Return closing pull requests from issue_read

[zwick]

Summary

issue_read with method=get now returns closed_by_pull_requests, a compact summary of the pull requests configured to close the issue, sourced from the GraphQL Issue.closedByPullRequestsReferences field.

Why

Answering "is there a PR that closes this issue?" previously meant listing up to 100 pull requests and grepping their bodies for closing keywords. That burns a large token budget and misses cross-repo and non-body links. GraphQL already models this relationship directly.

Tracking issue: github/plan-track-agentic-org#192

What changed

• Added closedByPullRequestsReferences(first: 5, includeClosedPrs: true, orderByState: true) with totalCount to the existing issueReadEnrichmentQuery, so the answer arrives in the same round-trip as the hierarchy signals. No new tool, no extra API call.
• Response shape is { "total_count": N, "references": [...] }. At most 5 references are embedded because this enrichment runs on every get; total_count is authoritative, so the rare issue with more linked PRs is never read as a complete list. Truncation is derivable from total_count > len(references), so no redundant flag is emitted.
• MinimalIssue.ClosedByPullRequests is a pointer: an enriched issue with no closing PRs still serializes a definitive total_count: 0, while list/search paths that never enrich omit the key entirely.
• Generalized isSafeParentContent into isSafeRefContent and reused it to filter closing PR references under lockdown.

includeClosedPrs is required because it defaults to false and hides merged and closed PRs, which are exactly what answers "which PR closed this?". orderByState keeps open PRs ahead of the cap.

MCP impact

• Tool schema or behavior changed — issue_read get gains a closed_by_pull_requests key; the method description was updated and the toolsnap regenerated.

Prompts tested (tool changes only)

Drove the built server over stdio against the live API:

• "Is there a PR that closes this issue?" — open closing PR returned as state: OPEN.
• Same issue after the PR merged — returned as state: MERGED, so the retrospective "which PR closed this?" case works.
• github/github-mcp-server#1 — returned PR fix: detect ungraceful stdin close and self-terminate #2325 with state: CLOSED (unmerged), which the default GraphQL args would have hidden.
• An issue with no linked PR — returned total_count: 0, references: [].
• An issue with 7 linked PRs — returned total_count: 7 with 5 open references, confirming truncation is visible.

Security / limits

• Data exposure, filtering, or token/size limits considered — closing PR titles are sanitized because they can originate from another repository; under lockdown, references whose author cannot be verified as safe content are omitted, matching the existing parent reference behavior. Capped at 5 embedded references to keep the always-on enrichment cheap.

Tool renaming

• I am not renaming tools as part of this PR

Lint & tests

• Linted locally with ./script/lint
• Tested locally with ./script/test

Table-driven coverage for populated results (including a cross-repo PR), empty results, truncation, title sanitization, lockdown filtering, and the enrichment-failure path.

Docs

• Updated (README / docs / examples) — regenerated via script/generate-docs.