Plugin skills not included in available_skills for main agent — only builtin skills visible

[zzatang]

Describe the bug

Plugin skills installed via marketplace are visible in the /skills UI (showing all 18 skills correctly), but are not injected into the <available_skills> block in the agent's system prompt. Only the builtin customize-cloud-agent skill appears. When the agent calls the skill tool for any plugin skill, it returns "Skill not found".

This differs from #2416 (sub-agent token truncation) — this affects the main/default agent and involves zero plugin skills appearing, not a truncated list.

Environment

• Copilot CLI version: 1.0.28
• OS: Windows 11
• Plugin: superpowers v5.0.7 from obra/superpowers-marketplace
• Install method: Marketplace (copilot plugin install via superpowers-marketplace)

Steps to reproduce

1. Install the superpowers plugin from marketplace
2. Verify /skills shows all 18 skills (17 plugin + 1 builtin) ✅
3. Start a conversation and ask the agent to invoke any plugin skill (e.g., using-superpowers)
4. Agent calls skill tool → returns "Skill not found"
5. Ask the agent what skills it can see — it only sees customize-cloud-agent (builtin)

Evidence

The ~/.copilot/config.json is correctly configured:

• Plugin is installed, enabled, cache_path points to the correct directory
• disabledSkills is empty
• Skills exist on disk at {cache_path}/skills/ with valid SKILL.md files
• Plugin agents (e.g., superpowers:code-reviewer) ARE correctly discovered and available via the task tool

Expected behavior

All enabled plugin skills should appear in <available_skills> and be invocable via the skill tool, matching what /skills shows in the UI.

Actual behavior

Only builtin skills appear in <available_skills>. Plugin skills are invisible to the agent despite being correctly installed, enabled, and visible in /skills.

Related issues

• Sub-agents cannot see skills from their own plugin due to <available_skills> token truncation #2416 — Sub-agent <available_skills> truncation (similar symptom, different scope)
• copilot plugin install from GitHub repo does not discover .github/plugin/plugin.json — skills and agents unavailable #2390 — Direct repo install path discovery issue (different root cause)

Workaround

Manually read the SKILL.md files via the view tool and follow instructions, bypassing the skill tool entirely.