docs: clarify GitHub Copilot CLI limitation for custom prompts (Fission-AI#676)

* docs: clarify GitHub Copilot CLI does not support custom prompt files

GitHub Copilot's .github/prompts/*.prompt.md files are only recognized
as custom slash commands in IDE extensions (VS Code, JetBrains, Visual
Studio). The Copilot CLI does not support them (github/copilot-cli#618).
This updates the docs to clarify the limitation and point users to the
.github/agents/ workaround.

Closes Fission-AI#671

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* docs: use distinct footnote markers for Codex and Copilot

Addresses review feedback: the shared `*` marker was ambiguous across
Markdown renderers. Now uses `*` for Codex and `**` for Copilot.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude <noreply@anthropic.com>

Author: 1code-async[bot]

docs/commands.md

@@ -568,11 +568,13 @@ Different AI tools use slightly different command syntax. Use the format that ma
 | Claude Code | `/opsx:new`, `/opsx:apply` |
 | Cursor | `/opsx-new`, `/opsx-apply` |
 | Windsurf | `/opsx-new`, `/opsx-apply` |
-| Copilot | `/opsx-new`, `/opsx-apply` |
+| Copilot (IDE) | `/opsx-new`, `/opsx-apply` |
 | Trae | `/openspec-new-change`, `/openspec-apply-change` |
 
 The functionality is identical regardless of syntax.
 
+> **Note:** GitHub Copilot commands (`.github/prompts/*.prompt.md`) are only available in IDE extensions (VS Code, JetBrains, Visual Studio). GitHub Copilot CLI does not currently support custom prompt files — see [Supported Tools](supported-tools.md) for details and workarounds.
+
 ---
 
 ## Legacy Commands

docs/migration-guide.md

@@ -46,7 +46,7 @@ Only OpenSpec-managed files that are being replaced:
 - Windsurf: `.windsurf/workflows/openspec-*.md`
 - Cline: `.clinerules/workflows/openspec-*.md`
 - Roo: `.roo/commands/openspec-*.md`
-- GitHub Copilot: `.github/prompts/openspec-*.prompt.md`
+- GitHub Copilot: `.github/prompts/openspec-*.prompt.md` (IDE extensions only; not supported in Copilot CLI)
 - And others (Augment, Continue, Amazon Q, etc.)
 
 The migration detects whichever tools you have configured and cleans up their legacy files.

docs/supported-tools.md

@@ -19,14 +19,14 @@ For each tool you select, OpenSpec installs:
 | Claude Code | `.claude/skills/` | `.claude/commands/opsx/` |
 | Cline | `.cline/skills/` | `.clinerules/workflows/` |
 | CodeBuddy | `.codebuddy/skills/` | `.codebuddy/commands/opsx/` |
-| Codex | `.codex/skills/` | `~/.codex/prompts/`* |
+| Codex | `.codex/skills/` | `~/.codex/prompts/`\* |
 | Continue | `.continue/skills/` | `.continue/prompts/` |
 | CoStrict | `.cospec/skills/` | `.cospec/openspec/commands/` |
 | Crush | `.crush/skills/` | `.crush/commands/opsx/` |
 | Cursor | `.cursor/skills/` | `.cursor/commands/` |
 | Factory Droid | `.factory/skills/` | `.factory/commands/` |
 | Gemini CLI | `.gemini/skills/` | `.gemini/commands/opsx/` |
-| GitHub Copilot | `.github/skills/` | `.github/prompts/` |
+| GitHub Copilot | `.github/skills/` | `.github/prompts/`\*\* |
 | iFlow | `.iflow/skills/` | `.iflow/commands/` |
 | Kilo Code | `.kilocode/skills/` | `.kilocode/workflows/` |
 | OpenCode | `.opencode/skills/` | `.opencode/command/` |
@@ -38,6 +38,8 @@ For each tool you select, OpenSpec installs:
 
 \* Codex commands are installed to the global home directory (`~/.codex/prompts/` or `$CODEX_HOME/prompts/`), not the project directory.
 
+\*\* GitHub Copilot's `.github/prompts/*.prompt.md` files are recognized as custom slash commands in **IDE extensions only** (VS Code, JetBrains, Visual Studio). GitHub Copilot CLI does not currently support custom prompts from this directory — see [github/copilot-cli#618](https://github.com/github/copilot-cli/issues/618). If you use Copilot CLI, you may need to manually set up [custom agents](https://docs.github.com/en/copilot/how-tos/use-copilot-agents/coding-agent/create-custom-agents) in `.github/agents/` as a workaround.
+
 ## Non-Interactive Setup
 
 For CI/CD or scripted setup, use the `--tools` flag: