Refactor: Reorganize `agent/` directory structure

[leandrodamascena]

The problem

The agent/ directory is a flat mix of everything - Python source code, Dockerfile, shell scripts, lock files, configs, tests, all sitting at the same level. When I was going through the project trying to understand how things fit together, it wasn't obvious what's source code and what's build infrastructure.

agent/                  <- current state
├── Dockerfile
├── README.md
├── entrypoint.py       <- source
├── server.py           <- source
├── memory.py           <- source
├── task_state.py       <- source
├── observability.py    <- source
├── system_prompt.py    <- source
├── prepare-commit-msg.sh  <- script
├── run.sh              <- script
├── mise.toml           <- config
├── pyproject.toml      <- config
├── uv.lock             <- lock file
├── prompts/            <- source
├── scripts/            <- scripts
└── tests/              <- tests

I think we have the following problems:

• Makes it harder than it should be to find what you're looking for, especially for someone new to the project
• AI coding assistants also benefit from clear separation - when everything is flat, models have to figure out what's source code vs infrastructure on every interaction
• As the entrypoint refactor (see follow-up issue) adds more modules, the flat structure will get even messier

Proposed solution

Move all Python source code into agent/src/. Build/infra files stay at the root:

agent/
├── Dockerfile
├── README.md
├── mise.toml
├── pyproject.toml
├── uv.lock
├── prepare-commit-msg.sh
├── run.sh
├── scripts/
├── tests/
│
└── src/
    ├── entrypoint.py
    ├── server.py
    ├── memory.py
    ├── task_state.py
    ├── observability.py
    ├── system_prompt.py
    └── prompts/
        ├── __init__.py
        ├── base.py
        ├── new_task.py
        ├── pr_iteration.py
        └── pr_review.py

Acknowledgements

• I may be able to implement this feature
• This might be a breaking change

[krokoko]

Absolutely, refactored in #23