Copilot SWE agent should auto-include 'Fixes #N' closing keyword in PR descriptions

[clubanderson]

Problem

When Copilot SWE agent is assigned to an issue and creates a PR, the PR description does not include GitHub closing keywords like Fixes #N, Closes #N, or Resolves #N. This means the original issue does not auto-close when the PR is merged, requiring manual cleanup.

Despite having the instruction in three separate places:

1. .github/copilot-instructions.md → Include Fixes #ISSUE_NUMBER in PR body
2. Workflow comment instructions → Create a PR with Fixes #$ISSUE_NUM in the description
3. Issue assignment comments → Same instruction

Copilot consistently ignores this instruction. Tested across 10+ PRs — none included closing keywords.

Expected Behavior

When Copilot creates a PR from an issue assignment, it should automatically include Fixes #<issue_number> in the PR description. The agent knows which issue it was assigned to — it should reference it with a closing keyword.

Current Workaround

We added a step in our copilot-automation.yml workflow that detects Copilot PRs missing closing keywords and auto-injects Fixes #N by:

1. Querying GraphQL closingIssuesReferences
2. Searching for open issues assigned to copilot-swe-agent[bot]
3. Extracting #N references from the PR body

This works but is unnecessary complexity that should be handled natively by the agent.

Proposal

When copilot-swe-agent[bot] creates a PR from an issue assignment, automatically include Fixes #<issue_number> in the PR body. This is a standard GitHub convention that every human developer follows — the agent should too.

Impact

• Every repo using Copilot SWE agent for automated issue fixing
• Without this, issues accumulate as open even after their fix PRs are merged
• Breaks CI/CD pipelines that rely on issue auto-close for state management