unity-agentic-tools 0.4.1 → 0.4.2

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: "0.4.2",
     description: "Fast, token-efficient Unity YAML parser for AI agents",
     exports: {
       ".": {
@@ -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)) {
@@ -3286,6 +3289,24 @@ function resolveScriptGuid(script, projectPath) {
         }
       } catch {}
     }
+    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;
 }
@@ -3440,8 +3461,8 @@ 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$/, "");
@@ -5223,48 +5244,320 @@ 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}${indent}  serializedVersion: 3
+`);
+  if (updated === raw) {
+    return false;
   }
-  const existingPattern = /(m_AddedComponents:[ \t]*\n(?:[ \t]+-[\s\S]*?(?=\n[ \t]+m_|$))*)/;
-  if (existingPattern.test(raw)) {
-    raw = raw.replace(existingPattern, `$1${entry}`);
-    piBlock.replace_raw(raw);
+  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);
+    }
+  }
+  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 +5684,17 @@ 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 +5847,14 @@ 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 +6337,7 @@ 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 +6484,7 @@ PrefabInstance:
   m_ObjectHideFlags: 0
   serializedVersion: 2
   m_Modification:
+    serializedVersion: 3
     m_TransformParent: {fileID: ${parentTransformIdStr}}
     m_Modifications:
     - target: {fileID: ${rootGoFileId}, guid: ${sourceGuid}, type: 3}
@@ -6476,6 +6789,8 @@ function is_valid_component_base(base_class, project_path, depth = 0) {
         }
         if (!fullPath.endsWith(".cs") || !import_fs8.existsSync(fullPath)) {
           if (match.kind === "class") {
+            if (fullPath.includes("Assembly-CSharp.dll"))
+              return true;
             return is_likely_component_base_name(base_class);
           }
         }
@@ -6620,11 +6935,11 @@ function addComponent(options) {
       };
     }
     if (resolved.base_class && !COMPONENT_BASE_CLASSES.has(resolved.base_class) && !is_valid_component_base(resolved.base_class, project_path)) {
-      return {
-        success: false,
-        file_path,
-        error: `"${component_type}" extends ${resolved.base_class}, which does not inherit from MonoBehaviour. Cannot add as a component. If this is incorrect, ensure the type registry is up to date ("setup" command).`
-      };
+      const warn = `"${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) {
@@ -6640,10 +6955,22 @@ 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 ${variantInfo.prefab_instance_id}`
+      };
+    }
   } else {
     const added = addComponentToGameObject(doc, gameObjectIdStr, componentIdStr);
     if (!added) {
@@ -7615,7 +7942,7 @@ function editComponentByFileId(options) {
     return {
       success: false,
       file_path,
-      error: `Could not resolve "${new_value}" to asset reference. Ensure GUID cache exists (run "setup <project>" first).`
+      error: `Could not resolve "${new_value}" to asset reference. Ensure GUID cache exists (run "setup" first, or "setup -p <path>").`
     };
   }
   if (resolved !== undefined) {
@@ -8192,6 +8519,193 @@ function findPrefabInstanceBlock(doc, identifier) {
   }
   return null;
 }
+function parsePrefabRef2(refText) {
+  const fileIdMatch = refText.match(/fileID:[ \t]*(-?\d+)/i);
+  if (!fileIdMatch)
+    return null;
+  const guidMatch = refText.match(/guid:[ \t]*([a-f0-9]{32})/i);
+  const typeMatch = refText.match(/type:[ \t]*(-?\d+)/i);
+  return {
+    file_id: fileIdMatch[1],
+    guid: guidMatch ? guidMatch[1].toLowerCase() : undefined,
+    type: typeMatch ? typeMatch[1] : undefined
+  };
+}
+function extractPrefabSourceGuid2(prefabInstanceRaw) {
+  const sourceMatch = prefabInstanceRaw.match(/m_SourcePrefab:[ \t]*\{[^}]*guid:[ \t]*([a-f0-9]{32})/i);
+  return sourceMatch ? sourceMatch[1].toLowerCase() : null;
+}
+function normalizePrefabRef2(refText, sourceGuid) {
+  const parsed = parsePrefabRef2(refText);
+  if (!parsed) {
+    return { error: `Invalid reference "${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 +8916,6 @@ 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 +8926,16 @@ 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:
-  - ${component_ref}
-`);
-  } else {
-    return { success: false, file_path, error: "m_RemovedComponents property not found in PrefabInstance" };
+  const mutation = mutatePrefabReferenceList({
+    target_block: targetBlock,
+    key: "m_RemovedComponents",
+    ref_text: component_ref,
+    action: "add",
+    item_label: "Component"
+  });
+  if (!mutation.success) {
+    return { success: false, file_path, error: mutation.error };
   }
-  targetBlock.replace_raw(rawText);
   if (!doc.validate()) {
     return { success: false, file_path, error: "Validation failed after adding removed component" };
   }
@@ -8456,13 +8964,16 @@ function removeRemovedComponent(options) {
   if (!targetBlock) {
     return { success: false, file_path, error: `PrefabInstance "${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 +8992,6 @@ 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 +9002,16 @@ 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:
-  - ${component_ref}
-`);
-  } else {
-    return { success: false, file_path, error: "m_RemovedGameObjects property not found in PrefabInstance" };
+  const mutation = mutatePrefabReferenceList({
+    target_block: targetBlock,
+    key: "m_RemovedGameObjects",
+    ref_text: component_ref,
+    action: "add",
+    item_label: "GameObject"
+  });
+  if (!mutation.success) {
+    return { success: false, file_path, error: mutation.error };
   }
-  targetBlock.replace_raw(rawText);
   if (!doc.validate()) {
     return { success: false, file_path, error: "Validation failed after adding removed GameObject" };
   }
@@ -8535,13 +9040,16 @@ function removeRemovedGameObject(options) {
   if (!targetBlock) {
     return { success: false, file_path, error: `PrefabInstance "${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" };
   }
@@ -9398,6 +9906,7 @@ 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 +9917,19 @@ 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 +9953,7 @@ 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 +10071,124 @@ 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 +10216,23 @@ 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";
@@ -10615,10 +11242,11 @@ 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;
@@ -10726,9 +11354,10 @@ 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;
@@ -11032,6 +11661,116 @@ init_scanner();
 var import_fs18 = require("fs");
 var import_path8 = 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(`
 `);
@@ -11735,9 +12474,16 @@ 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 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_path8.dirname(file));
           const resolved = resolve_source_prefab(doc, file, projectPath ?? undefined);
           if (resolved) {
@@ -11772,6 +12518,7 @@ 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}; ${variantNote}` : variantNote;
             }
@@ -11782,8 +12529,13 @@ function build_read_command(getScanner) {
         try {
           const fileSize = import_fs18.statSync(file).size;
           if (fileSize > 100) {
-            const corruptWarning = "File has valid Unity YAML header but contains no parseable GameObjects -- file may be corrupt or malformed";
-            result.warning = result.warning ? `${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 {}
       }
@@ -12056,38 +12808,41 @@ 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 +12905,10 @@ 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 +12917,14 @@ 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));
@@ -12418,9 +13184,7 @@ 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)) {
       console.log(JSON.stringify({ error: `Editor.log not found${logPath ? `: ${logPath}` : ". Could not detect platform log path."}` }, null, 2));
@@ -12429,9 +13193,9 @@ function build_read_command(getScanner) {
     const content = import_fs18.readFileSync(logPath, "utf-8");
     let lines = content.split(/\r?\n/);
     if (options.project) {
-      const projectPath2 = import_path8.resolve(options.project);
-      const projectName = import_path8.basename(projectPath2);
-      const escapedPath = projectPath2.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+      const projectPath = import_path8.resolve(options.project);
+      const projectName = import_path8.basename(projectPath);
+      const escapedPath = projectPath.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
       const escapedName = projectName.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
       const session_markers = [
         new RegExp(`Loading project at '${escapedPath}'`),
@@ -12876,7 +13640,7 @@ function build_read_command(getScanner) {
       }
       const states_out = { file, states_by_layer: by_layer };
       if (needs_setup_hint)
-        states_out._hint = "Run 'setup <project>' to resolve motion paths";
+        states_out._hint = "Run 'setup' (or 'setup -p <path>') to resolve motion paths";
       console.log(JSON.stringify(states_out, null, 2));
       return;
     }
@@ -12925,14 +13689,15 @@ function build_read_command(getScanner) {
       }))
     };
     if (needs_setup_hint)
-      default_out._hint = "Run 'setup <project>' to resolve motion paths";
+      default_out._hint = "Run 'setup' (or 'setup -p <path>') to resolve motion paths";
     console.log(JSON.stringify(default_out, null, 2));
   });
-  cmd.command("dependents <project_path> <guid>").description("Find which files reference a given GUID (reverse dependency lookup)").option("--type <type>", "Filter to specific file types (scene, prefab, mat, etc.)").option("-j, --json", "Output as JSON").action((project_path, guid, options) => {
+  cmd.command("dependents <guid>").description("Find which files reference a given GUID (reverse dependency lookup)").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("--type <type>", "Filter to specific file types (scene, prefab, mat, etc.)").option("-j, --json", "Output as JSON").action((guid, options) => {
     if (!/^[0-9a-f]{32}$/i.test(guid)) {
       console.log(JSON.stringify({ error: "GUID must be a 32-character hexadecimal string" }, null, 2));
       process.exit(1);
     }
+    const project_path = resolve_project_path(options.project);
     const assetsDir = import_path8.join(import_path8.resolve(project_path), "Assets");
     if (!import_fs18.existsSync(assetsDir)) {
       console.log(JSON.stringify({ error: `Assets directory not found in "${project_path}"` }, null, 2));
@@ -12990,11 +13755,11 @@ function build_read_command(getScanner) {
       by_type
     }, null, 2));
   });
-  cmd.command("unused <project_path>").description("Find potentially unused assets (zero inbound GUID references)").option("--type <type>", "Filter to specific asset types").option("--ignore <glob>", "Exclude paths matching this pattern").option("--max <n>", "Maximum results to return (default 200)", "200").option("-j, --json", "Output as JSON").action((project_path, options) => {
-    const resolvedProject = import_path8.resolve(project_path);
+  cmd.command("unused").description("Find potentially unused assets (zero inbound GUID references)").option("-p, --project <path>", "Unity project path (defaults to cwd)").option("--type <type>", "Filter to specific asset types").option("--ignore <glob>", "Exclude paths matching this pattern").option("--max <n>", "Maximum results to return (default 200)", "200").option("-j, --json", "Output as JSON").action((options) => {
+    const resolvedProject = resolve_project_path(options.project);
     const assetsDir = import_path8.join(resolvedProject, "Assets");
     if (!import_fs18.existsSync(assetsDir)) {
-      console.log(JSON.stringify({ error: `Assets directory not found in "${project_path}"` }, null, 2));
+      console.log(JSON.stringify({ error: `Assets directory not found in "${resolvedProject}"` }, null, 2));
       process.exit(1);
     }
     const guidCacheObj = load_guid_cache(resolvedProject);
@@ -13085,7 +13850,8 @@ 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));
@@ -13404,13 +14170,14 @@ 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 +14186,14 @@ 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 +14201,10 @@ 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 +14212,14 @@ 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
     });
@@ -13549,20 +14319,21 @@ 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;
@@ -15256,9 +16027,10 @@ 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;
@@ -15276,9 +16048,10 @@ 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("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;
@@ -15565,7 +16338,7 @@ function generate_id() {
 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;
@@ -15757,9 +16530,9 @@ 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 +16540,9 @@ 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;
@@ -16100,11 +16873,12 @@ 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 +16906,9 @@ 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) {