Fix package.json (#1080)

Fixes #554 #1049 
    
<!-- This is an auto-generated description by cubic. -->
---

## Summary by cubic
Stop mutating package.json when reading files. readFileWithCache now
returns raw content so all fields are preserved (e.g., packageManager).
Fixes #554 and #1049.

- **Bug Fixes**
  - Removed package.json "cleaning" logic and the cleanContent helper.
- Return and cache unmodified file content from both fs and
virtualFileSystem.

<!-- End of auto-generated description by cubic. -->

src/utils/codebase.ts

@@ -178,7 +178,7 @@ export async function readFileWithCache(
     if (virtualFileSystem) {
       const virtualContent = await virtualFileSystem.readFile(filePath);
       if (virtualContent != null) {
-        return cleanContent({ content: virtualContent, filePath });
+        return virtualContent;
       }
     }
 
@@ -196,7 +196,7 @@ export async function readFileWithCache(
 
     // Read file and update cache
     const rawContent = await fsAsync.readFile(filePath, "utf-8");
-    const content = cleanContent({ content: rawContent, filePath });
+    const content = rawContent;
     fileContentCache.set(filePath, {
       content,
       mtime: currentMtime,
@@ -221,32 +221,6 @@ export async function readFileWithCache(
   }
 }
 
-function cleanContent({
-  content,
-  filePath,
-}: {
-  content: string;
-  filePath: string;
-}): string {
-  // Why are we cleaning package.json?
-  // 1. It contains unnecessary information for LLM context
-  // 2. Fields like packageManager cause diffs in e2e test snapshots.
-  if (path.basename(filePath) === "package.json") {
-    try {
-      const { dependencies, devDependencies } = JSON.parse(content);
-      const cleanPackageJson = {
-        dependencies,
-        devDependencies,
-      };
-      return JSON.stringify(cleanPackageJson, null, 2);
-    } catch (error) {
-      logger.error(`Error cleaning package.json: ${filePath}`, error);
-      return content;
-    }
-  }
-  return content;
-}
-
 /**
  * Recursively walk a directory and collect all relevant files
  */