My auto research template features - always in worktree - git hooks reminding and protecting files - explicit human,meta,agent files, explicit frozen files - everything is a file, with a pipeline from idea -> worktrees -> research reports - stronger and explicit ideation and interpreations (weak points of current agents) See also - https://github.com/karpathy/autoresearch/blob/master/program.md - https://github.com/NousResearch/autonovel/blob/master/program.md