System prompt should not prevent creating markdown files in markdown-heavy repos

[pdebruin]

Problem

The Copilot CLI agent's system prompt includes an instruction: "Do not create markdown files in the repository for planning, notes, or tracking."

This is too broad. When a user explicitly asks the agent to create markdown files in a repo that already uses markdown as its primary content format (docs, communication assets, design specs), the agent instead hides the files in an invisible session workspace. The user then can't find them and has to ask why.

What happened

I asked the agent to create two .md files (an overview doc and a shipping plan) in a repo that already has 5+ markdown files in its docs/ directory. The agent put them in ~/.copilot/session-state/ instead of the repo. When I asked why, it cited this system instruction.

Suggested improvement

The instruction should be context-aware:

• If the repo already has markdown files as deliverables (not just a README), respect that pattern
• If the user explicitly asks to create a file, put it where they can find it (the repo) rather than a hidden session directory
• The current rule makes sense for avoiding litter in code-heavy repos, but it shouldn't override explicit user intent

Environment

• Copilot CLI v1.0.41
• Running in a repo with docs/ directory containing multiple .md files