docs: point the upgrade guide's Copilot checks at .github/skills (#5010)

* docs: point the upgrade guide's Copilot checks at .github/skills

Copilot has installed skills under .github/skills/ by default since #3976
(feat(copilot): default integration to skills). .github/prompts/ is only
created by the opt-in commands layout (--integration-options="--commands"),
next to .github/agents/.

The upgrade guide still told Copilot users to verify their install with
`ls -la .github/prompts/`, which fails with "No such file or directory"
on a default `specify init --integration copilot` project, and it listed
.github/prompts/ as Copilot's command location in three other places.

Point those references at .github/skills/ and name the commands-layout
directories in the verification step.

Assisted-by: Claude Code (model: Claude Opus 5.5, autonomous)
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* docs: name the Copilot commands-layout check in the upgrade guide

Projects created before Copilot defaulted to skills keep the commands
layout when upgraded (see test_upgrade_preserves_historical_copilot_
commands_without_options), so `ls .github/skills/` reports a missing
directory for them. Give the commands layout its own check alongside the
skills one.

Assisted-by: Claude Code (model: Claude Opus 5.5, autonomous)
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

Author: yxshee

docs/upgrade.md

@@ -95,7 +95,7 @@ When Spec Kit releases new features (like new slash commands, updated templates,
 
 For existing Spec Kit projects, use the manifest-aware upgrade path first:
 
-- ✅ **Integration command/skill files** (`.claude/skills/`, `.github/prompts/`, `.agents/skills/`, etc.)
+- ✅ **Integration command/skill files** (`.claude/skills/`, `.github/skills/`, `.agents/skills/`, etc.)
 - ✅ **Managed shared scripts and templates** (`.specify/scripts/`, `.specify/templates/`) when they are unchanged from the previous managed copy
 - ✅ **Installed extensions** when you run `specify extension update`
 
@@ -420,7 +420,7 @@ This warning appears when you run `specify init --here` (or `specify init .`) in
 
 Only Spec Kit infrastructure files:
 
-- Agent command/skill files (`.claude/skills/`, `.github/prompts/`, etc.)
+- Agent command/skill files (`.claude/skills/`, `.github/skills/`, etc.)
 - Scripts in `.specify/scripts/`
 - Templates in `.specify/templates/`
 - Missing memory files such as `.specify/memory/constitution.md` may be created from templates; an existing constitution is preserved
@@ -498,15 +498,19 @@ The `specify` CLI tool is used for:
 - **Fallback recovery:** `specify init --here --force` when integration metadata is missing or the manifest-aware path cannot be used
 - **Diagnostics:** `specify check` to verify tool installation
 
-Once you've run `specify init`, the slash commands (like `/speckit.specify`, `/speckit.plan`, etc.) are **permanently installed** in your project's agent folder (`.claude/`, `.github/prompts/`, `.pi/prompts/`, `.omp/commands/`, etc.). Your AI coding agent reads these command files directly—no need to run `specify` again.
+Once you've run `specify init`, the slash commands (like `/speckit.specify`, `/speckit.plan`, etc.) are **permanently installed** in your project's agent folder (`.claude/`, `.github/skills/`, `.pi/prompts/`, `.omp/commands/`, etc.). Your AI coding agent reads these command files directly—no need to run `specify` again.
 
 **If your agent isn't recognizing slash commands:**
 
 1. **Verify command files exist:**
 
    ```bash
-   # For GitHub Copilot
-   ls -la .github/prompts/
+   # For GitHub Copilot (default skills layout)
+   ls -la .github/skills/
+
+   # For GitHub Copilot with the commands layout (--integration-options="--commands",
+   # or a project created before skills became the default and upgraded since)
+   ls -la .github/agents/ .github/prompts/
 
    # For Claude
    ls -la .claude/skills/