Fixes #554 #1049 
    
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## 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.

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