The agent reads your project and runs analysis commands freely, because that is most of the work. It also publishes its reports, with the charts, scripts and other results it made under output/, to the project your folder is linked to without asking, and tells you each time with the link: only members of that project’s organisation can read them. It stops and asks before it does anything else that changes your environment or shares your data. Before a job that would run for a long time or cost much, the agent proposes it in the conversation and waits for your answer. When your question needs data from a service you use, it proposes connecting it and walks you through it; the connection itself still waits for your approval.

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Questions

When a choice is yours to make, the agent asks a question with options. Use ↑ ↓ to choose, Enter to confirm, or type your own answer. Several questions appear as tabs; review them on the last tab before you submit. A key or password for a connection is asked for in a hidden field instead: it shows dots, never the key, and the review shows it as “hidden”. See Keys and passwords.
A question in the AIUS terminal asking whether to attach the analysis code, executed notebook and aggregate results to the report, with the options Approve evidence attachments, Report text only and Type your own answer

The agent asks which evidence to attach to a report

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Permission prompts

When a command or tool needs permission, the terminal shows the exact command and three choices: allow it once, allow it always for this project, or reject it. Reject leaves everything as it was, and the agent looks for another way.
A Permission required prompt in the AIUS terminal for the shell command uv pip install --python .venv/bin/python six, with the options Allow once, Allow always and Reject

A permission prompt before a package install

aius --auto approves every request that is not explicitly denied, including package installs and publishing. Use it only in a disposable environment.
To be asked before every report as well, tell the agent “Always ask before publishing”. It saves that in your settings, as "artifact_publish": "ask" and "aius_platform_report_publish": "ask" under permission. AIUS reads its settings only from ~/.config/aius-agent/aius.json and, in a project, from aius.json or .aius/aius.json. Settings written for other coding agents never change what AIUS asks before it acts.