: \d+\}\n)*)/m;
-  const addedCompMatch = piBlock.raw.match(addedCompPattern);
-  if (addedCompMatch) {
-    const addedCompSection = addedCompMatch[1];
-    const compMatches = addedCompSection.matchAll(/fileID:[ \t]*(\d+)/g);
-    for (const match of compMatches) {
-      allToRemove.add(match[1]);
-    }
+  for (const componentId of collectAddedObjectFileIdsFromArray(piBlock.raw, "m_AddedComponents")) {
+    allToRemove.add(componentId);
   }
   const parentMatch = piBlock.raw.match(/m_TransformParent:[ \t]*\{fileID:[ \t]*(\d+)\}/);
   const parentTransformId = parentMatch ? parentMatch[1] : "0";
@@ -9634,6 +10662,70 @@ function deletePrefabInstance(options) {
     deleted_count: allToRemove.size
   };
 }
+function deleteAssetFile(options) {
+  const { file_path } = options;
+  const pathError = validate_file_path(file_path, "write");
+  if (pathError) {
+    return { success: false, file_path, error: pathError };
+  }
+  if (!import_fs13.existsSync(file_path)) {
+    return { success: false, file_path, error: `File not found: ${file_path}` };
+  }
+  const supportedExtensions = new Set([
+    ".unity",
+    ".prefab",
+    ".mat",
+    ".anim",
+    ".controller",
+    ".inputactions",
+    ".asset"
+  ]);
+  const extension = import_path6.extname(file_path).toLowerCase();
+  if (!supportedExtensions.has(extension)) {
+    return {
+      success: false,
+      file_path,
+      error: `Unsupported asset type "${extension}". Supported extensions: .unity, .prefab, .mat, .anim, .controller, .inputactions, .asset`
+    };
+  }
+  const metaPath = `${file_path}.meta`;
+  const hasMeta = import_fs13.existsSync(metaPath);
+  try {
+    import_fs13.unlinkSync(file_path);
+  } catch (err) {
+    return {
+      success: false,
+      file_path,
+      error: `Failed to delete file: ${err instanceof Error ? err.message : String(err)}`
+    };
+  }
+  if (hasMeta) {
+    try {
+      import_fs13.unlinkSync(metaPath);
+      return {
+        success: true,
+        file_path,
+        deleted_file: true,
+        deleted_meta: true
+      };
+    } catch (err) {
+      return {
+        success: true,
+        file_path,
+        deleted_file: true,
+        deleted_meta: false,
+        warning: `Deleted asset file but failed to delete .meta file: ${err instanceof Error ? err.message : String(err)}`
+      };
+    }
+  }
+  return {
+    success: true,
+    file_path,
+    deleted_file: true,
+    deleted_meta: false,
+    warning: `Asset file deleted, but no .meta file found at ${metaPath}`
+  };
+}
 // src/editor/duplicate.ts
 var import_fs14 = require("fs");
 var path6 = __toESM(require("path"));
@@ -10278,9 +11370,9 @@ function move_scene(projectPath, scenePath, newPosition) {
 
 // src/packages.ts
 var import_fs15 = require("fs");
-var import_path6 = require("path");
+var import_path7 = require("path");
 function load_manifest(project_path) {
-  const manifest_path = import_path6.join(project_path, "Packages", "manifest.json");
+  const manifest_path = import_path7.join(project_path, "Packages", "manifest.json");
   if (!import_fs15.existsSync(manifest_path)) {
     return { error: `manifest.json not found at ${manifest_path}` };
   }
@@ -10474,24 +11566,381 @@ function remove_control_scheme(data, name) {
   return data;
 }
 
-// src/cmd-create.ts
-function build_create_command() {
-  const cmd = new Command("create").description("Create Unity objects (GameObjects, scenes, prefabs, components)");
-  cmd.command("gameobject <file> [name]").description("Create a new GameObject in a Unity file").option("-p, --parent <name|id>", "Parent GameObject name or Transform fileID").option("-n, --name <name>", "GameObject name (alternative to positional arg)").option("-j, --json", "Output as JSON").action((file, name_positional, options) => {
-    const name = name_positional || options.name;
-    if (!name) {
-      console.log(JSON.stringify({
-        success: false,
-        error: "Missing required name. Provide as positional argument or --name flag.",
-        correct_usage: [
-          "unity-agentic-tools create gameobject <file> <name>",
-          "unity-agentic-tools create gameobject <file> --name <name>"
-        ]
-      }, null, 2));
-      process.exitCode = 1;
-      return;
+// src/loaded-protection.ts
+var import_path9 = require("path");
+
+// src/editor-client.ts
+var import_fs17 = require("fs");
+var import_path8 = require("path");
+function read_editor_config(project_path) {
+  const config_path = import_path8.join(project_path, ".unity-agentic", "editor.json");
+  if (!import_fs17.existsSync(config_path)) {
+    return { error: `Editor bridge not found at ${config_path}. Is the Unity Editor running with the bridge package installed?` };
+  }
+  let config;
+  try {
+    const raw = import_fs17.readFileSync(config_path, "utf-8");
+    config = JSON.parse(raw);
+  } catch (err) {
+    return { error: `Failed to parse editor.json: ${err instanceof Error ? err.message : String(err)}` };
+  }
+  if (typeof config.port !== "number" || typeof config.pid !== "number") {
+    return { error: "Invalid editor.json: missing port or pid" };
+  }
+  if (!is_pid_alive(config.pid)) {
+    return { error: `Unity Editor process (PID ${config.pid}) is not running. The editor may have been closed.` };
+  }
+  return config;
+}
+var RETRYABLE_CODES = new Set([-32000, -32002, -32003]);
+var RETRY_DELAYS = [500, 1000, 2000];
+async function call_editor(options) {
+  const maxRetries = options.retries ?? 2;
+  let lastResponse;
+  for (let attempt = 0;attempt <= maxRetries; attempt++) {
+    lastResponse = await call_editor_once(options);
+    if (!lastResponse.error || !RETRYABLE_CODES.has(lastResponse.error.code)) {
+      return lastResponse;
     }
-    const ext = file.toLowerCase().split(".").pop();
+    if (attempt < maxRetries) {
+      const delay = RETRY_DELAYS[Math.min(attempt, RETRY_DELAYS.length - 1)];
+      await new Promise((r) => setTimeout(r, delay));
+    }
+  }
+  return lastResponse;
+}
+function call_editor_once(options) {
+  const { method, params, timeout = 1e4, no_wait } = options;
+  const config = resolve_config(options);
+  if ("error" in config) {
+    return Promise.resolve({
+      jsonrpc: "2.0",
+      id: "0",
+      error: { code: -32000, message: config.error }
+    });
+  }
+  const url = `ws://127.0.0.1:${config.port}/unity-agentic`;
+  const request_id = generate_id();
+  const wire_params = { ...params };
+  if (timeout !== 1e4)
+    wire_params._timeout = timeout;
+  if (no_wait)
+    wire_params.no_wait = true;
+  const request = {
+    jsonrpc: "2.0",
+    id: request_id,
+    method,
+    ...Object.keys(wire_params).length > 0 ? { params: wire_params } : {}
+  };
+  return new Promise((resolve5) => {
+    let resolved = false;
+    let ws;
+    const timer = setTimeout(() => {
+      if (!resolved) {
+        resolved = true;
+        try {
+          ws?.close();
+        } catch {}
+        resolve5({
+          jsonrpc: "2.0",
+          id: request_id,
+          error: { code: -32001, message: `Timeout after ${timeout}ms waiting for response to ${method}` }
+        });
+      }
+    }, timeout);
+    try {
+      ws = new WebSocket(url);
+      ws.onopen = () => {
+        ws.send(JSON.stringify(request));
+        if (no_wait && !resolved) {
+          resolved = true;
+          clearTimeout(timer);
+          setTimeout(() => {
+            try {
+              ws.close();
+            } catch {}
+          }, 200);
+          resolve5({
+            jsonrpc: "2.0",
+            id: request_id,
+            result: { queued: true }
+          });
+        }
+      };
+      ws.onmessage = (event) => {
+        try {
+          const data = JSON.parse(String(event.data));
+          if (data.id === request_id) {
+            if (!resolved) {
+              resolved = true;
+              clearTimeout(timer);
+              ws.close();
+              resolve5(data);
+            }
+          }
+        } catch {}
+      };
+      ws.onerror = () => {
+        if (!resolved) {
+          resolved = true;
+          clearTimeout(timer);
+          resolve5({
+            jsonrpc: "2.0",
+            id: request_id,
+            error: { code: -32002, message: `WebSocket connection failed to ${url}. Is the Unity Editor running?` }
+          });
+        }
+      };
+      ws.onclose = () => {
+        if (!resolved) {
+          resolved = true;
+          clearTimeout(timer);
+          resolve5({
+            jsonrpc: "2.0",
+            id: request_id,
+            error: { code: -32003, message: "WebSocket connection closed before response received" }
+          });
+        }
+      };
+    } catch (err) {
+      if (!resolved) {
+        resolved = true;
+        clearTimeout(timer);
+        resolve5({
+          jsonrpc: "2.0",
+          id: request_id,
+          error: { code: -32002, message: `Failed to connect: ${err instanceof Error ? err.message : String(err)}` }
+        });
+      }
+    }
+  });
+}
+async function stream_editor(options) {
+  const { method, params, timeout = 30000, on_event } = options;
+  const config = resolve_config(options);
+  if ("error" in config) {
+    throw new Error(config.error);
+  }
+  const MAX_RECONNECTS = 5;
+  let reconnect_count = 0;
+  let stopped = false;
+  return new Promise((resolve5, reject) => {
+    let resolved = false;
+    function connect(url) {
+      const ws = new WebSocket(url);
+      const request_id = generate_id();
+      const request = {
+        jsonrpc: "2.0",
+        id: request_id,
+        method,
+        ...params ? { params } : {}
+      };
+      let connected = false;
+      const timer = !resolved ? setTimeout(() => {
+        if (!connected && !resolved) {
+          reject(new Error(`Timeout connecting to ${url}`));
+        }
+      }, timeout) : null;
+      ws.onopen = () => {
+        connected = true;
+        if (timer)
+          clearTimeout(timer);
+        reconnect_count = 0;
+        ws.send(JSON.stringify(request));
+        if (!resolved) {
+          resolved = true;
+          resolve5({ close: () => {
+            stopped = true;
+            ws.close();
+          } });
+        }
+      };
+      ws.onmessage = (event) => {
+        try {
+          const data = JSON.parse(String(event.data));
+          if ("method" in data && !("id" in data)) {
+            on_event(data);
+          }
+        } catch {}
+      };
+      ws.onerror = () => {
+        if (!connected && !resolved) {
+          if (timer)
+            clearTimeout(timer);
+          reject(new Error(`WebSocket connection failed to ${url}`));
+        }
+      };
+      ws.onclose = () => {
+        if (stopped)
+          return;
+        if (!connected && !resolved)
+          return;
+        if (reconnect_count >= MAX_RECONNECTS)
+          return;
+        reconnect_count++;
+        const delay = Math.min(500 * reconnect_count, 3000);
+        setTimeout(() => {
+          if (stopped)
+            return;
+          const fresh_config = resolve_config(options);
+          if ("error" in fresh_config)
+            return;
+          connect(`ws://127.0.0.1:${fresh_config.port}/unity-agentic`);
+        }, delay);
+      };
+    }
+    connect(`ws://127.0.0.1:${config.port}/unity-agentic`);
+  });
+}
+async function ping_editor(port, timeout_ms = 2000) {
+  return new Promise((resolve5) => {
+    const timer = setTimeout(() => {
+      resolve5({ reachable: false, error: `Timeout after ${timeout_ms}ms` });
+    }, timeout_ms);
+    try {
+      const ws = new WebSocket(`ws://127.0.0.1:${port}/unity-agentic`);
+      ws.onopen = () => {
+        clearTimeout(timer);
+        try {
+          ws.close();
+        } catch {}
+        resolve5({ reachable: true });
+      };
+      ws.onerror = (err) => {
+        clearTimeout(timer);
+        resolve5({ reachable: false, error: String(err) });
+      };
+    } catch (err) {
+      clearTimeout(timer);
+      resolve5({ reachable: false, error: String(err) });
+    }
+  });
+}
+function resolve_config(options) {
+  if (options.port) {
+    return { port: options.port, pid: 0, version: "unknown" };
+  }
+  return read_editor_config(options.project_path);
+}
+function is_pid_alive(pid) {
+  try {
+    process.kill(pid, 0);
+    return true;
+  } catch {
+    return false;
+  }
+}
+function generate_id() {
+  return `${Date.now()}-${Math.random().toString(36).substring(2, 8)}`;
+}
+
+// src/loaded-protection.ts
+function normalize_slashes(value) {
+  return value.replace(/\\/g, "/");
+}
+function to_project_asset_path(file_path, project_path) {
+  const abs_file = import_path9.resolve(file_path);
+  const abs_project = import_path9.resolve(project_path);
+  const rel = import_path9.relative(abs_project, abs_file);
+  if (!rel || rel.startsWith("..") || rel.includes(`..${import_path9.sep}`)) {
+    if (/^Assets[\\/]/.test(file_path)) {
+      return normalize_slashes(file_path);
+    }
+    return null;
+  }
+  return normalize_slashes(rel);
+}
+function normalize_loaded_paths(paths) {
+  return new Set(paths.map((p) => normalize_slashes(p)));
+}
+async function get_loaded_state(project_path) {
+  const config = read_editor_config(project_path);
+  if ("error" in config)
+    return null;
+  const ping = await ping_editor(config.port, 1200);
+  if (!ping.reachable)
+    return null;
+  const response = await call_editor({
+    project_path,
+    method: "editor.scene.loaded",
+    timeout: 2500
+  });
+  if (response.error || !response.result || typeof response.result !== "object") {
+    return null;
+  }
+  const result = response.result;
+  const loaded = Array.isArray(result.loaded_scene_paths) ? result.loaded_scene_paths.filter((v) => typeof v === "string") : [];
+  return {
+    loaded_scene_paths: loaded,
+    active_scene_path: typeof result.active_scene_path === "string" ? result.active_scene_path : undefined,
+    prefab_stage_path: typeof result.prefab_stage_path === "string" ? result.prefab_stage_path : undefined
+  };
+}
+async function is_editor_connected_for_project(project_path) {
+  const resolved_project = resolve_project_path(project_path);
+  const config = read_editor_config(resolved_project);
+  if ("error" in config)
+    return false;
+  const ping = await ping_editor(config.port, 1200);
+  return ping.reachable;
+}
+async function enforce_loaded_edit_protection(file_path, bypass, project_path) {
+  if (bypass)
+    return { allowed: true };
+  const ext = file_path.toLowerCase().split(".").pop();
+  if (!ext || ext !== "unity" && ext !== "prefab") {
+    return { allowed: true };
+  }
+  const inferred_project = project_path ? resolve_project_path(project_path) : find_unity_project_root(import_path9.dirname(import_path9.resolve(file_path))) || process.cwd();
+  const loaded_state = await get_loaded_state(inferred_project);
+  if (!loaded_state) {
+    return { allowed: true };
+  }
+  const target_asset_path = to_project_asset_path(file_path, inferred_project);
+  if (!target_asset_path) {
+    return { allowed: true };
+  }
+  const loaded_scenes = normalize_loaded_paths(loaded_state.loaded_scene_paths);
+  const active_scene = loaded_state.active_scene_path ? normalize_slashes(loaded_state.active_scene_path) : "";
+  const prefab_stage = loaded_state.prefab_stage_path ? normalize_slashes(loaded_state.prefab_stage_path) : "";
+  if (target_asset_path.endsWith(".unity")) {
+    if (loaded_scenes.has(target_asset_path)) {
+      const reason = active_scene === target_asset_path ? "it is currently the active scene in the Unity Editor" : "it is currently loaded in the Unity Editor";
+      return {
+        allowed: false,
+        error: `Refusing to edit ${target_asset_path}: ${reason}. Use --bypass-loaded-protection to force file-based edits while editor is connected.`
+      };
+    }
+  }
+  if (target_asset_path.endsWith(".prefab")) {
+    if (prefab_stage === target_asset_path) {
+      return {
+        allowed: false,
+        error: `Refusing to edit ${target_asset_path}: it is currently open in Prefab Mode. Use --bypass-loaded-protection to force file-based edits while editor is connected.`
+      };
+    }
+  }
+  return { allowed: true };
+}
+
+// src/cmd-create.ts
+function build_create_command() {
+  const cmd = new Command("create").description("Create Unity objects (GameObjects, scenes, prefabs, components)");
+  cmd.command("gameobject <file> [name]").description("Create a new GameObject in a Unity file").option("-p, --parent <name|id>", "Parent GameObject name or Transform fileID").option("-n, --name <name>", "GameObject name (alternative to positional arg)").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").option("-j, --json", "Output as JSON").action(async (file, name_positional, options) => {
+    const name = name_positional || options.name;
+    if (!name) {
+      console.log(JSON.stringify({
+        success: false,
+        error: "Missing required name. Provide as positional argument or --name flag.",
+        correct_usage: [
+          "unity-agentic-tools create gameobject <file> <name>",
+          "unity-agentic-tools create gameobject <file> --name <name>"
+        ]
+      }, null, 2));
+      process.exitCode = 1;
+      return;
+    }
+    const ext = file.toLowerCase().split(".").pop();
     if (!ext || !["unity", "prefab", "asset"].includes(ext)) {
       console.log(JSON.stringify({ success: false, error: `Invalid file type ".${ext}". create gameobject only works with .unity, .prefab, or .asset files` }, null, 2));
       process.exitCode = 1;
@@ -10502,6 +11951,12 @@ function build_create_command() {
       const asNumber = parseInt(options.parent, 10);
       parent = isNaN(asNumber) ? options.parent : asNumber;
     }
+    const guard = await enforce_loaded_edit_protection(file, options.bypassLoadedProtection);
+    if (!guard.allowed) {
+      console.log(JSON.stringify({ success: false, file_path: file, error: guard.error }, null, 2));
+      process.exitCode = 1;
+      return;
+    }
     const result = createGameObject({
       file_path: file,
       name,
@@ -10530,7 +11985,7 @@ function build_create_command() {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("prefab-instance <scene_file> <prefab_path>").description("Instantiate a prefab into a scene file").option("-n, --name <name>", "Instance name (defaults to prefab filename)").option("-p, --parent <name|id>", "Parent GameObject name or Transform fileID").option("--position <x,y,z>", "Local position (default: 0,0,0)").option("-j, --json", "Output as JSON").action((scene_file, prefab_path_arg, options) => {
+  cmd.command("prefab-instance <scene_file> <prefab_path>").description("Instantiate a prefab into a scene file").option("-n, --name <name>", "Instance name (defaults to prefab filename)").option("-p, --parent <name|id>", "Parent GameObject name or Transform fileID").option("--position <x,y,z>", "Local position (default: 0,0,0)").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").option("-j, --json", "Output as JSON").action(async (scene_file, prefab_path_arg, options) => {
     let position;
     if (options.position) {
       const parts = options.position.split(",").map(Number);
@@ -10549,6 +12004,12 @@ function build_create_command() {
       const asNumber = parseInt(options.parent, 10);
       parent = isNaN(asNumber) ? options.parent : asNumber;
     }
+    const guard = await enforce_loaded_edit_protection(scene_file, options.bypassLoadedProtection);
+    if (!guard.allowed) {
+      console.log(JSON.stringify({ success: false, file_path: scene_file, error: guard.error }, null, 2));
+      process.exitCode = 1;
+      return;
+    }
     const result = createPrefabInstance({
       scene_path: scene_file,
       prefab_path: prefab_path_arg,
@@ -10589,12 +12050,18 @@ function build_create_command() {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("component <file> <object_name> <component>").description("Add a Unity component (e.g., MeshRenderer, Animator, Rigidbody) or custom script").option("-p, --project <path>", "Unity project path (for script GUID lookup)").option("-j, --json", "Output as JSON").action((file, object_name, component, options) => {
+  cmd.command("component <file> <object_name> <component>").description("Add a Unity component (e.g., MeshRenderer, Animator, Rigidbody) or custom script").option("-p, --project <path>", "Unity project path (for script GUID lookup)").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").option("-j, --json", "Output as JSON").action(async (file, object_name, component, options) => {
     if (!component || component.trim() === "") {
       console.log(JSON.stringify({ success: false, file_path: file, error: "Component name must not be empty" }, null, 2));
       process.exitCode = 1;
       return;
     }
+    const guard = await enforce_loaded_edit_protection(file, options.bypassLoadedProtection, options.project);
+    if (!guard.allowed) {
+      console.log(JSON.stringify({ success: false, file_path: file, error: guard.error }, null, 2));
+      process.exitCode = 1;
+      return;
+    }
     const result = addComponent({
       file_path: file,
       game_object_name: object_name,
@@ -10605,7 +12072,13 @@ function build_create_command() {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("component-copy <file> <source_file_id> <target_object_name>").description("Copy a component to a target GameObject").option("-j, --json", "Output as JSON").action((file, source_file_id, target_object_name, _options) => {
+  cmd.command("component-copy <file> <source_file_id> <target_object_name>").description("Copy a component to a target GameObject").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").option("-j, --json", "Output as JSON").action(async (file, source_file_id, target_object_name, options) => {
+    const guard = await enforce_loaded_edit_protection(file, options.bypassLoadedProtection);
+    if (!guard.allowed) {
+      console.log(JSON.stringify({ success: false, file_path: file, error: guard.error }, null, 2));
+      process.exitCode = 1;
+      return;
+    }
     const result = copyComponent({
       file_path: file,
       source_file_id,
@@ -10615,10 +12088,11 @@ function build_create_command() {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("build <project_path> <scene_path>").description("Add a scene to build settings").option("--index <n>", "Insert at position (0-based)").option("-j, --json", "Output as JSON").action((project_path, scene_path, options) => {
+  cmd.command("build <scene_path>").description("Add a scene to build settings").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("--index <n>", "Insert at position (0-based)").option("-j, --json", "Output as JSON").action((scene_path, options) => {
     try {
+      const resolvedProjectPath = resolve_project_path(options.project);
       const position = options.index !== undefined ? parseInt(options.index, 10) : undefined;
-      const result = add_scene(project_path, scene_path, { position });
+      const result = add_scene(resolvedProjectPath, scene_path, { position });
       console.log(JSON.stringify(result, null, 2));
       if (!result.success)
         process.exitCode = 1;
@@ -10632,7 +12106,7 @@ function build_create_command() {
       console.log(JSON.stringify({ success: false, error: "--shader <guid> is required" }, null, 2));
       process.exit(1);
     }
-    if (import_fs17.existsSync(output_path)) {
+    if (import_fs18.existsSync(output_path)) {
       console.log(JSON.stringify({ success: false, error: `File already exists: ${output_path}` }, null, 2));
       process.exit(1);
     }
@@ -10705,7 +12179,7 @@ Material:
   m_BuildTextureStacks: []
 `;
     ensure_parent_dir(output_path);
-    import_fs17.writeFileSync(output_path, mat_content, "utf-8");
+    import_fs18.writeFileSync(output_path, mat_content, "utf-8");
     const guid = import_crypto2.randomBytes(16).toString("hex");
     const meta_content = `fileFormatVersion: 2
 guid: ${guid}
@@ -10716,7 +12190,7 @@ NativeFormatImporter:
   assetBundleName:
   assetBundleVariant:
 `;
-    import_fs17.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
+    import_fs18.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
     console.log(JSON.stringify({
       success: true,
       file: output_path,
@@ -10726,9 +12200,10 @@ NativeFormatImporter:
       shader_guid
     }, null, 2));
   });
-  cmd.command("package <project_path> <name> <version>").description("Add a package to Packages/manifest.json").option("-j, --json", "Output as JSON").action((project_path, name, version, _options) => {
+  cmd.command("package <name> <version>").description("Add a package to Packages/manifest.json").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-j, --json", "Output as JSON").action((name, version, options) => {
     try {
-      const result = add_package(project_path, name, version);
+      const resolvedProjectPath = resolve_project_path(options.project);
+      const result = add_package(resolvedProjectPath, name, version);
       if ("error" in result) {
         console.log(JSON.stringify({ success: false, error: result.error }, null, 2));
         process.exitCode = 1;
@@ -10746,7 +12221,7 @@ NativeFormatImporter:
       process.exitCode = 1;
       return;
     }
-    if (import_fs17.existsSync(output_path)) {
+    if (import_fs18.existsSync(output_path)) {
       console.log(JSON.stringify({ success: false, error: `File already exists: ${output_path}` }, null, 2));
       process.exitCode = 1;
       return;
@@ -10773,7 +12248,7 @@ ScriptedImporter:
   wrapperClassName:
   wrapperCodeNamespace:
 `;
-    import_fs17.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
+    import_fs18.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
     console.log(JSON.stringify({
       success: true,
       file: output_path,
@@ -10788,8 +12263,8 @@ ScriptedImporter:
       process.exitCode = 1;
       return;
     }
-    const name = name_arg || import_path7.basename(output_path).replace(/\.anim$/i, "");
-    if (import_fs17.existsSync(output_path)) {
+    const name = name_arg || import_path10.basename(output_path).replace(/\.anim$/i, "");
+    if (import_fs18.existsSync(output_path)) {
       console.log(JSON.stringify({ success: false, error: `File already exists: ${output_path}` }, null, 2));
       process.exitCode = 1;
       return;
@@ -10857,7 +12332,7 @@ AnimationClip:
   m_Events: []
 `;
     ensure_parent_dir(output_path);
-    import_fs17.writeFileSync(output_path, anim_content, "utf-8");
+    import_fs18.writeFileSync(output_path, anim_content, "utf-8");
     const guid = import_crypto2.randomBytes(16).toString("hex");
     const meta_content = `fileFormatVersion: 2
 guid: ${guid}
@@ -10868,7 +12343,7 @@ NativeFormatImporter:
   assetBundleName:
   assetBundleVariant:
 `;
-    import_fs17.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
+    import_fs18.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
     console.log(JSON.stringify({
       success: true,
       file: output_path,
@@ -10880,13 +12355,13 @@ NativeFormatImporter:
     }, null, 2));
   });
   cmd.command("animator <output_path> [name]").description("Create a blank .controller AnimatorController file (name defaults to filename without extension)").option("--layer <name>", 'Name of the initial layer (default: "Base Layer")', "Base Layer").option("-j, --json", "Output as JSON").action((output_path, name_arg, options) => {
-    const name = name_arg || import_path7.basename(output_path).replace(/\.controller$/i, "");
+    const name = name_arg || import_path10.basename(output_path).replace(/\.controller$/i, "");
     if (!output_path.toLowerCase().endsWith(".controller")) {
       console.log(JSON.stringify({ success: false, error: "Output path must end with .controller" }, null, 2));
       process.exitCode = 1;
       return;
     }
-    if (import_fs17.existsSync(output_path)) {
+    if (import_fs18.existsSync(output_path)) {
       console.log(JSON.stringify({ success: false, error: `File already exists: ${output_path}` }, null, 2));
       process.exitCode = 1;
       return;
@@ -10937,7 +12412,7 @@ AnimatorStateMachine:
   m_DefaultState: {fileID: 0}
 `;
     ensure_parent_dir(output_path);
-    import_fs17.writeFileSync(output_path, ctrl_content, "utf-8");
+    import_fs18.writeFileSync(output_path, ctrl_content, "utf-8");
     const guid = import_crypto2.randomBytes(16).toString("hex");
     const meta_content = `fileFormatVersion: 2
 guid: ${guid}
@@ -10948,7 +12423,7 @@ NativeFormatImporter:
   assetBundleName:
   assetBundleVariant:
 `;
-    import_fs17.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
+    import_fs18.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
     console.log(JSON.stringify({
       success: true,
       file: output_path,
@@ -10959,13 +12434,13 @@ NativeFormatImporter:
     }, null, 2));
   });
   cmd.command("prefab <output_path> [name]").description("Create a blank .prefab file (name defaults to filename without extension)").option("-j, --json", "Output as JSON").action((output_path, name_arg) => {
-    const name = name_arg || import_path7.basename(output_path).replace(/\.prefab$/i, "");
+    const name = name_arg || import_path10.basename(output_path).replace(/\.prefab$/i, "");
     if (!output_path.toLowerCase().endsWith(".prefab")) {
       console.log(JSON.stringify({ success: false, error: "Output path must end with .prefab" }, null, 2));
       process.exitCode = 1;
       return;
     }
-    if (import_fs17.existsSync(output_path)) {
+    if (import_fs18.existsSync(output_path)) {
       console.log(JSON.stringify({ success: false, error: `File already exists: ${output_path}` }, null, 2));
       process.exitCode = 1;
       return;
@@ -11005,7 +12480,7 @@ Transform:
   m_LocalEulerAnglesHint: {x: 0, y: 0, z: 0}
 `;
     ensure_parent_dir(output_path);
-    import_fs17.writeFileSync(output_path, prefab_content, "utf-8");
+    import_fs18.writeFileSync(output_path, prefab_content, "utf-8");
     const guid = import_crypto2.randomBytes(16).toString("hex");
     const meta_content = `fileFormatVersion: 2
 guid: ${guid}
@@ -11015,7 +12490,7 @@ PrefabImporter:
   assetBundleName:
   assetBundleVariant:
 `;
-    import_fs17.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
+    import_fs18.writeFileSync(`${output_path}.meta`, meta_content, "utf-8");
     console.log(JSON.stringify({
       success: true,
       file: output_path,
@@ -11029,9 +12504,119 @@ PrefabImporter:
 
 // src/cmd-read.ts
 init_scanner();
-var import_fs18 = require("fs");
-var import_path8 = require("path");
+var import_fs19 = require("fs");
+var import_path11 = require("path");
 var import_os = require("os");
+function parse_unity_ref(ref_text) {
+  const file_id_match = ref_text.match(/fileID:[ \t]*(-?\d+)/i);
+  if (!file_id_match)
+    return null;
+  const guid_match = ref_text.match(/guid:[ \t]*([a-f0-9]{32})/i);
+  const type_match = ref_text.match(/type:[ \t]*(-?\d+)/i);
+  const parsed = { file_id: file_id_match[1] };
+  if (guid_match)
+    parsed.guid = guid_match[1].toLowerCase();
+  if (type_match)
+    parsed.type = parseInt(type_match[1], 10);
+  return parsed;
+}
+function extract_prefab_list_section(raw, key) {
+  const lines = raw.split(`
+`);
+  const key_pattern = new RegExp(`^(\\s*)${key}:[ \\t]*(.*)$`);
+  let key_index = -1;
+  let key_indent = 0;
+  for (let i = 0;i < lines.length; i++) {
+    const match = lines[i].match(key_pattern);
+    if (match) {
+      key_index = i;
+      key_indent = match[1].length;
+      break;
+    }
+  }
+  if (key_index === -1)
+    return null;
+  const section_lines = [lines[key_index]];
+  for (let i = key_index + 1;i < lines.length; i++) {
+    const line = lines[i];
+    const trimmed = line.trim();
+    if (trimmed.length === 0) {
+      section_lines.push(line);
+      continue;
+    }
+    const indent = (line.match(/^\s*/) || [""])[0].length;
+    if (indent < key_indent)
+      break;
+    if (indent === key_indent && !trimmed.startsWith("-") && /^[A-Za-z_][A-Za-z0-9_]*:/.test(trimmed)) {
+      break;
+    }
+    section_lines.push(line);
+  }
+  return { key_indent, section_lines };
+}
+function parse_removed_list(raw, key) {
+  const section = extract_prefab_list_section(raw, key);
+  if (!section)
+    return [];
+  const key_line = section.section_lines[0].trim();
+  if (key_line.endsWith("[]"))
+    return [];
+  const refs = section.section_lines.join(`
+`).match(/\{[^}]*fileID:[^}]*\}/g) || [];
+  const dedup = new Map;
+  for (const ref of refs) {
+    const parsed = parse_unity_ref(ref);
+    if (!parsed)
+      continue;
+    const key_text = `${parsed.file_id}|${parsed.guid ?? ""}|${parsed.type ?? ""}`;
+    if (!dedup.has(key_text))
+      dedup.set(key_text, parsed);
+  }
+  return [...dedup.values()];
+}
+function parse_added_list(raw, key) {
+  const section = extract_prefab_list_section(raw, key);
+  if (!section)
+    return [];
+  const key_line = section.section_lines[0].trim();
+  if (key_line.endsWith("[]"))
+    return [];
+  const lines = section.section_lines.slice(1);
+  const entries = [];
+  let i = 0;
+  while (i < lines.length) {
+    const line = lines[i];
+    const trimmed = line.trimStart();
+    if (!trimmed.startsWith("-")) {
+      i++;
+      continue;
+    }
+    const entry_indent = (line.match(/^\s*/) || [""])[0].length;
+    const entry_lines = [line];
+    i++;
+    while (i < lines.length) {
+      const next = lines[i];
+      const next_trimmed = next.trim();
+      const next_indent = (next.match(/^\s*/) || [""])[0].length;
+      if (next_trimmed.length > 0 && next_indent === entry_indent && next_trimmed.startsWith("-")) {
+        break;
+      }
+      entry_lines.push(next);
+      i++;
+    }
+    const entry_text = entry_lines.join(`
+`);
+    const target_match = entry_text.match(/targetCorrespondingSourceObject:[ \t]*(\{[^}]+\})/);
+    const insert_match = entry_text.match(/insertIndex:[ \t]*(-?\d+)/);
+    const added_match = entry_text.match(/addedObject:[ \t]*(\{[^}]+\})/);
+    entries.push({
+      target_corresponding_source_object: target_match ? parse_unity_ref(target_match[1]) : null,
+      insert_index: insert_match ? parseInt(insert_match[1], 10) : null,
+      added_object: added_match ? parse_unity_ref(added_match[1]) : null
+    });
+  }
+  return entries;
+}
 function parse_material_yaml(content) {
   const lines = content.replace(/\r/g, "").split(`
 `);
@@ -11230,7 +12815,7 @@ function parse_material_yaml(content) {
   return result;
 }
 function categorize_asset(filePath) {
-  const ext = import_path8.extname(filePath).toLowerCase();
+  const ext = import_path11.extname(filePath).toLowerCase();
   const categories = {
     ".cs": "script",
     ".mat": "material",
@@ -11274,12 +12859,12 @@ function categorize_asset(filePath) {
   return categories[ext] || "other";
 }
 function find_project_root_from_file(filePath) {
-  let dir = import_path8.dirname(import_path8.resolve(filePath));
+  let dir = import_path11.dirname(import_path11.resolve(filePath));
   for (let i = 0;i < 20; i++) {
-    if (import_fs18.existsSync(import_path8.join(dir, "Assets")) && import_fs18.existsSync(import_path8.join(dir, "ProjectSettings"))) {
+    if (import_fs19.existsSync(import_path11.join(dir, "Assets")) && import_fs19.existsSync(import_path11.join(dir, "ProjectSettings"))) {
       return dir;
     }
-    const parent = import_path8.dirname(dir);
+    const parent = import_path11.dirname(dir);
     if (parent === dir)
       break;
     dir = parent;
@@ -11289,13 +12874,13 @@ function find_project_root_from_file(filePath) {
 function get_editor_log_path() {
   const p = import_os.platform();
   if (p === "darwin")
-    return import_path8.join(import_os.homedir(), "Library", "Logs", "Unity", "Editor.log");
+    return import_path11.join(import_os.homedir(), "Library", "Logs", "Unity", "Editor.log");
   if (p === "win32") {
-    const localAppData = process.env.LOCALAPPDATA || import_path8.join(import_os.homedir(), "AppData", "Local");
-    return import_path8.join(localAppData, "Unity", "Editor", "Editor.log");
+    const localAppData = process.env.LOCALAPPDATA || import_path11.join(import_os.homedir(), "AppData", "Local");
+    return import_path11.join(localAppData, "Unity", "Editor", "Editor.log");
   }
   if (p === "linux")
-    return import_path8.join(import_os.homedir(), ".config", "unity3d", "Editor.log");
+    return import_path11.join(import_os.homedir(), ".config", "unity3d", "Editor.log");
   return null;
 }
 function parse_log_line_timestamp(line) {
@@ -11626,19 +13211,19 @@ function walk_files(dir, extensions) {
     const current = stack.pop();
     let entries;
     try {
-      entries = import_fs18.readdirSync(current);
+      entries = import_fs19.readdirSync(current);
     } catch {
       continue;
     }
     for (const entry of entries) {
       if (entry.startsWith("."))
         continue;
-      const full = import_path8.join(current, entry);
+      const full = import_path11.join(current, entry);
       try {
-        const stat = import_fs18.statSync(full);
+        const stat = import_fs19.statSync(full);
         if (stat.isDirectory()) {
           stack.push(full);
-        } else if (extensions.has(import_path8.extname(full).toLowerCase())) {
+        } else if (extensions.has(import_path11.extname(full).toLowerCase())) {
           results.push(full);
         }
       } catch {
@@ -11649,7 +13234,7 @@ function walk_files(dir, extensions) {
   return results;
 }
 function validate_unity_yaml(file) {
-  if (!import_fs18.existsSync(file)) {
+  if (!import_fs19.existsSync(file)) {
     return `File not found: ${file}`;
   }
   try {
@@ -11735,10 +13320,17 @@ function build_read_command(getScanner) {
     }
     if (result.total === 0 && !result.error) {
       const prefabInstances = result.prefabInstances;
+      let variantDetected = false;
+      let variantResolvedFromSource = false;
       if (prefabInstances && prefabInstances.length > 0) {
+        variantDetected = true;
         try {
           const doc = UnityDocument.from_file(file);
-          const projectPath = find_unity_project_root(import_path8.dirname(file));
+          const strippedGoCount = doc.blocks.filter((b) => b.class_id === 1 && b.is_stripped).length;
+          if (strippedGoCount > 0) {
+            variantDetected = true;
+          }
+          const projectPath = find_unity_project_root(import_path11.dirname(file));
           const resolved = resolve_source_prefab(doc, file, projectPath ?? undefined);
           if (resolved) {
             const sourceResult = getScanner().inspect_all_paginated({
@@ -11772,6 +13364,7 @@ function build_read_command(getScanner) {
               resultRecord.resolvedFromSource = true;
               resultRecord.sourcePrefab = resolved.source_path;
               resultRecord.sourceGuid = resolved.source_guid;
+              variantResolvedFromSource = true;
               const variantNote = `PrefabVariant resolved from source prefab: ${resolved.source_path}`;
               result.warning = result.warning ? `${result.warning}; ${variantNote}` : variantNote;
             }
@@ -11780,10 +13373,15 @@ function build_read_command(getScanner) {
       }
       if (result.total === 0) {
         try {
-          const fileSize = import_fs18.statSync(file).size;
+          const fileSize = import_fs19.statSync(file).size;
           if (fileSize > 100) {
-            const corruptWarning = "File has valid Unity YAML header but contains no parseable GameObjects -- file may be corrupt or malformed";
-            result.warning = result.warning ? `${result.warning}; ${corruptWarning}` : corruptWarning;
+            if (variantDetected && !variantResolvedFromSource) {
+              const variantWarning = "PrefabVariant detected but source prefab hierarchy could not be resolved (missing project context or GUID cache). Use --project or run setup to resolve source hierarchy.";
+              result.warning = result.warning ? `${result.warning}; ${variantWarning}` : variantWarning;
+            } else {
+              const corruptWarning = "File has valid Unity YAML header but contains no parseable GameObjects -- file may be corrupt or malformed";
+              result.warning = result.warning ? `${result.warning}; ${corruptWarning}` : corruptWarning;
+            }
           }
         } catch {}
       }
@@ -11893,7 +13491,7 @@ function build_read_command(getScanner) {
       console.log(JSON.stringify({ error: matValidationError }, null, 2));
       process.exit(1);
     }
-    const content = import_fs18.readFileSync(file, "utf-8");
+    const content = import_fs19.readFileSync(file, "utf-8");
     if (!content.includes("Material:")) {
       console.log(JSON.stringify({ error: `File "${file}" does not contain a Material block. Use 'read asset' for generic Unity YAML files.` }, null, 2));
       process.exit(1);
@@ -11935,13 +13533,13 @@ function build_read_command(getScanner) {
     }, null, 2));
   });
   cmd.command("dependencies <file>").description("List asset dependencies (GUIDs referenced by this file)").option("--project <path>", "Unity project root (for GUID resolution)").option("--unresolved", "Show only GUIDs that could not be resolved").option("--recursive [depth]", "Follow dependency chain N levels deep (default: 3)").option("-j, --json", "Output as JSON").action((file, options) => {
-    if (!import_fs18.existsSync(file)) {
+    if (!import_fs19.existsSync(file)) {
       console.log(JSON.stringify({ error: `File not found: ${file}` }, null, 2));
       process.exit(1);
     }
     let content;
     try {
-      content = import_fs18.readFileSync(file, "utf-8");
+      content = import_fs19.readFileSync(file, "utf-8");
     } catch {
       console.log(JSON.stringify({ error: `Cannot read file: ${file}` }, null, 2));
       process.exit(1);
@@ -11982,7 +13580,7 @@ function build_read_command(getScanner) {
         const result = [];
         let fileContent;
         try {
-          fileContent = import_fs18.readFileSync(filePath, "utf-8");
+          fileContent = import_fs19.readFileSync(filePath, "utf-8");
         } catch {
           return [];
         }
@@ -11999,7 +13597,7 @@ function build_read_command(getScanner) {
           const rAbsPath = cache.resolve_absolute(g);
           const rType = rPath ? categorize_asset(rPath) : "unknown";
           const dep = { guid: g, path: rPath, type: rType, depth };
-          if (rAbsPath && depth < max_depth && import_fs18.existsSync(rAbsPath)) {
+          if (rAbsPath && depth < max_depth && import_fs19.existsSync(rAbsPath)) {
             const subs = traverse_file(rAbsPath, depth + 1);
             if (subs.length > 0)
               dep.sub_dependencies = subs;
@@ -12028,7 +13626,7 @@ function build_read_command(getScanner) {
         const rDep = { guid: dep.guid, path: dep.path, type: dep.type, depth: 0 };
         if (dep.path) {
           const absPath = cache.resolve_absolute(dep.guid);
-          if (absPath && import_fs18.existsSync(absPath)) {
+          if (absPath && import_fs19.existsSync(absPath)) {
             const subs = traverse_file(absPath, 1);
             if (subs.length > 0)
               rDep.sub_dependencies = subs;
@@ -12056,38 +13654,41 @@ function build_read_command(getScanner) {
       by_type: options.unresolved ? undefined : byType
     };
     if (!cache) {
-      output._hint = "Run 'setup <project>' to resolve GUID paths";
+      output._hint = "Run 'setup' (or 'setup -p <path>') to resolve GUID paths";
     }
     console.log(JSON.stringify(output, null, 2));
   });
-  cmd.command("settings <project_path>").description("Read Unity project settings (TagManager, DynamicsManager, QualitySettings, TimeManager, etc.)").option("-s, --setting <name>", "Setting name or alias (tags, physics, quality, time)", "TagManager").option("-j, --json", "Output as JSON").action((project_path, options) => {
+  cmd.command("settings").description("Read Unity project settings (TagManager, DynamicsManager, QualitySettings, TimeManager, etc.)").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-s, --setting <name>", "Setting name or alias (tags, physics, quality, time)", "TagManager").option("-j, --json", "Output as JSON").action((options) => {
+    const resolvedProjectPath = resolve_project_path(options.project);
     const result = read_settings({
-      project_path,
+      project_path: resolvedProjectPath,
       setting: options.setting
     });
     console.log(JSON.stringify(result, null, 2));
     if (!result.success)
       process.exit(1);
   });
-  cmd.command("build <project_path>").description("Read build settings (scene list, build profiles)").option("-j, --json", "Output as JSON").action((project_path, _options) => {
+  cmd.command("build").description("Read build settings (scene list, build profiles)").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-j, --json", "Output as JSON").action((options) => {
+    const resolvedProjectPath = resolve_project_path(options.project);
     try {
-      const result = get_build_settings(project_path);
+      const result = get_build_settings(resolvedProjectPath);
       console.log(JSON.stringify(result, null, 2));
     } catch (err) {
       console.log(JSON.stringify({ success: false, error: err instanceof Error ? err.message : String(err) }, null, 2));
       process.exitCode = 1;
     }
   });
-  cmd.command("scenes <project_path>").description('Read build scenes (alias for "read build")').option("-j, --json", "Output as JSON").action((project_path, _options) => {
+  cmd.command("scenes").description('Read build scenes (alias for "read build")').option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-j, --json", "Output as JSON").action((options) => {
+    const resolvedProjectPath = resolve_project_path(options.project);
     try {
-      const result = get_build_settings(project_path);
+      const result = get_build_settings(resolvedProjectPath);
       console.log(JSON.stringify(result, null, 2));
     } catch (err) {
       console.log(JSON.stringify({ success: false, error: err instanceof Error ? err.message : String(err) }, null, 2));
       process.exitCode = 1;
     }
   });
-  cmd.command("overrides <file> <prefab_instance>").description("Read PrefabInstance override modifications").option("--flat", "Output simplified list").option("-j, --json", "Output as JSON").action((file, prefab_instance, options) => {
+  cmd.command("overrides <file> <prefab_instance>").description("Read PrefabInstance overrides (modifications + removed/added state)").option("--flat", "Output simplified list").option("-j, --json", "Output as JSON").action((file, prefab_instance, options) => {
     try {
       const doc = UnityDocument.from_file(file);
       let block = null;
@@ -12150,6 +13751,10 @@ function build_read_command(getScanner) {
           i++;
         }
       }
+      const removed_components = parse_removed_list(block.raw, "m_RemovedComponents");
+      const removed_gameobjects = parse_removed_list(block.raw, "m_RemovedGameObjects");
+      const added_gameobjects = parse_added_list(block.raw, "m_AddedGameObjects");
+      const added_components = parse_added_list(block.raw, "m_AddedComponents");
       if (options.flat) {
         const flat = modifications.map((m) => ({
           property_path: m.property_path,
@@ -12158,7 +13763,14 @@ function build_read_command(getScanner) {
         }));
         console.log(JSON.stringify(flat, null, 2));
       } else {
-        console.log(JSON.stringify(modifications, null, 2));
+        console.log(JSON.stringify({
+          prefab_instance_id: block.file_id,
+          modifications,
+          removed_components,
+          removed_gameobjects,
+          added_gameobjects,
+          added_components
+        }, null, 2));
       }
     } catch (err) {
       console.log(JSON.stringify({ error: err instanceof Error ? err.message : String(err) }, null, 2));
@@ -12213,7 +13825,7 @@ function build_read_command(getScanner) {
   });
   cmd.command("target <file> <gameobject_name> [component_type]").description("Build a --target reference string for prefab override commands").option("-p, --project <path>", "Unity project path").option("-j, --json", "Output as JSON").action((file, gameobject_name, component_type, options) => {
     try {
-      if (!import_fs18.existsSync(file)) {
+      if (!import_fs19.existsSync(file)) {
         console.log(JSON.stringify({ error: `File not found: ${file}` }, null, 2));
         process.exit(1);
       }
@@ -12274,12 +13886,12 @@ function build_read_command(getScanner) {
             if (classId === null && compBlock.class_id === 114) {
               const scriptMatch = compBlock.raw.match(/m_Script:[ \t]*\{[^}]*guid:[ \t]*([a-f0-9]{32})/);
               if (scriptMatch) {
-                const project = options.project || find_unity_project_root(import_path8.dirname(file));
+                const project = options.project || find_unity_project_root(import_path11.dirname(file));
                 if (project) {
                   const cache = load_guid_cache(project);
                   if (cache) {
                     const scriptPath = cache.resolve(scriptMatch[1]);
-                    if (scriptPath && import_path8.basename(scriptPath, ".cs").toLowerCase() === component_type.toLowerCase().replace(/\.cs$/, "")) {
+                    if (scriptPath && import_path11.basename(scriptPath, ".cs").toLowerCase() === component_type.toLowerCase().replace(/\.cs$/, "")) {
                       targetFileId = refId;
                       compFound = true;
                       break;
@@ -12294,7 +13906,7 @@ function build_read_command(getScanner) {
             process.exit(1);
           }
         } else {
-          const project = options.project || find_unity_project_root(import_path8.dirname(file));
+          const project = options.project || find_unity_project_root(import_path11.dirname(file));
           const resolved = resolve_source_prefab(doc, file, project ?? undefined);
           if (resolved) {
             const sourceDoc = UnityDocument.from_file(resolved.source_path);
@@ -12333,7 +13945,7 @@ function build_read_command(getScanner) {
     }
   });
   cmd.command("script <file>").description("Extract C# type declarations from a .cs file or .NET DLL").option("-j, --json", "Output as JSON").action((file, _options) => {
-    if (!import_fs18.existsSync(file)) {
+    if (!import_fs19.existsSync(file)) {
       console.log(JSON.stringify({ error: `File not found: ${file}` }, null, 2));
       process.exit(1);
     }
@@ -12369,7 +13981,7 @@ function build_read_command(getScanner) {
       console.log(JSON.stringify({ error: "Native module not available" }, null, 2));
       process.exit(1);
     }
-    const projectPath = import_path8.resolve(options.project);
+    const projectPath = import_path11.resolve(options.project);
     const validSources = ["assets", "packages", "dlls", "all"];
     if (!validSources.includes(options.source)) {
       console.log(JSON.stringify({ error: `Invalid --source "${options.source}". Valid values: ${validSources.join(", ")}` }, null, 2));
@@ -12418,20 +14030,18 @@ function build_read_command(getScanner) {
       types: displayed
     }, null, 2));
   });
-  cmd.command("log [project-path]").description("Read and filter the Unity Editor.log").option("--path <file>", "Path to Editor.log (auto-detected if omitted)").option("--project <path>", "Filter to log entries from a specific Unity project session").option("--tail <n>", "Show last N lines (default 50)", "50").option("--errors", "Show only error entries").option("--warnings", "Show only warning entries").option("--compile-errors", "Show only C# compilation errors").option("--import-errors", "Show only asset import errors").option("--since <timestamp>", "Filter entries after this timestamp (YYYY-MM-DD or HH:MM:SS)").option("--search <pattern>", "Regex filter on log content").option("-j, --json", "Output as JSON").action((projectPath, options) => {
-    if (projectPath && !options.project)
-      options.project = projectPath;
+  cmd.command("log").description("Read and filter the Unity Editor.log").option("--path <file>", "Path to Editor.log (auto-detected if omitted)").option("--project <path>", "Filter to log entries from a specific Unity project session").option("--tail <n>", "Show last N lines (default 50)", "50").option("--errors", "Show only error entries").option("--warnings", "Show only warning entries").option("--compile-errors", "Show only C# compilation errors").option("--import-errors", "Show only asset import errors").option("--since <timestamp>", "Filter entries after this timestamp (YYYY-MM-DD or HH:MM:SS)").option("--search <pattern>", "Regex filter on log content").option("-j, --json", "Output as JSON").action((options) => {
     const logPath = options.path || get_editor_log_path();
-    if (!logPath || !import_fs18.existsSync(logPath)) {
+    if (!logPath || !import_fs19.existsSync(logPath)) {
       console.log(JSON.stringify({ error: `Editor.log not found${logPath ? `: ${logPath}` : ". Could not detect platform log path."}` }, null, 2));
       process.exit(1);
     }
-    const content = import_fs18.readFileSync(logPath, "utf-8");
+    const content = import_fs19.readFileSync(logPath, "utf-8");
     let lines = content.split(/\r?\n/);
     if (options.project) {
-      const projectPath2 = import_path8.resolve(options.project);
-      const projectName = import_path8.basename(projectPath2);
-      const escapedPath = projectPath2.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+      const projectPath = import_path11.resolve(options.project);
+      const projectName = import_path11.basename(projectPath);
+      const escapedPath = projectPath.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
       const escapedName = projectName.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
       const session_markers = [
         new RegExp(`Loading project at '${escapedPath}'`),
@@ -12551,11 +14161,11 @@ function build_read_command(getScanner) {
   });
   cmd.command("meta <file>").description("Read a Unity .meta file and show importer settings").option("--summary", "Show importer type and key settings only").option("-j, --json", "Output as JSON").action((file, options) => {
     const metaPath = file.endsWith(".meta") ? file : `${file}.meta`;
-    if (!import_fs18.existsSync(metaPath)) {
+    if (!import_fs19.existsSync(metaPath)) {
       console.log(JSON.stringify({ error: `Meta file not found: ${metaPath}` }, null, 2));
       process.exit(1);
     }
-    const content = import_fs18.readFileSync(metaPath, "utf-8");
+    const content = import_fs19.readFileSync(metaPath, "utf-8");
     const lines = content.split(/\r?\n/);
     let guid = "";
     let importer_type = "Unknown";
@@ -12643,7 +14253,7 @@ function build_read_command(getScanner) {
       console.log(JSON.stringify({ error: animValidationError }, null, 2));
       process.exit(1);
     }
-    const content = import_fs18.readFileSync(file, "utf-8");
+    const content = import_fs19.readFileSync(file, "utf-8");
     const clip = parse_animation_yaml(content, options.curves === true);
     if (!clip) {
       console.log(JSON.stringify({ error: `No AnimationClip found in "${file}". Is this an .anim file?` }, null, 2));
@@ -12704,7 +14314,7 @@ function build_read_command(getScanner) {
       console.log(JSON.stringify({ error: ctrlValidationError }, null, 2));
       process.exit(1);
     }
-    const content = import_fs18.readFileSync(file, "utf-8");
+    const content = import_fs19.readFileSync(file, "utf-8");
     const blocks = split_yaml_blocks(content);
     const controller_block = blocks.find((b) => b.class_id === 91);
     if (!controller_block) {
@@ -12876,7 +14486,7 @@ function build_read_command(getScanner) {
       }
       const states_out = { file, states_by_layer: by_layer };
       if (needs_setup_hint)
-        states_out._hint = "Run 'setup <project>' to resolve motion paths";
+        states_out._hint = "Run 'setup' (or 'setup -p <path>') to resolve motion paths";
       console.log(JSON.stringify(states_out, null, 2));
       return;
     }
@@ -12895,7 +14505,7 @@ function build_read_command(getScanner) {
     if (options.summary) {
       console.log(JSON.stringify({
         file,
-        name: yaml_field(controller_block.raw, "m_Name") || import_path8.basename(file),
+        name: yaml_field(controller_block.raw, "m_Name") || import_path11.basename(file),
         parameter_count: params.length,
         layer_count: layers.length,
         state_count: states.length,
@@ -12908,7 +14518,7 @@ function build_read_command(getScanner) {
       default_state_names[s.file_id] = s.name;
     const default_out = {
       file,
-      name: yaml_field(controller_block.raw, "m_Name") || import_path8.basename(file),
+      name: yaml_field(controller_block.raw, "m_Name") || import_path11.basename(file),
       parameters: params,
       layers: layers.map((l) => l.name),
       states: states.map((s) => ({
@@ -12925,16 +14535,17 @@ function build_read_command(getScanner) {
       }))
     };
     if (needs_setup_hint)
-      default_out._hint = "Run 'setup <project>' to resolve motion paths";
+      default_out._hint = "Run 'setup' (or 'setup -p <path>') to resolve motion paths";
     console.log(JSON.stringify(default_out, null, 2));
   });
-  cmd.command("dependents <project_path> <guid>").description("Find which files reference a given GUID (reverse dependency lookup)").option("--type <type>", "Filter to specific file types (scene, prefab, mat, etc.)").option("-j, --json", "Output as JSON").action((project_path, guid, options) => {
+  cmd.command("dependents <guid>").description("Find which files reference a given GUID (reverse dependency lookup)").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("--type <type>", "Filter to specific file types (scene, prefab, mat, etc.)").option("-j, --json", "Output as JSON").action((guid, options) => {
     if (!/^[0-9a-f]{32}$/i.test(guid)) {
       console.log(JSON.stringify({ error: "GUID must be a 32-character hexadecimal string" }, null, 2));
       process.exit(1);
     }
-    const assetsDir = import_path8.join(import_path8.resolve(project_path), "Assets");
-    if (!import_fs18.existsSync(assetsDir)) {
+    const project_path = resolve_project_path(options.project);
+    const assetsDir = import_path11.join(import_path11.resolve(project_path), "Assets");
+    if (!import_fs19.existsSync(assetsDir)) {
       console.log(JSON.stringify({ error: `Assets directory not found in "${project_path}"` }, null, 2));
       process.exit(1);
     }
@@ -12963,9 +14574,9 @@ function build_read_command(getScanner) {
     const guid_pattern = `guid: ${guid}`;
     for (const f of files) {
       try {
-        const fc = import_fs18.readFileSync(f, "utf-8");
+        const fc = import_fs19.readFileSync(f, "utf-8");
         if (fc.includes(guid_pattern)) {
-          const rel = import_path8.relative(import_path8.resolve(project_path), f);
+          const rel = import_path11.relative(import_path11.resolve(project_path), f);
           const ftype = categorize_asset(f);
           referencing.push({ path: rel, type: ftype });
         }
@@ -12984,17 +14595,17 @@ function build_read_command(getScanner) {
       by_type[r.type].push(r.path);
     }
     console.log(JSON.stringify({
-      project_path: import_path8.resolve(project_path),
+      project_path: import_path11.resolve(project_path),
       guid,
       total_references: filtered.length,
       by_type
     }, null, 2));
   });
-  cmd.command("unused <project_path>").description("Find potentially unused assets (zero inbound GUID references)").option("--type <type>", "Filter to specific asset types").option("--ignore <glob>", "Exclude paths matching this pattern").option("--max <n>", "Maximum results to return (default 200)", "200").option("-j, --json", "Output as JSON").action((project_path, options) => {
-    const resolvedProject = import_path8.resolve(project_path);
-    const assetsDir = import_path8.join(resolvedProject, "Assets");
-    if (!import_fs18.existsSync(assetsDir)) {
-      console.log(JSON.stringify({ error: `Assets directory not found in "${project_path}"` }, null, 2));
+  cmd.command("unused").description("Find potentially unused assets (zero inbound GUID references)").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("--type <type>", "Filter to specific asset types").option("--ignore <glob>", "Exclude paths matching this pattern").option("--max <n>", "Maximum results to return (default 200)", "200").option("-j, --json", "Output as JSON").action((options) => {
+    const resolvedProject = resolve_project_path(options.project);
+    const assetsDir = import_path11.join(resolvedProject, "Assets");
+    if (!import_fs19.existsSync(assetsDir)) {
+      console.log(JSON.stringify({ error: `Assets directory not found in "${resolvedProject}"` }, null, 2));
       process.exit(1);
     }
     const guidCacheObj = load_guid_cache(resolvedProject);
@@ -13021,7 +14632,7 @@ function build_read_command(getScanner) {
     const guid_re = /guid:\s*([a-f0-9]{32})/g;
     for (const f of files) {
       try {
-        const fc = import_fs18.readFileSync(f, "utf-8");
+        const fc = import_fs19.readFileSync(f, "utf-8");
         let gm;
         while ((gm = guid_re.exec(fc)) !== null) {
           referenced_guids.add(gm[1]);
@@ -13030,10 +14641,10 @@ function build_read_command(getScanner) {
         continue;
       }
     }
-    const buildSettingsPath = import_path8.join(resolvedProject, "ProjectSettings", "EditorBuildSettings.asset");
+    const buildSettingsPath = import_path11.join(resolvedProject, "ProjectSettings", "EditorBuildSettings.asset");
     const build_scene_guids = new Set;
-    if (import_fs18.existsSync(buildSettingsPath)) {
-      const bsc = import_fs18.readFileSync(buildSettingsPath, "utf-8");
+    if (import_fs19.existsSync(buildSettingsPath)) {
+      const bsc = import_fs19.readFileSync(buildSettingsPath, "utf-8");
       let bm;
       while ((bm = guid_re.exec(bsc)) !== null) {
         build_scene_guids.add(bm[1]);
@@ -13054,7 +14665,7 @@ function build_read_command(getScanner) {
         continue;
       if (ignore_pattern && ignore_pattern.test(asset_path))
         continue;
-      if (import_path8.extname(asset_path) === "")
+      if (import_path11.extname(asset_path) === "")
         continue;
       const asset_type = categorize_asset(asset_path);
       if (options.type && asset_type !== options.type)
@@ -13085,7 +14696,8 @@ function build_read_command(getScanner) {
       by_type
     }, null, 2));
   });
-  cmd.command("manifest <project_path>").description("List packages from Packages/manifest.json").option("--search <pattern>", "Filter packages by name pattern").option("-j, --json", "Output as JSON").action((project_path, options) => {
+  cmd.command("manifest").description("List packages from Packages/manifest.json").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("--search <pattern>", "Filter packages by name pattern").option("-j, --json", "Output as JSON").action((options) => {
+    const project_path = resolve_project_path(options.project);
     const result = list_packages(project_path, options.search);
     if ("error" in result) {
       console.log(JSON.stringify({ success: false, error: result.error }, null, 2));
@@ -13155,8 +14767,8 @@ function build_read_command(getScanner) {
 }
 
 // src/cmd-update.ts
-var import_fs19 = require("fs");
-var import_path9 = require("path");
+var import_fs20 = require("fs");
+var import_path12 = require("path");
 
 // src/animator-utils.ts
 function split_yaml_blocks2(content) {
@@ -13285,7 +14897,13 @@ function parseVector(str) {
   }
   return { x: parts[0], y: parts[1], z: parts[2] };
 }
-function resolve_transform_id(scanner, file, identifier) {
+function resolve_transform_id(scanner, file, identifier, by_id = false) {
+  if (by_id) {
+    if (!/^-?\d+$/.test(identifier)) {
+      return { error: `Invalid fileID: "${identifier}" \u2014 expected a numeric value when using --by-id` };
+    }
+    return { transform_id: identifier };
+  }
   let resolved_id = identifier;
   if (!/^-?\d+$/.test(identifier)) {
     const matches = scanner.find_by_name(file, identifier, false);
@@ -13310,7 +14928,17 @@ function resolve_transform_id(scanner, file, identifier) {
 }
 function build_update_command(getScanner) {
   const cmd = new Command("update").description("Update Unity object properties, transforms, settings, and hierarchy");
-  cmd.command("gameobject <file> <object_name> <property> <value>").description("Edit GameObject property value safely").option("-j, --json", "Output as JSON").option("-p, --project <path>", "Unity project path (for tag validation)").action((file, object_name, property, value, options) => {
+  async function check_loaded_edit_protection(file, bypass, project_path) {
+    const guard = await enforce_loaded_edit_protection(file, bypass, project_path);
+    if (guard.allowed)
+      return true;
+    console.log(JSON.stringify({ success: false, file_path: file, error: guard.error }, null, 2));
+    process.exitCode = 1;
+    return false;
+  }
+  cmd.command("gameobject <file> <object_name> <property> <value>").description("Edit GameObject property value safely").option("-j, --json", "Output as JSON").option("-p, --project <path>", "Unity project path (for tag validation)").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, object_name, property, value, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection, options.project))
+      return;
     const result = editProperty({
       file_path: file,
       object_name,
@@ -13322,7 +14950,7 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("component <file> <file_id> <property> <value>").description("Edit any component property by file ID. Supports dotted paths (m_LocalPosition.x) and array paths (m_Materials.Array.data[0]). Quote paths with brackets or use dot notation (data.0) to avoid shell glob expansion").option("-j, --json", "Output as JSON").option("-p, --project <path>", "Unity project path (for asset reference resolution)").action((file, file_id, property, value, options) => {
+  cmd.command("component <file> <file_id> <property> <value>").description("Edit any component property by file ID. Supports dotted paths (m_LocalPosition.x) and array paths (m_Materials.Array.data[0]). Quote paths with brackets or use dot notation (data.0) to avoid shell glob expansion").option("-j, --json", "Output as JSON").option("-p, --project <path>", "Unity project path (for asset reference resolution)").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, file_id, property, value, options) => {
     if (property === "m_RootOrder") {
       const num = Number(value);
       if (!Number.isInteger(num) || num < 0) {
@@ -13331,6 +14959,8 @@ function build_update_command(getScanner) {
         return;
       }
     }
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection, options.project))
+      return;
     const result = editComponentByFileId({
       file_path: file,
       file_id,
@@ -13342,7 +14972,7 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("transform <file> <identifier>").description("Edit Transform by GameObject name or transform fileID").option("-p, --position <x,y,z>", "Set local position").option("-r, --rotation <x,y,z>", "Set local rotation (Euler angles in degrees)").option("-s, --scale <x,y,z>", "Set local scale").option("-j, --json", "Output as JSON").action((file, identifier, options) => {
+  cmd.command("transform <file> <identifier>").description("Edit Transform by GameObject name or transform fileID. Use --by-id to force numeric fileID mode").option("-p, --position <x,y,z>", "Set local position").option("-r, --rotation <x,y,z>", "Set local rotation (Euler angles in degrees)").option("-s, --scale <x,y,z>", "Set local scale").option("--by-id", "Treat identifier as a numeric fileID instead of name lookup").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, identifier, options) => {
     if (!options.position && !options.rotation && !options.scale) {
       console.log(JSON.stringify({
         success: false,
@@ -13352,7 +14982,9 @@ function build_update_command(getScanner) {
       process.exitCode = 1;
       return;
     }
-    const resolved = resolve_transform_id(getScanner(), file, identifier);
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
+    const resolved = resolve_transform_id(getScanner(), file, identifier, options.byId);
     if ("error" in resolved) {
       console.log(JSON.stringify({
         success: false,
@@ -13404,13 +15036,14 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("settings <project_path>").description("Edit a property in any ProjectSettings/*.asset file").option("-s, --setting <name>", "Setting name or alias").option("--property <name>", "Property name to edit").option("--value <value>", "New value").option("-j, --json", "Output as JSON").action((project_path, options) => {
+  cmd.command("settings").description("Edit a property in any ProjectSettings/*.asset file").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-s, --setting <name>", "Setting name or alias").option("--property <name>", "Property name to edit").option("--value <value>", "New value").option("-j, --json", "Output as JSON").action((options) => {
     if (!options.setting || !options.property || !options.value) {
       console.log(JSON.stringify({ success: false, error: "Required: --setting, --property, --value" }, null, 2));
       process.exit(1);
     }
+    const resolvedProjectPath = resolve_project_path(options.project);
     const result = edit_settings({
-      project_path,
+      project_path: resolvedProjectPath,
       setting: options.setting,
       property: options.property,
       value: options.value
@@ -13419,13 +15052,14 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("tag <project_path> <action> <tag>").description("Add or remove a tag in the TagManager").option("-j, --json", "Output as JSON").action((project_path, action, tag, _options) => {
+  cmd.command("tag <action> <tag>").description("Add or remove a tag in the TagManager").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-j, --json", "Output as JSON").action((action, tag, options) => {
     if (action !== "add" && action !== "remove") {
       console.log(JSON.stringify({ success: false, error: 'Action must be "add" or "remove"' }, null, 2));
       process.exit(1);
     }
+    const resolvedProjectPath = resolve_project_path(options.project);
     const result = edit_tag({
-      project_path,
+      project_path: resolvedProjectPath,
       action,
       tag
     });
@@ -13433,9 +15067,10 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("layer <project_path> <index> <name>").description("Set a named layer at a specific index (3-31)").option("-j, --json", "Output as JSON").action((project_path, index, name, _options) => {
+  cmd.command("layer <index> <name>").description("Set a named layer at a specific index (3-31)").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-j, --json", "Output as JSON").action((index, name, options) => {
+    const resolvedProjectPath = resolve_project_path(options.project);
     const result = edit_layer({
-      project_path,
+      project_path: resolvedProjectPath,
       index: parseInt(index, 10),
       name
     });
@@ -13443,13 +15078,14 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("sorting-layer <project_path> <action> <name>").description("Add or remove a sorting layer").option("-j, --json", "Output as JSON").action((project_path, action, name, _options) => {
+  cmd.command("sorting-layer <action> <name>").description("Add or remove a sorting layer").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-j, --json", "Output as JSON").action((action, name, options) => {
     if (action !== "add" && action !== "remove") {
       console.log(JSON.stringify({ success: false, error: 'Action must be "add" or "remove"' }, null, 2));
       process.exit(1);
     }
+    const resolvedProjectPath = resolve_project_path(options.project);
     const result = edit_sorting_layer({
-      project_path,
+      project_path: resolvedProjectPath,
       action,
       name
     });
@@ -13457,7 +15093,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("parent <file> <object_name> <new_parent>").description('Move a GameObject under a new parent. Use "root" to move to scene root. Use --by-id to specify fileIDs instead of names').option("-j, --json", "Output as JSON").option("--by-id", "Treat object_name and new_parent as numeric fileIDs instead of names").action((file, object_name, new_parent, options) => {
+  cmd.command("parent <file> <object_name> <new_parent>").description('Move a GameObject under a new parent. Use "root" to move to scene root. Use --by-id to specify fileIDs instead of names').option("-j, --json", "Output as JSON").option("--by-id", "Treat object_name and new_parent as numeric fileIDs instead of names").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, object_name, new_parent, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     const result = reparentGameObject({
       file_path: file,
       object_name,
@@ -13469,7 +15107,9 @@ function build_update_command(getScanner) {
       process.exitCode = 1;
   });
   const prefab_cmd = new Command("prefab").description("Prefab operations (unpack, override, remove-override, remove/restore component/gameobject)");
-  prefab_cmd.command("unpack <file> <prefab_instance>").description("Unpack a PrefabInstance into standalone GameObjects").option("-p, --project <path>", "Unity project path (for GUID cache lookup)").option("-j, --json", "Output as JSON").action((file, prefab_instance, options) => {
+  prefab_cmd.command("unpack <file> <prefab_instance>").description("Unpack a PrefabInstance into standalone GameObjects").option("-p, --project <path>", "Unity project path (for GUID cache lookup)").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, prefab_instance, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection, options.project))
+      return;
     const result = unpackPrefab({
       file_path: file,
       prefab_instance,
@@ -13479,7 +15119,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  prefab_cmd.command("override <file> <prefab_instance> <property_path> <value>").description("Edit or add a property override in a PrefabInstance m_Modifications list. Quote paths with brackets or use dot notation (data.0) to avoid shell glob expansion").option("--object-reference <ref>", "Object reference value (default: {fileID: 0})").option("--managed-reference <id>", "Managed reference ID -- placed in value: field, forces objectReference: {fileID: 0}").option("--target <target>", 'Target reference for new entries (e.g., "{fileID: 400000, guid: abc, type: 3}")').option("-j, --json", "Output as JSON").action((file, prefab_instance, property_path, value, options) => {
+  prefab_cmd.command("override <file> <prefab_instance> <property_path> <value>").description("Edit or add a property override in a PrefabInstance m_Modifications list. Quote paths with brackets or use dot notation (data.0) to avoid shell glob expansion").option("--object-reference <ref>", "Object reference value (default: {fileID: 0})").option("--managed-reference <id>", "Managed reference ID -- placed in value: field, forces objectReference: {fileID: 0}").option("--target <target>", 'Target reference for new entries (e.g., "{fileID: 400000, guid: abc, type: 3}")').option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, prefab_instance, property_path, value, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     if (options.objectReference && !/^\{fileID:/.test(options.objectReference)) {
       console.error(`Warning: --object-reference "${options.objectReference}" does not look like a Unity object reference ({fileID: ...}). For managed reference IDs, use --managed-reference instead or pass the ID as the <value> argument.`);
     }
@@ -13496,7 +15138,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  prefab_cmd.command("batch-overrides <file> <prefab_instance> <edits_json>").description('Batch edit multiple property overrides in a PrefabInstance. JSON format: [{"property_path":"...","value":"...","target":"...","object_reference":"..."}]').option("-j, --json", "Output as JSON").action((file, prefab_instance, edits_json, _options) => {
+  prefab_cmd.command("batch-overrides <file> <prefab_instance> <edits_json>").description('Batch edit multiple property overrides in a PrefabInstance. JSON format: [{"property_path":"...","value":"...","target":"...","object_reference":"..."}]').option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, prefab_instance, edits_json, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     let raw_edits;
     try {
       const parsed = JSON.parse(edits_json);
@@ -13535,7 +15179,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  prefab_cmd.command("managed-reference <file> <prefab_instance> <field_path> <type_name>").description("Add a [SerializeReference] managed reference to a prefab override. Auto-generates rid and creates type/data/version override entries.").requiredOption("--target <ref>", 'Target reference (e.g., "{fileID: 400000, guid: ..., type: 3}")').option("--index <n>", "Array index (default: 0)", "0").option("-p, --project <path>", "Unity project path (for type registry)").option("-j, --json", "Output as JSON").action((file, prefab_instance, field_path, type_name, options) => {
+  prefab_cmd.command("managed-reference <file> <prefab_instance> <field_path> <type_name>").description("Add a [SerializeReference] managed reference to a prefab override. Auto-generates rid and creates type/data/version override entries.").requiredOption("--target <ref>", 'Target reference (e.g., "{fileID: 400000, guid: ..., type: 3}")').option("--index <n>", "Array index (default: 0)", "0").option("-p, --project <path>", "Unity project path (for type registry)").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, prefab_instance, field_path, type_name, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection, options.project))
+      return;
     const result = addPrefabManagedReference({
       file_path: file,
       prefab_instance,
@@ -13549,20 +15195,21 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("build <project_path> <scene_path>").description("Enable, disable, or move a scene in build settings").option("--enable", "Enable the scene").option("--disable", "Disable the scene").option("--move <index>", "Move scene to position").option("-j, --json", "Output as JSON").action((project_path, scene_path, options) => {
+  cmd.command("build <scene_path>").description("Enable, disable, or move a scene in build settings").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("--enable", "Enable the scene").option("--disable", "Disable the scene").option("--move <index>", "Move scene to position").option("-j, --json", "Output as JSON").action((scene_path, options) => {
     try {
+      const resolvedProjectPath = resolve_project_path(options.project);
       if (options.move !== undefined) {
-        const result = move_scene(project_path, scene_path, parseInt(options.move, 10));
+        const result = move_scene(resolvedProjectPath, scene_path, parseInt(options.move, 10));
         console.log(JSON.stringify(result, null, 2));
         if (!result.success)
           process.exitCode = 1;
       } else if (options.enable) {
-        const result = enable_scene(project_path, scene_path);
+        const result = enable_scene(resolvedProjectPath, scene_path);
         console.log(JSON.stringify(result, null, 2));
         if (!result.success)
           process.exitCode = 1;
       } else if (options.disable) {
-        const result = disable_scene(project_path, scene_path);
+        const result = disable_scene(resolvedProjectPath, scene_path);
         console.log(JSON.stringify(result, null, 2));
         if (!result.success)
           process.exitCode = 1;
@@ -13575,7 +15222,7 @@ function build_update_command(getScanner) {
       process.exitCode = 1;
     }
   });
-  cmd.command("array <file> <file_id> <array_property> <action> [args...]").description("Insert, append, or remove array elements in a component. Insert: <index> <value> or <value> --index <n>. Append: <value>. Remove: <index> or --index <n>. Quote paths with brackets or use dot notation (data.0) to avoid shell glob expansion").option("--index <n>", "Index for insert/remove").option("-j, --json", "Output as JSON").action((file, file_id, array_property, action, args, options) => {
+  cmd.command("array <file> <file_id> <array_property> <action> [args...]").description("Insert, append, or remove array elements in a component. Insert: <index> <value> or <value> --index <n>. Append: <value>. Remove: <index> or --index <n>. Quote paths with brackets or use dot notation (data.0) to avoid shell glob expansion").option("--index <n>", "Index for insert/remove").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, file_id, array_property, action, args, options) => {
     if (action !== "insert" && action !== "append" && action !== "remove") {
       console.log(JSON.stringify({ success: false, error: 'Action must be "insert", "append", or "remove"' }, null, 2));
       process.exit(1);
@@ -13616,6 +15263,8 @@ function build_update_command(getScanner) {
         }
       }
     }
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     const result = editArray({
       file_path: file,
       file_id,
@@ -13628,7 +15277,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("batch <file> <edits_json>").description('Batch edit multiple GameObject properties in a single file operation. JSON format: [{"object_name":"...","property":"...","value":"..."}]').option("-j, --json", "Output as JSON").action((file, edits_json, _options) => {
+  cmd.command("batch <file> <edits_json>").description('Batch edit multiple GameObject properties in a single file operation. JSON format: [{"object_name":"...","property":"...","value":"..."}]').option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, edits_json, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     let raw_edits;
     try {
       const parsed = JSON.parse(edits_json);
@@ -13669,7 +15320,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("batch-components <file> <edits_json>").description('Batch edit multiple component properties by fileID in a single operation. JSON format: [{"file_id":"...","property":"...","value":"..."}]').option("-j, --json", "Output as JSON").action((file, edits_json, _options) => {
+  cmd.command("batch-components <file> <edits_json>").description('Batch edit multiple component properties by fileID in a single operation. JSON format: [{"file_id":"...","property":"...","value":"..."}]').option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, edits_json, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     let raw_edits;
     try {
       const parsed = JSON.parse(edits_json);
@@ -13710,7 +15363,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  prefab_cmd.command("remove-override <file> <prefab_instance> <property_path>").description("Remove a property override from a PrefabInstance. Quote paths with brackets or use dot notation (data.0) to avoid shell glob expansion").option("--target <ref>", "Target reference to match (for disambiguation)").option("-j, --json", "Output as JSON").action((file, prefab_instance, property_path, options) => {
+  prefab_cmd.command("remove-override <file> <prefab_instance> <property_path>").description("Remove a property override from a PrefabInstance. Quote paths with brackets or use dot notation (data.0) to avoid shell glob expansion").option("--target <ref>", "Target reference to match (for disambiguation)").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, prefab_instance, property_path, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     const result = removePrefabOverride({
       file_path: file,
       prefab_instance,
@@ -13721,7 +15376,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  prefab_cmd.command("remove-component <file> <prefab_instance> <component_ref>").description("Add a component to the PrefabInstance m_RemovedComponents list").option("-j, --json", "Output as JSON").action((file, prefab_instance, component_ref, _options) => {
+  prefab_cmd.command("remove-component <file> <prefab_instance> <component_ref>").description("Add a component to the PrefabInstance m_RemovedComponents list").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, prefab_instance, component_ref, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     const result = addRemovedComponent({
       file_path: file,
       prefab_instance,
@@ -13731,7 +15388,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  prefab_cmd.command("restore-component <file> <prefab_instance> <component_ref>").description("Remove a component from the PrefabInstance m_RemovedComponents list (restore it)").option("-j, --json", "Output as JSON").action((file, prefab_instance, component_ref, _options) => {
+  prefab_cmd.command("restore-component <file> <prefab_instance> <component_ref>").description("Remove a component from the PrefabInstance m_RemovedComponents list (restore it)").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, prefab_instance, component_ref, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     const result = removeRemovedComponent({
       file_path: file,
       prefab_instance,
@@ -13741,7 +15400,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  prefab_cmd.command("remove-gameobject <file> <prefab_instance> <gameobject_ref>").description("Add a GameObject to the PrefabInstance m_RemovedGameObjects list").option("-j, --json", "Output as JSON").action((file, prefab_instance, gameobject_ref, _options) => {
+  prefab_cmd.command("remove-gameobject <file> <prefab_instance> <gameobject_ref>").description("Add a GameObject to the PrefabInstance m_RemovedGameObjects list").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, prefab_instance, gameobject_ref, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     const result = addRemovedGameObject({
       file_path: file,
       prefab_instance,
@@ -13751,7 +15412,9 @@ function build_update_command(getScanner) {
     if (!result.success)
       process.exitCode = 1;
   });
-  prefab_cmd.command("restore-gameobject <file> <prefab_instance> <gameobject_ref>").description("Remove a GameObject from the PrefabInstance m_RemovedGameObjects list (restore it)").option("-j, --json", "Output as JSON").action((file, prefab_instance, gameobject_ref, _options) => {
+  prefab_cmd.command("restore-gameobject <file> <prefab_instance> <gameobject_ref>").description("Remove a GameObject from the PrefabInstance m_RemovedGameObjects list (restore it)").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, prefab_instance, gameobject_ref, options) => {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
     const result = removeRemovedGameObject({
       file_path: file,
       prefab_instance,
@@ -13771,11 +15434,11 @@ function build_update_command(getScanner) {
       }
     }
   }).action((file, options) => {
-    if (!import_fs19.existsSync(file)) {
+    if (!import_fs20.existsSync(file)) {
       console.log(JSON.stringify({ success: false, error: `File not found: ${file}` }, null, 2));
       process.exit(1);
     }
-    let content = import_fs19.readFileSync(file, "utf-8");
+    let content = import_fs20.readFileSync(file, "utf-8");
     const changes = [];
     if (options.shader) {
       const guid = options.shader;
@@ -13924,7 +15587,7 @@ ${lm[1]}  - ${kw}
       process.exitCode = 1;
       return;
     }
-    import_fs19.writeFileSync(file, content, "utf-8");
+    import_fs20.writeFileSync(file, content, "utf-8");
     console.log(JSON.stringify({ success: true, file, changes }, null, 2));
   });
   cmd.command("meta [file]").description("Edit Unity .meta file importer settings").option("--set <key=value>", "Set an importer setting (e.g., isReadable=1)", (v, p) => [...p, v], []).option("--max-size <n>", "Set TextureImporter maxTextureSize").option("--compression <type>", "Set textureCompression (0=None, 1=LowQuality, 2=Normal, 3=HighQuality)").option("--filter-mode <mode>", "Set filterMode (0=Point, 1=Bilinear, 2=Trilinear)").option("--read-write", "Enable isReadable").option("--no-read-write", "Disable isReadable").option("--batch <glob>", "Apply to all matching files").option("--dry-run", "Preview changes without writing").option("-j, --json", "Output as JSON").action((file, options) => {
@@ -13980,14 +15643,14 @@ ${lm[1]}  - ${kw}
       const glob_pattern = options.batch;
       const pattern = glob_pattern.endsWith(".meta") ? glob_pattern : `${glob_pattern}.meta`;
       const first_glob = pattern.search(/[*?[\]{}]/);
-      const dir_part = first_glob >= 0 ? pattern.slice(0, pattern.lastIndexOf("/", first_glob)) : import_path9.dirname(pattern);
-      const dir = import_path9.resolve(dir_part);
-      const suffix = import_path9.basename(pattern).replace(/^\*+/, "");
+      const dir_part = first_glob >= 0 ? pattern.slice(0, pattern.lastIndexOf("/", first_glob)) : import_path12.dirname(pattern);
+      const dir = import_path12.resolve(dir_part);
+      const suffix = import_path12.basename(pattern).replace(/^\*+/, "");
       const meta_files = [];
       const scan = (d) => {
-        for (const entry of import_fs19.readdirSync(d)) {
-          const full = import_path9.join(d, entry);
-          if (import_fs19.statSync(full).isDirectory()) {
+        for (const entry of import_fs20.readdirSync(d)) {
+          const full = import_path12.join(d, entry);
+          if (import_fs20.statSync(full).isDirectory()) {
             if (pattern.includes("**"))
               scan(full);
           } else if (entry.endsWith(suffix)) {
@@ -13995,7 +15658,7 @@ ${lm[1]}  - ${kw}
           }
         }
       };
-      if (import_fs19.existsSync(dir))
+      if (import_fs20.existsSync(dir))
         scan(dir);
       if (meta_files.length === 0) {
         console.log(JSON.stringify({ success: false, error: `No files matched pattern: ${glob_pattern}` }, null, 2));
@@ -14003,7 +15666,7 @@ ${lm[1]}  - ${kw}
       }
       const results = [];
       for (const mf of meta_files) {
-        let mc = import_fs19.readFileSync(mf, "utf-8");
+        let mc = import_fs20.readFileSync(mf, "utf-8");
         const file_changes = [];
         for (const edit of edits) {
           const re = new RegExp(`^(\\s*${edit.key}:)[ \\t]*.*$`, "m");
@@ -14014,7 +15677,7 @@ ${lm[1]}  - ${kw}
         }
         if (file_changes.length > 0) {
           if (!options.dryRun)
-            import_fs19.writeFileSync(mf, mc, "utf-8");
+            import_fs20.writeFileSync(mf, mc, "utf-8");
           results.push({ file: mf, changes: file_changes });
         }
       }
@@ -14027,11 +15690,11 @@ ${lm[1]}  - ${kw}
       }, null, 2));
       return;
     }
-    if (!import_fs19.existsSync(metaPath)) {
+    if (!import_fs20.existsSync(metaPath)) {
       console.log(JSON.stringify({ success: false, error: `Meta file not found: ${metaPath}` }, null, 2));
       process.exit(1);
     }
-    let content = import_fs19.readFileSync(metaPath, "utf-8");
+    let content = import_fs20.readFileSync(metaPath, "utf-8");
     const changes = [];
     for (const edit of edits) {
       const re = new RegExp(`^(\\s*${edit.key}:)[ \\t]*.*$`, "m");
@@ -14046,11 +15709,11 @@ ${lm[1]}  - ${kw}
       console.log(JSON.stringify({ success: true, dry_run: true, file: metaPath, changes }, null, 2));
       return;
     }
-    import_fs19.writeFileSync(metaPath, content, "utf-8");
+    import_fs20.writeFileSync(metaPath, content, "utf-8");
     console.log(JSON.stringify({ success: true, file: metaPath, changes }, null, 2));
   });
   cmd.command("animation <file>").description("Edit AnimationClip settings and events").option("--set <property=value>", "Set a clip property (e.g., wrap-mode=2 for Loop)", (v, p) => [...p, v], []).option("--add-event <time,function[,data]>", "Add an animation event (e.g., 0.5,OnFootstep,left)", (v, p) => [...p, v], []).option("--remove-event <index>", "Remove an animation event by index (0-based)").option("-j, --json", "Output as JSON").action((file, options) => {
-    if (!import_fs19.existsSync(file)) {
+    if (!import_fs20.existsSync(file)) {
       console.log(JSON.stringify({ success: false, error: `File not found: ${file}` }, null, 2));
       process.exit(1);
     }
@@ -14058,7 +15721,7 @@ ${lm[1]}  - ${kw}
       console.log(JSON.stringify({ success: false, error: `File is not an AnimationClip (.anim): ${file}` }, null, 2));
       process.exit(1);
     }
-    let content = import_fs19.readFileSync(file, "utf-8");
+    let content = import_fs20.readFileSync(file, "utf-8");
     const changes = [];
     const property_map = {
       "wrap-mode": "m_WrapMode",
@@ -14219,16 +15882,16 @@ ${event_yaml}
       process.exitCode = 1;
       return;
     }
-    import_fs19.writeFileSync(file, content, "utf-8");
+    import_fs20.writeFileSync(file, content, "utf-8");
     console.log(JSON.stringify({ success: true, file, changes }, null, 2));
   });
   const PARAM_TYPE_MAP = { float: 1, int: 3, bool: 4, trigger: 9 };
   cmd.command("animator <file>").description("Edit AnimatorController parameters").option("--add-parameter <name>", "Add a new parameter").option("--type <float|int|bool|trigger>", "Parameter type (required with --add-parameter)").option("--remove-parameter <name>", "Remove a parameter by name").option("--set-default <param=value>", "Set parameter default value (e.g., Speed=1.5)", (v, p) => [...p, v], []).option("-j, --json", "Output as JSON").action((file, options) => {
-    if (!import_fs19.existsSync(file)) {
+    if (!import_fs20.existsSync(file)) {
       console.log(JSON.stringify({ success: false, error: `File not found: ${file}` }, null, 2));
       process.exit(1);
     }
-    let content = import_fs19.readFileSync(file, "utf-8");
+    let content = import_fs20.readFileSync(file, "utf-8");
     const had_crlf = content.includes(`\r
 `);
     if (had_crlf)
@@ -14330,17 +15993,19 @@ $1`);
     if (had_crlf)
       content = content.replace(/\n/g, `\r
 `);
-    import_fs19.writeFileSync(file, content, "utf-8");
+    import_fs20.writeFileSync(file, content, "utf-8");
     console.log(JSON.stringify({ success: true, file, changes }, null, 2));
   });
-  cmd.command("sibling-index <file> <object_name> <index>").description("Set the sibling index of a GameObject, renumbering all siblings").option("-j, --json", "Output as JSON").action((file, object_name, index_str, _options) => {
+  cmd.command("sibling-index <file> <object_name> <index>").description("Set the sibling index of a GameObject, renumbering all siblings").option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, object_name, index_str, options) => {
     const target_index = parseInt(index_str, 10);
     if (!Number.isFinite(target_index) || target_index < 0) {
       console.log(JSON.stringify({ success: false, error: "Index must be a non-negative integer" }, null, 2));
       process.exitCode = 1;
       return;
     }
-    if (!import_fs19.existsSync(file)) {
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection))
+      return;
+    if (!import_fs20.existsSync(file)) {
       console.log(JSON.stringify({ success: false, error: `File not found: ${file}` }, null, 2));
       process.exitCode = 1;
       return;
@@ -14535,7 +16200,7 @@ $1`);
     console.log(JSON.stringify({ success: true, file, changes }, null, 2));
   });
   cmd.command("animation-curves <file>").description("Add, remove, or modify animation curves in an .anim file").option("--add-curve <json>", 'Add a curve (JSON: {"type":"float","path":"Body","attribute":"m_Alpha","classID":23,"keyframes":[{"time":0,"value":1}]})').option("--remove-curve <spec>", "Remove a curve by path:attribute (e.g., Body/Mesh:m_Alpha)").option("--set-keyframes <json>", 'Replace keyframes (JSON: {"curve":"path:attribute","keyframes":[{"time":0,"value":10}]})').option("-j, --json", "Output as JSON").action((file, options) => {
-    if (!import_fs19.existsSync(file)) {
+    if (!import_fs20.existsSync(file)) {
       console.log(JSON.stringify({ success: false, error: `File not found: ${file}` }, null, 2));
       process.exitCode = 1;
       return;
@@ -14545,7 +16210,7 @@ $1`);
       process.exitCode = 1;
       return;
     }
-    let content = import_fs19.readFileSync(file, "utf-8");
+    let content = import_fs20.readFileSync(file, "utf-8");
     const had_crlf = content.includes(`\r
 `);
     if (had_crlf)
@@ -14843,16 +16508,16 @@ ${curve_yaml}`);
     if (had_crlf)
       content = content.replace(/\n/g, `\r
 `);
-    import_fs19.writeFileSync(file, content, "utf-8");
+    import_fs20.writeFileSync(file, content, "utf-8");
     console.log(JSON.stringify({ success: true, file, changes }, null, 2));
   });
   cmd.command("animator-state <file>").description("Add/remove states and transitions in an AnimatorController").option("--add-state <name>", "Add a new AnimatorState").option("--motion <guid-or-path>", "Motion clip GUID or file path (companion to --add-state)").option("--layer <name>", "Target layer name (default: first layer)").option("--speed <n>", "State speed (companion to --add-state, default: 1)").option("--remove-state <name>", "Remove a state and all its transitions").option("--add-transition <src:dst>", 'Add a transition (use "any" for AnyState source)').option("--condition <param,mode,threshold>", "Transition condition (repeatable)", (v, p) => [...p, v], []).option("--has-exit-time", "Enable exit time on transition").option("--exit-time <n>", "Exit time value (default: 0.75)").option("--duration <n>", "Transition duration (default: 0.25)").option("--remove-transition <src:dst>", "Remove a transition by source:destination state names").option("--set-default-state <name>", "Set the default state in the state machine").option("-j, --json", "Output as JSON").action((file, options) => {
-    if (!import_fs19.existsSync(file)) {
+    if (!import_fs20.existsSync(file)) {
       console.log(JSON.stringify({ success: false, error: `File not found: ${file}` }, null, 2));
       process.exitCode = 1;
       return;
     }
-    let content = import_fs19.readFileSync(file, "utf-8");
+    let content = import_fs20.readFileSync(file, "utf-8");
     const had_crlf = content.includes(`\r
 `);
     if (had_crlf)
@@ -15191,11 +16856,11 @@ $1`);
     if (had_crlf)
       content = content.replace(/\n/g, `\r
 `);
-    import_fs19.writeFileSync(file, content, "utf-8");
+    import_fs20.writeFileSync(file, content, "utf-8");
     console.log(JSON.stringify({ success: true, file, changes }, null, 2));
   });
   cmd.addCommand(prefab_cmd);
-  cmd.command("managed-reference <file> <component_id> <field_path> <type_name>").description('Add a managed reference (SerializeReference) to a component field. Type can be "Namespace.ClassName" (registry lookup) or "Assembly Namespace.ClassName" (manual).').option("-p, --project <path>", "Unity project path (for type registry)").option("--append", "Append to array (do not update field rid)").option("--properties <json>", `JSON object of initial field values for the data block (e.g. '{"damage": "10"}')`).option("-j, --json", "Output as JSON").action((file, component_id, field_path, type_name, options) => {
+  cmd.command("managed-reference <file> <component_id> <field_path> <type_name>").description('Add a managed reference (SerializeReference) to a component field. Type can be "Namespace.ClassName" (registry lookup) or "Assembly Namespace.ClassName" (manual).').option("-p, --project <path>", "Unity project path (for type registry)").option("--append", "Append to array (do not update field rid)").option("--properties <json>", `JSON object of initial field values for the data block (e.g. '{"damage": "10"}')`).option("-j, --json", "Output as JSON").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").action(async (file, component_id, field_path, type_name, options) => {
     let initial_values;
     if (options.properties) {
       try {
@@ -15206,6 +16871,8 @@ $1`);
         return;
       }
     }
+    if (!await check_loaded_edit_protection(file, options.bypassLoadedProtection, options.project))
+      return;
     const result = editManagedReference({
       file_path: file,
       file_id: component_id,
@@ -15225,7 +16892,13 @@ $1`);
 // src/cmd-delete.ts
 function build_delete_command() {
   const cmd = new Command("delete").description("Delete Unity objects (GameObjects, components)");
-  cmd.command("gameobject <file> <object_name>").description("Delete a GameObject and its hierarchy from a Unity file").option("-j, --json", "Output as JSON").action((file, object_name, _options) => {
+  cmd.command("gameobject <file> <object_name>").description("Delete a GameObject and its hierarchy from a Unity file").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").option("-j, --json", "Output as JSON").action(async (file, object_name, options) => {
+    const guard = await enforce_loaded_edit_protection(file, options.bypassLoadedProtection);
+    if (!guard.allowed) {
+      console.log(JSON.stringify({ success: false, file_path: file, error: guard.error }, null, 2));
+      process.exitCode = 1;
+      return;
+    }
     const result = deleteGameObject({
       file_path: file,
       object_name
@@ -15234,10 +16907,22 @@ function build_delete_command() {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("component <file_or_project> <component>").description('Remove a component by file ID or type name (e.g., "Rigidbody", "StandaloneInputModule")').option("--on <game_object>", "Scope to a specific GameObject (name or fileID)").option("-p, --project <path>", "Unity project path (for script GUID lookup)").option("--all", "Remove from all scenes and prefabs in the project (first arg becomes project path)").option("-j, --json", "Output as JSON").action((file_or_project, component, options) => {
+  cmd.command("component <file_or_project> <component>").description('Remove a component by file ID or type name (e.g., "Rigidbody", "StandaloneInputModule")').option("--on <game_object>", "Scope to a specific GameObject (name or fileID)").option("-p, --project <path>", "Unity project path (for script GUID lookup)").option("--all", "Remove from all scenes and prefabs in the project (first arg becomes project path)").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").option("-j, --json", "Output as JSON").action(async (file_or_project, component, options) => {
     if (options.all) {
+      const resolvedProjectPath = resolve_project_path(file_or_project);
+      if (!options.bypassLoadedProtection) {
+        const connected = await is_editor_connected_for_project(resolvedProjectPath);
+        if (connected) {
+          console.log(JSON.stringify({
+            success: false,
+            error: "Refusing to run project-wide delete while editor is connected. Use --bypass-loaded-protection to force file-based edits."
+          }, null, 2));
+          process.exitCode = 1;
+          return;
+        }
+      }
       const result = removeComponentBatch({
-        project_path: file_or_project,
+        project_path: resolvedProjectPath,
         component_type: component,
         game_object: options.on
       });
@@ -15245,6 +16930,12 @@ function build_delete_command() {
       if (!result.success)
         process.exitCode = 1;
     } else {
+      const guard = await enforce_loaded_edit_protection(file_or_project, options.bypassLoadedProtection, options.project);
+      if (!guard.allowed) {
+        console.log(JSON.stringify({ success: false, file_path: file_or_project, error: guard.error }, null, 2));
+        process.exitCode = 1;
+        return;
+      }
       const result = removeComponent({
         file_path: file_or_project,
         file_id: component,
@@ -15256,9 +16947,10 @@ function build_delete_command() {
         process.exitCode = 1;
     }
   });
-  cmd.command("build <project_path> <scene_path>").description("Remove a scene from build settings").option("-j, --json", "Output as JSON").action((project_path, scene_path, _options) => {
+  cmd.command("build <scene_path>").description("Remove a scene from build settings").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-j, --json", "Output as JSON").action((scene_path, options) => {
+    const resolvedProjectPath = resolve_project_path(options.project);
     try {
-      const result = remove_scene(project_path, scene_path);
+      const result = remove_scene(resolvedProjectPath, scene_path);
       console.log(JSON.stringify(result, null, 2));
       if (!result.success)
         process.exitCode = 1;
@@ -15267,7 +16959,13 @@ function build_delete_command() {
       process.exitCode = 1;
     }
   });
-  cmd.command("prefab <file> <prefab_instance>").description("Delete a PrefabInstance and all its stripped/added blocks from a Unity file").option("-j, --json", "Output as JSON").action((file, prefab_instance, _options) => {
+  cmd.command("prefab <file> <prefab_instance>").description("Delete a PrefabInstance and all its stripped/added blocks from a Unity file").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").option("-j, --json", "Output as JSON").action(async (file, prefab_instance, options) => {
+    const guard = await enforce_loaded_edit_protection(file, options.bypassLoadedProtection);
+    if (!guard.allowed) {
+      console.log(JSON.stringify({ success: false, file_path: file, error: guard.error }, null, 2));
+      process.exitCode = 1;
+      return;
+    }
     const result = deletePrefabInstance({
       file_path: file,
       prefab_instance
@@ -15276,9 +16974,22 @@ function build_delete_command() {
     if (!result.success)
       process.exitCode = 1;
   });
-  cmd.command("package <project_path> <name>").description("Remove a package from Packages/manifest.json").option("-j, --json", "Output as JSON").action((project_path, name, _options) => {
+  cmd.command("asset <file>").description("Delete an asset file and its .meta sidecar (missing .meta => warning)").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").option("-j, --json", "Output as JSON").action(async (file, options) => {
+    const guard = await enforce_loaded_edit_protection(file, options.bypassLoadedProtection);
+    if (!guard.allowed) {
+      console.log(JSON.stringify({ success: false, file_path: file, error: guard.error }, null, 2));
+      process.exitCode = 1;
+      return;
+    }
+    const result = deleteAssetFile({ file_path: file });
+    console.log(JSON.stringify(result, null, 2));
+    if (!result.success)
+      process.exitCode = 1;
+  });
+  cmd.command("package <name>").description("Remove a package from Packages/manifest.json").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-j, --json", "Output as JSON").action((name, options) => {
     try {
-      const result = remove_package(project_path, name);
+      const resolvedProjectPath = resolve_project_path(options.project);
+      const result = remove_package(resolvedProjectPath, name);
       if ("error" in result) {
         console.log(JSON.stringify({ success: false, error: result.error }, null, 2));
         process.exitCode = 1;
@@ -15294,278 +17005,11 @@ function build_delete_command() {
 }
 
 // src/cmd-editor.ts
-var import_path11 = require("path");
-
-// src/editor-client.ts
-var import_fs20 = require("fs");
-var import_path10 = require("path");
-function read_editor_config(project_path) {
-  const config_path = import_path10.join(project_path, ".unity-agentic", "editor.json");
-  if (!import_fs20.existsSync(config_path)) {
-    return { error: `Editor bridge not found at ${config_path}. Is the Unity Editor running with the bridge package installed?` };
-  }
-  let config;
-  try {
-    const raw = import_fs20.readFileSync(config_path, "utf-8");
-    config = JSON.parse(raw);
-  } catch (err) {
-    return { error: `Failed to parse editor.json: ${err instanceof Error ? err.message : String(err)}` };
-  }
-  if (typeof config.port !== "number" || typeof config.pid !== "number") {
-    return { error: "Invalid editor.json: missing port or pid" };
-  }
-  if (!is_pid_alive(config.pid)) {
-    return { error: `Unity Editor process (PID ${config.pid}) is not running. The editor may have been closed.` };
-  }
-  return config;
-}
-var RETRYABLE_CODES = new Set([-32000, -32002, -32003]);
-var RETRY_DELAYS = [500, 1000, 2000];
-async function call_editor(options) {
-  const maxRetries = options.retries ?? 2;
-  let lastResponse;
-  for (let attempt = 0;attempt <= maxRetries; attempt++) {
-    lastResponse = await call_editor_once(options);
-    if (!lastResponse.error || !RETRYABLE_CODES.has(lastResponse.error.code)) {
-      return lastResponse;
-    }
-    if (attempt < maxRetries) {
-      const delay = RETRY_DELAYS[Math.min(attempt, RETRY_DELAYS.length - 1)];
-      await new Promise((r) => setTimeout(r, delay));
-    }
-  }
-  return lastResponse;
-}
-function call_editor_once(options) {
-  const { method, params, timeout = 1e4, no_wait } = options;
-  const config = resolve_config(options);
-  if ("error" in config) {
-    return Promise.resolve({
-      jsonrpc: "2.0",
-      id: "0",
-      error: { code: -32000, message: config.error }
-    });
-  }
-  const url = `ws://127.0.0.1:${config.port}/unity-agentic`;
-  const request_id = generate_id();
-  const wire_params = { ...params };
-  if (timeout !== 1e4)
-    wire_params._timeout = timeout;
-  if (no_wait)
-    wire_params.no_wait = true;
-  const request = {
-    jsonrpc: "2.0",
-    id: request_id,
-    method,
-    ...Object.keys(wire_params).length > 0 ? { params: wire_params } : {}
-  };
-  return new Promise((resolve7) => {
-    let resolved = false;
-    let ws;
-    const timer = setTimeout(() => {
-      if (!resolved) {
-        resolved = true;
-        try {
-          ws?.close();
-        } catch {}
-        resolve7({
-          jsonrpc: "2.0",
-          id: request_id,
-          error: { code: -32001, message: `Timeout after ${timeout}ms waiting for response to ${method}` }
-        });
-      }
-    }, timeout);
-    try {
-      ws = new WebSocket(url);
-      ws.onopen = () => {
-        ws.send(JSON.stringify(request));
-        if (no_wait && !resolved) {
-          resolved = true;
-          clearTimeout(timer);
-          setTimeout(() => {
-            try {
-              ws.close();
-            } catch {}
-          }, 200);
-          resolve7({
-            jsonrpc: "2.0",
-            id: request_id,
-            result: { queued: true }
-          });
-        }
-      };
-      ws.onmessage = (event) => {
-        try {
-          const data = JSON.parse(String(event.data));
-          if (data.id === request_id) {
-            if (!resolved) {
-              resolved = true;
-              clearTimeout(timer);
-              ws.close();
-              resolve7(data);
-            }
-          }
-        } catch {}
-      };
-      ws.onerror = () => {
-        if (!resolved) {
-          resolved = true;
-          clearTimeout(timer);
-          resolve7({
-            jsonrpc: "2.0",
-            id: request_id,
-            error: { code: -32002, message: `WebSocket connection failed to ${url}. Is the Unity Editor running?` }
-          });
-        }
-      };
-      ws.onclose = () => {
-        if (!resolved) {
-          resolved = true;
-          clearTimeout(timer);
-          resolve7({
-            jsonrpc: "2.0",
-            id: request_id,
-            error: { code: -32003, message: "WebSocket connection closed before response received" }
-          });
-        }
-      };
-    } catch (err) {
-      if (!resolved) {
-        resolved = true;
-        clearTimeout(timer);
-        resolve7({
-          jsonrpc: "2.0",
-          id: request_id,
-          error: { code: -32002, message: `Failed to connect: ${err instanceof Error ? err.message : String(err)}` }
-        });
-      }
-    }
-  });
-}
-async function stream_editor(options) {
-  const { method, params, timeout = 30000, on_event } = options;
-  const config = resolve_config(options);
-  if ("error" in config) {
-    throw new Error(config.error);
-  }
-  const MAX_RECONNECTS = 5;
-  let reconnect_count = 0;
-  let stopped = false;
-  return new Promise((resolve7, reject) => {
-    let resolved = false;
-    function connect(url) {
-      const ws = new WebSocket(url);
-      const request_id = generate_id();
-      const request = {
-        jsonrpc: "2.0",
-        id: request_id,
-        method,
-        ...params ? { params } : {}
-      };
-      let connected = false;
-      const timer = !resolved ? setTimeout(() => {
-        if (!connected && !resolved) {
-          reject(new Error(`Timeout connecting to ${url}`));
-        }
-      }, timeout) : null;
-      ws.onopen = () => {
-        connected = true;
-        if (timer)
-          clearTimeout(timer);
-        reconnect_count = 0;
-        ws.send(JSON.stringify(request));
-        if (!resolved) {
-          resolved = true;
-          resolve7({ close: () => {
-            stopped = true;
-            ws.close();
-          } });
-        }
-      };
-      ws.onmessage = (event) => {
-        try {
-          const data = JSON.parse(String(event.data));
-          if ("method" in data && !("id" in data)) {
-            on_event(data);
-          }
-        } catch {}
-      };
-      ws.onerror = () => {
-        if (!connected && !resolved) {
-          if (timer)
-            clearTimeout(timer);
-          reject(new Error(`WebSocket connection failed to ${url}`));
-        }
-      };
-      ws.onclose = () => {
-        if (stopped)
-          return;
-        if (!connected && !resolved)
-          return;
-        if (reconnect_count >= MAX_RECONNECTS)
-          return;
-        reconnect_count++;
-        const delay = Math.min(500 * reconnect_count, 3000);
-        setTimeout(() => {
-          if (stopped)
-            return;
-          const fresh_config = resolve_config(options);
-          if ("error" in fresh_config)
-            return;
-          connect(`ws://127.0.0.1:${fresh_config.port}/unity-agentic`);
-        }, delay);
-      };
-    }
-    connect(`ws://127.0.0.1:${config.port}/unity-agentic`);
-  });
-}
-async function ping_editor(port, timeout_ms = 2000) {
-  return new Promise((resolve7) => {
-    const timer = setTimeout(() => {
-      resolve7({ reachable: false, error: `Timeout after ${timeout_ms}ms` });
-    }, timeout_ms);
-    try {
-      const ws = new WebSocket(`ws://127.0.0.1:${port}/unity-agentic`);
-      ws.onopen = () => {
-        clearTimeout(timer);
-        try {
-          ws.close();
-        } catch {}
-        resolve7({ reachable: true });
-      };
-      ws.onerror = (err) => {
-        clearTimeout(timer);
-        resolve7({ reachable: false, error: String(err) });
-      };
-    } catch (err) {
-      clearTimeout(timer);
-      resolve7({ reachable: false, error: String(err) });
-    }
-  });
-}
-function resolve_config(options) {
-  if (options.port) {
-    return { port: options.port, pid: 0, version: "unknown" };
-  }
-  return read_editor_config(options.project_path);
-}
-function is_pid_alive(pid) {
-  try {
-    process.kill(pid, 0);
-    return true;
-  } catch {
-    return false;
-  }
-}
-function generate_id() {
-  return `${Date.now()}-${Math.random().toString(36).substring(2, 8)}`;
-}
-
-// src/cmd-editor.ts
+var import_path13 = require("path");
 var BRIDGE_PACKAGE_NAME = "com.unity-agentic-tools.editor-bridge";
 var BRIDGE_PACKAGE_VERSION = "https://github.com/taconotsandwich/unity-agentic-tools.git?path=unity-package";
 function get_common_options(cmd) {
-  let current = cmd.parent;
+  let current = cmd;
   let project;
   let timeout_str;
   let port_str;
@@ -15579,7 +17023,7 @@ function get_common_options(cmd) {
       port_str = opts.port;
     current = current.parent;
   }
-  const project_path = import_path11.resolve(project || process.cwd());
+  const project_path = import_path13.resolve(project || process.cwd());
   const timeout = parseInt(timeout_str || "10000", 10);
   const port = port_str ? parseInt(port_str, 10) : undefined;
   return { project_path, timeout, port };
@@ -15757,9 +17201,9 @@ function build_editor_command() {
       params.mode = options.mode;
     await handle_rpc(this, "editor.tests.run", params);
   });
-  cmd.command("install <project_path>").description("Install the editor bridge package into a Unity project").action((_project_path) => {
-    const resolved_path = import_path11.resolve(_project_path);
-    const result = add_package(resolved_path, BRIDGE_PACKAGE_NAME, BRIDGE_PACKAGE_VERSION);
+  cmd.command("install").description("Install the editor bridge package into a Unity project").option("-p, --project <path>", "Path to Unity project (defaults to cwd)").action(function() {
+    const { project_path } = get_common_options(this);
+    const result = add_package(project_path, BRIDGE_PACKAGE_NAME, BRIDGE_PACKAGE_VERSION);
     if ("error" in result) {
       console.log(JSON.stringify({ success: false, error: result.error }, null, 2));
       process.exitCode = 1;
@@ -15767,9 +17211,9 @@ function build_editor_command() {
     }
     console.log(JSON.stringify(result, null, 2));
   });
-  cmd.command("uninstall <project_path>").description("Remove the editor bridge package from a Unity project").action((_project_path) => {
-    const resolved_path = import_path11.resolve(_project_path);
-    const result = remove_package(resolved_path, BRIDGE_PACKAGE_NAME);
+  cmd.command("uninstall").description("Remove the editor bridge package from a Unity project").option("-p, --project <path>", "Path to Unity project (defaults to cwd)").action(function() {
+    const { project_path } = get_common_options(this);
+    const result = remove_package(project_path, BRIDGE_PACKAGE_NAME);
     if ("error" in result) {
       console.log(JSON.stringify({ success: false, error: result.error }, null, 2));
       process.exitCode = 1;
@@ -15994,7 +17438,13 @@ program.addCommand(build_read_command(getScanner));
 program.addCommand(build_update_command(getScanner));
 program.addCommand(build_delete_command());
 program.addCommand(build_editor_command());
-program.command("clone <file> <object_name>").description("Duplicate a GameObject and its hierarchy").option("-n, --name <new_name>", "Name for the duplicated object").option("-j, --json", "Output as JSON").action((file, object_name, options) => {
+program.command("clone <file> <object_name>").description("Duplicate a GameObject and its hierarchy").option("-n, --name <new_name>", "Name for the duplicated object").option("--bypass-loaded-protection", "Allow editing files currently loaded in Unity Editor").option("-j, --json", "Output as JSON").action(async (file, object_name, options) => {
+  const guard = await enforce_loaded_edit_protection(file, options.bypassLoadedProtection);
+  if (!guard.allowed) {
+    console.log(JSON.stringify({ success: false, file_path: file, error: guard.error }, null, 2));
+    process.exitCode = 1;
+    return;
+  }
   const result = duplicateGameObject({
     file_path: file,
     object_name,
@@ -16100,11 +17550,12 @@ program.command("search <path> [pattern]").description("Search for GameObjects.
     console.log(JSON.stringify(result, null, 2));
   }
 });
-program.command("grep <project_path> <pattern>").description("Search for a regex pattern across project files").option("--type <type>", "File type filter: cs, yaml, unity, prefab, asset, all", "all").option("-m, --max <n>", "Max results (default: 100)", "100").option("-C, --context <n>", "Context lines around matches", "0").option("-j, --json", "Output as JSON").action((project_path, pattern, options) => {
+program.command("grep <pattern>").description("Search for a regex pattern across project files").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("--type <type>", "File type filter: cs, yaml, unity, prefab, asset, all", "all").option("-m, --max <n>", "Max results (default: 100)", "100").option("-C, --context <n>", "Context lines around matches", "0").option("-j, --json", "Output as JSON").action((pattern, options) => {
   if (!pattern || pattern.trim() === "") {
     console.log(JSON.stringify({ success: false, error: "Pattern must not be empty" }, null, 2));
     process.exit(1);
   }
+  let project_path = resolve_project_path(options.project);
   const abs_path = path9.resolve(project_path);
   const project_root = find_unity_project_root(abs_path);
   if (project_root) {
@@ -16132,8 +17583,9 @@ program.command("grep <project_path> <pattern>").description("Search for a regex
   if (!result.success)
     process.exitCode = 1;
 });
-program.command("version <project_path>").description("Read Unity project version").option("-j, --json", "Output as JSON").action((project_path, _options) => {
+program.command("version").description("Read Unity project version").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("-j, --json", "Output as JSON").action((options) => {
   try {
+    const project_path = resolve_project_path(options.project);
     const version = read_project_version(project_path);
     console.log(JSON.stringify(version, null, 2));
   } catch (err) {