JetBrains Copilot plugin does not discover agent/prompt files created outside of IDE UI

[Patas106]

🏷️ Discussion Type

Bug

💬 Feature/Topic Area

Copilot in GitHub

Body

Description

Agent files (.agent.md) and prompt files (.prompt.md) are not discovered
by the JetBrains GitHub Copilot plugin when created in any of these ways:

• Created by the Copilot plugin itself (asked in chat to create an agent or prompt)
• Created via terminal / CLI
• Created by another tool (e.g. Copilot CLI)

The files are never available — even after full IDE restart, cache invalidation,
or plugin restart.

Steps to reproduce

Scenario A — Plugin creates an agent file itself

1. Open JetBrains IDE with GitHub Copilot plugin
2. In Copilot chat, ask: "Create a new agent for reviewing Scala code"
3. Plugin creates .github/agents/scala-reviewer.agent.md ✅
4. Try to use the agent → not listed, not available ❌
5. Restart IDE → still not available ❌

Scenario B — Plugin creates a prompt file itself

1. In Copilot chat, ask: "Create a prompt file for PR review checklist"
2. Plugin creates .github/prompts/kontrola-pred-pr.prompt.md ✅
3. Type /kontrola-pred-pr in chat → not offered ❌
4. Restart IDE → still not available ❌

Scenario C — File created externally (terminal / CLI)

1. Create a prompt file via terminal:
   echo "" > .github/prompts/kontrola-pred-pr.prompt.md
2. Open Copilot chat in JetBrains
3. Type /kontrola-pred-pr → not offered ❌
4. Restart IDE → still not available ❌

Expected behavior

All files in .github/agents/ and .github/prompts/ should be discovered
and available regardless of how they were created.

Workarounds tried

• Full IDE restart → does not help
• Invalidate Caches & Restart → does not help
• Opening the file in the IDE editor → does not help
• Disabling/enabling the plugin → does not help

The only files that seem to work are those created
directly through the settings in ide for github copilot

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[Patas106]

When I create the file this way in the IDE, it still doesn't work — the plugin doesn't offer or list it.