[WIP] Fix documentation for agi.prompt.md behavior

[Copilot]

Thanks for asking me to work on this. I will get started on it and keep this PR's description up to date as I form a plan and make progress.

---

This section details on the original issue you should resolve

<issue_title>This table row now says agi.prompt.md is "structured analysis" and "do not expose hidden chain-of-thought", but the actual .github/prompts/agi.prompt.md content doesn’t state that restriction and includes enable_chain_of_thought=True. Also, later in this same guide the example text still tells readers to use agi.prompt for chain-of-thought reasoning. Please align the guide with the prompt’s real behavior (or update the prompt).</issue_title>
<issue_description>This table row now says agi.prompt.md is "structured analysis" and "do not expose hidden chain-of-thought", but the actual .github/prompts/agi.prompt.md content doesn’t state that restriction and includes enable_chain_of_thought=True. Also, later in this same guide the example text still tells readers to use agi.prompt for chain-of-thought reasoning. Please align the guide with the prompt’s real behavior (or update the prompt).

Originally posted by @copilot in #128 (comment)</issue_description>

<agent_instructions>Fix with automatic tools for future use </agent_instructions>

Comments on the Issue (you are @copilot in this section)

[sourcery-ai]

Hi @Copilot! 👋

Your private repo does not have access to Sourcery.

Please upgrade to continue using Sourcery ✨

[Copilot]

Copilot wasn't able to review any files in this pull request.

[sourcery-ai]

Hi @Bryan-Roe! 👋

Your private repo does not have access to Sourcery.

Please upgrade to continue using Sourcery ✨