The agent reads your project and runs analysis commands freely, because that is most of the work. It stops and asks before it does anything that changes your environment or shares your data.
The agent asks beforeWhy
Installing or syncing Python packages (pip, uv, conda, poetry)It changes your environment
Reading .env filesThey often hold secrets
Working outside the project folderIt is outside the task you gave it
Uploading files and publishing reportsIt shares data with your organisation
Recording runs to the project’s WorkIt shares measurements of your work
Creating a public share linkAnyone with the link can read the report

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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 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

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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
aius --auto approves every request that is not explicitly denied, including package installs and publishing. Use it only in a disposable environment.
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.