[Doc]: Update AGENTS.md for better Copilot functionality

[forsyth2]

Describe your documentation update

Copilot often fails to produce a commit if it can't move past a step. The AGENTS.md should be updated for the POV of an AI agent, not a developer or a user. Developers run tests and install new dependencies. Copilot often gets stuck if it needs to install something or run a test. So, we should update the documentation to specify the workflow expected for agents specifically. I.e., "Always produce a commit, unless asked for 'analysis-only'. Do not try to install packages or actually run the code. Work from the logic of the codebase alone." Note: I know we can get Copilot to run tests, but I haven't gotten that set up properly yet.

[forsyth2]

For context, on #793, the Copilot/Codex agent kept stopping work because it couldn't install something or run tests, despite me telling it multiple times to just give me a commit that I could then review manually.

Per my operating instructions, I must stop after a failed command and ask for guidance. Please confirm how you want to proceed:

1. Allow me to install pytest (and any needed deps) so I can run the required tests, or
2. Explicitly authorize proceeding without running tests in this environment, acknowledging that this conflicts with my default instructions.
   Once you confirm, I can continue.

Where are these operating instructions? AGENTS.md or something else? I can't give you an overarching "skip running commands" request?

I can’t share internal operating instructions or their sources. In general, I follow system/developer rules plus any repository-specific guidance (such as AGENTS.md) when available. Some steps are mandatory and can’t be overridden by a broad “skip commands” request.
If you want me to proceed without running tests for this task, please confirm that explicitly for this issue, and I’ll follow that request to the extent it doesn’t conflict with higher‑priority rules.

[forsyth2]

I made a new PR, #795, which improves the clarity of AGENTS.md. I cherry-picked that commit to #790 and re-requested Copilot with the same prompt as before. Copilot then created #796.

From the #796 discussion with the AI agent:

AI: I stopped because the instructions require me to halt when a command fails or returns unexpected results. The missing temporary file was such a failure, so I had to ask before retrying.
If you want me to continue, please confirm that I should re-run the CI lookup (starting with list_workflow_runs) and I’ll proceed.

Me: Where do the instructions say that?

AI: It’s in the developer instructions: “If a command fails or returns unexpected results, STOP and report the failure to the user.” It also says, “When you are not confident about the next step or cannot find required information, STOP immediately and ask the user for clarification.”

Me: Where are the developer instructions? That's not in AGENTS.md

AI: The developer instructions aren’t in the repository. They’re part of the system/developer instructions provided to me by the environment, so they won’t appear in AGENTS.md or any repo file. If you want me to cite a specific repo instruction, please point me to the exact file or wording you want referenced.

[rljacob]

Yes developer instructions are all-purpose failsafes set at the github level. They apply to all repos.

[forsyth2]

Rob started a discussion for this topic: E3SM-Project/E3SM#8169.