docs: clarify GitHub Copilot CLI limitation for custom prompts

[1code-async]

Summary

• Clarifies across docs that GitHub Copilot's .github/prompts/*.prompt.md files only work in IDE extensions (VS Code, JetBrains, Visual Studio), not in GitHub Copilot CLI
• Links to the upstream feature request github/copilot-cli#618
• Points users to the .github/agents/ custom agents workaround for CLI usage

Files changed

• docs/supported-tools.md — Added footnote explaining the IDE-only limitation with links to the upstream issue and workaround docs
• docs/commands.md — Renamed "Copilot" to "Copilot (IDE)" in syntax table; added blockquote note about the CLI limitation
• docs/migration-guide.md — Added parenthetical clarification to the legacy file reference

Test plan

• Verify footnote renders correctly in supported-tools.md (markdown table asterisk + footnote paragraph)
• Verify blockquote note renders correctly in commands.md
• Confirm all external links resolve (copilot-cli#618, GitHub custom agents docs)

Closes #671

🤖 Generated with Claude Code

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Greptile Overview

Greptile Summary

• Updates docs to clarify that GitHub Copilot custom prompt files (.github/prompts/*.prompt.md) are supported in Copilot IDE extensions, not in Copilot CLI.
• Adjusts the commands syntax table to label Copilot as IDE-specific and adds a cross-link to Supported Tools for details/workarounds.
• Adds a migration-guide clarification about the Copilot legacy prompt file location being IDE-only.
• Adds a Supported Tools footnote linking the upstream Copilot CLI feature request and pointing to .github/agents/ as a workaround for CLI users.

Confidence Score: 4/5

• Safe to merge after fixing a minor docs rendering ambiguity.
• Changes are documentation-only and internally consistent; the only merge-blocking issue is the ambiguous reuse of * footnote markers in a Markdown table, which can render confusingly across common Markdown renderers.
• docs/supported-tools.md (footnote markers/formatting)

Important Files Changed

Filename	Overview
docs/commands.md	Renames Copilot entry to “Copilot (IDE)” and adds a note clarifying .github/prompts/*.prompt.md custom prompts don’t work in Copilot CLI.
docs/migration-guide.md	Adds an explicit parenthetical that the GitHub Copilot .github/prompts/*.prompt.md legacy location is IDE-only and not supported in Copilot CLI.
docs/supported-tools.md	Adds a Copilot CLI limitation footnote and workaround link; introduces ambiguous reuse of * footnote markers between Codex and Copilot rows.

Sequence Diagram

sequenceDiagram
  participant U as User
  participant D as Docs (commands/supported-tools/migration-guide)
  participant IDE as Copilot IDE Extension
  participant CLI as Copilot CLI
  participant Agents as .github/agents/

  U->>D: Reads OpenSpec command/tool docs
  D-->>U: `.github/prompts/*.prompt.md` works in IDE extensions only
  U->>IDE: Uses `/opsx-*` via `.github/prompts/*.prompt.md`
  IDE-->>U: Commands available
  U->>CLI: Tries same custom prompts
  CLI-->>U: Not supported (per docs)
  D-->>U: Workaround: set up custom agents
  U->>Agents: Configure `.github/agents/`
  Agents-->>CLI: Enables CLI workflow via agents

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Footnote marker ambiguity

docs/supported-tools.md uses * footnotes for both Codex and GitHub Copilot, but the table marks Copilot’s Commands Location as .github/prompts/* (docs/supported-tools.md:29) while Codex is the earlier *-footnoted row. Many Markdown renderers don’t reliably associate repeated * markers in tables with the intended note, so this can render confusingly (Copilot may appear to reference the Codex home-directory note). Consider using distinct markers (e.g., * and **, or 1/2) to ensure the Copilot CLI limitation note is unambiguous.

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