[Follow-up] Implement an automated mechanism (using an API cal (PR #995)

[github-actions]

## Why
PR #995 addressed issue #994 but verification identified concerns (verdict: **CONCERNS**). This follow-up addresses the remaining gaps with improved task structure to ensure automated cross-referencing and accurate task tracking.

## Source
- Original PR: #995
- Parent issue: #994

## Tasks
- [ ] Implement an automated mechanism to create cross-references between the PR and related issues (#992, #991, #994, #989) using an API call or dedicated comment.
- [ ] Modify `keepalive_loop.js` to accurately update `tasksCompletedSinceLastRound` by calculating the difference between new and previous task counts.
- [ ] Add unit and integration tests for the new cross-referencing feature and the updated task progress logic in `keepalive_loop.js`.

## Acceptance Criteria
- [ ] The system automatically creates a comment on the PR linking issues #992, #991, #994, and #989 when the PR is submitted.
- [ ] The issues #992, #991, #994, and #989 remain open after the PR is submitted and linked.
- [ ] The `tasksCompletedSinceLastRound` variable in `keepalive_loop.js` correctly reflects the number of tasks completed, even when tasks are added or removed during the same round.
- [ ] All unit tests in `tests/pr_linking_tests.js` pass, covering scenarios of PR submission with and without related issues.
- [ ] All integration tests in `tests/keepalive_loop_tests.js` pass, including scenarios where tasks are added, removed, and completed concurrently.

## Implementation Notes
- Focus on `pr_linking_module.js` and `api_integration.js` for the cross-referencing feature.
- Ensure `keepalive_loop.js` accurately tracks task completion without resetting unexpectedly.
- Develop comprehensive tests in `tests/pr_linking_tests.js` and `tests/keepalive_loop_tests.js` to cover all scenarios.

<details>
<summary>Background (previous attempt context)</summary>

- The previous attempt only changed comment text to advise linking issues rather than implementing an automated linking mechanism. Advisory text does not enforce the necessary behavior nor does it provide a verifiable linkage between the PR and the issues. Develop and integrate a mechanism that programmatically generates cross-references between the PR and the target issues, ensuring these links are established as part of the PR process.
- The `tasksCompletedSinceLastRound` counter reset logic in `keepalive_loop.js` did not account for concurrent modifications, forcing the value to 0 unexpectedly. Relying solely on matching total checkbox counts leads to incorrect reset behavior when tasks are modified during the same round. Implement a more granular tracking system that computes the difference in completed tasks rather than a binary reset, ensuring proper progress maintenance even when the task list changes.

</details>

[github-actions]

Branch codex/issue-1001 created from main.

Option 1 (Invite) is enforced on issue events. PR creation is disabled by design so you are the PR author. Codex only engages on human-authored PRs.

Please open the PR as the author so Codex can work on it:

• Compare link: https://github.com/stranske/Workflows/compare/main...codex/issue-1001?expand=1
• Suggested title: Codex bootstrap for #1001
• Suggested body (copy/paste):

<!-- meta:issue:1001 -->

@codex Your objective is to satisfy the **Acceptance Criteria** by completing each **Task** within the defined **Scope**.

## Keepalive Next Task

**This round you MUST:**
1. Implement actual code or test changes that advance at least one incomplete task toward acceptance.
2. Commit meaningful source code (.py, .yml, .js, etc.)—not just status/docs updates.
3. Mark a task checkbox complete ONLY after verifying the implementation works.
4. Focus on the FIRST unchecked task unless blocked, then move to the next.

**Guidelines:**
- Keep edits scoped to the current task rather than reshaping the entire PR.
- Use repository instructions, conventions, and tests to validate work.
- Prefer small, reviewable commits; leave clear notes when follow-up is required.
- Do NOT work on unrelated improvements until all PR tasks are complete.

**COVERAGE TASKS - SPECIAL RULES:**
If a task mentions "coverage" or a percentage target (e.g., "≥95%", "to 95%"), you MUST:
1. After adding tests, run TARGETED coverage verification to avoid timeouts:
   - For a specific script like `scripts/foo.py`, run:
     `pytest tests/scripts/test_foo.py --cov=scripts/foo --cov-report=term-missing -m "not slow"`
   - If no matching test file exists, run:
     `pytest tests/ --cov=scripts/foo --cov-report=term-missing -m "not slow" -x`
2. Find the specific script in the coverage output table
3. Verify the `Cover` column shows the target percentage or higher
4. Only mark the task complete if the actual coverage meets the target
5. If coverage is below target, add more tests until it meets the target

IMPORTANT: Always use `-m "not slow"` to skip slow integration tests that may timeout.
IMPORTANT: Use targeted `--cov=scripts/specific_module` instead of `--cov=scripts` for faster feedback.

A coverage task is NOT complete just because you added tests. It is complete ONLY when the coverage command output confirms the target is met.

**The Tasks and Acceptance Criteria are provided in the appendix below.** Work through them in order.

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