TL;DR —codeep --helpand the README now say what--yololeaves unchecked: a shell command runs without asking and can write the files the file tools still ask about.
Fixed
--yolo's help no longer overstates what still asks.codeep --help,
the README and the 3.9.0 notes said writes to files that decide what runs later (.git/config, git hooks, MCP server lists) are still confirmed under --yolo. That holds for the agent's file tools only. A shell command is not checked that way, and under --yolo it runs without asking, so it can write those same files. The help now says so. It also no longer says "nothing is saved": the folder access and the confirmation settings are not, but the conversation is saved as a session, as usual.