Resolve direct PR links in issue-scoped tools

[alvarosanchez]

Summary

• resolve issue-scoped PR tools from durable paperclip-github-plugin.pull-request-link entities when the Paperclip issue has no GitHub issue-origin link
• merge direct PR references with GitHub issue-derived PR references without weakening repository ambiguity checks
• reject explicit repository/PR selections that are not directly linked
• document the direct-link resolution contract

Closes #167.

Why

create_pull_request already persisted a durable direct PR link for native Paperclip issues, but later tools such as get_pull_request({ paperclipIssueId }) only consulted GitHub issue-origin metadata. That made the atomic create flow succeed and link the PR while immediate follow-up reads incorrectly reported that the issue was not linked.

Verification

• pnpm typecheck
• pnpm test — 262 passing
• pnpm build
• git diff --check

Staging

Deployed an unreleased 0.14.1-issue167.1 build to the staging plugin worker and invoked the same get_pull_request call with the original native Paperclip issue and completed staging run context.

Before the fix:

This Paperclip issue is not linked to GitHub yet.

After the fix:

• HTTP 200
• no tool error
• resolved alvarosanchez/paperclip#3
• state: closed
• head SHA: 6f24ec5bb463231f5473bd98333efda1a1c0c139

The regression test covers atomic create_pull_request → durable direct link → get_pull_request({ paperclipIssueId }). A second test covers same-number direct PRs across repositories and requires an explicit matching repository.

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