Convert Astro syntax to GitHub flavored markdown

[Copilot]

AGENTS.md and .github/aw/*.md files contained Astro-specific syntax that doesn't render on GitHub.

Changes

• Link syntax: <a>file.md</a> → [file.md](file.md) (2 instances in AGENTS.md)
• Alert directive: :::note[Title] → > [!NOTE] with GitHub alert syntax (1 instance in upgrade-agentic-workflows.md)

Before

See <a>specs/yaml-version-gotchas.md</a> for details

:::note[Command Execution]
When running in GitHub Copilot Cloud...
:::

After

See [specs/yaml-version-gotchas.md](specs/yaml-version-gotchas.md) for details

> [!NOTE]
> **Command Execution**
>
> When running in GitHub Copilot Cloud...

All markdown now renders correctly in GitHub's native renderer.

Original prompt

Ensure that the agent.md and .github/aw/*.md files are using the github flavored markdown syntax, not Astro syntax. Aslo use github alerts syntax.

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