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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This uses Gemini's native [thinking
summaries](https://cloud.google.com/vertex-ai/generative-ai/docs/thinking#thought-summaries)
which were recently added to the API.
Why? The grafted thinking would sometimes cause weird issues where the
model, especially Gemini 2.5 Flash, got confused and put dyad tags like
`<dyad-write>` inside the `<think>` tags.
This also improves the UX because you can see the native thoughts rather
than having the Gemini response load for a while without any feedback.
I tried adding Anthropic extended thinking, however it requires temp to
be set at 1, which isn't ideal for Dyad's use case where we need precise
syntax following.
