Fixes#1037
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## Summary by cubic
Enable JSON file support in codebase scanning so common configs and data
(e.g., package.json, vercel.json, translations) are included. Adds .json
to the allowed extensions and removes special-casing for
package.json/vercel.json.
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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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