The disconnect might be that there is a separation between "generating the final answer for the user" and "researching/thinking to get information needed for that answer". Saying "deeply" prompts it to read more of the file (as in, actually use the `read` tool to grab more parts of the file into context), and generate more "thinking" tokens (as in, tokens that are not shown to the user but that the model writes to refine its thoughts and improve the quality of its answer).