I'm reading a 180-page thesis from another lab, closely related to mine. I uploaded the whole PDF to an assistant with a long context window and asked it to compare their method in chapter 4 with ours.
It answered confidently, but the details came from the introduction and conclusion, not chapter 4. When I asked about a specific table in chapter 4, it described a table that doesn't exist.
The context window is supposedly big enough for the whole thing. Is the model just not reading the middle? What's the workflow people use for long documents that actually works?