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. -->
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