fix(keepalive): count visible tasks outside generated summaries

.github/scripts/__tests__/agents-pr-meta-update-body.test.js

@@ -334,7 +334,7 @@ test('extractBlock returns empty string if markers not found', () => {
 
 // ========== stripPrTemplateContent tests ==========
 
-test('stripPrTemplateContent removes content before pr-preamble marker', () => {
+test('stripPrTemplateContent preserves checkbox-bearing content before pr-preamble marker', () => {
   const body = `# Summary
 
 One sentence.
@@ -356,9 +356,7 @@ Add labels.
 
   const result = stripPrTemplateContent(body);
 
-  assert.ok(result.startsWith('<!-- pr-preamble:start -->'));
-  assert.ok(!result.includes('# Summary'));
-  assert.ok(!result.includes('Checklist'));
+  assert.equal(result, body);
 });
 
 test('stripPrTemplateContent removes content before auto-status-summary if no preamble', () => {
@@ -1598,3 +1596,41 @@ test('upsertBlock preserves triple newlines in single-pair case (no duplicates)'
   assert.ok(result.includes('After'));
   assert.ok(result.includes('\n\n\n'), 'should preserve existing triple newlines when no duplicates removed');
 });
+
+
+test('metadata regeneration preserves outside task lines before and after the summary', () => {
+  const before = '## Reviewer tasks\n- [ ] Exercise the error path\n  and retain its output.\n\n';
+  const after = '\n\n## More acceptance\n- [ ] Verify the packaged command';
+  const oldSummary = '<!-- auto-status-summary:start -->\n## Tasks\n- [x] Source task\n<!-- auto-status-summary:end -->';
+  const newSummary = '<!-- auto-status-summary:start -->\n## Tasks\n- [x] Refreshed source task\n<!-- auto-status-summary:end -->';
+  const preamble = '<!-- pr-preamble:start -->\nCloses #3441\n<!-- pr-preamble:end -->';
+  const refresh = (body) => upsertBlock(upsertBlock(stripPrTemplateContent(body), 'pr-preamble', preamble), 'auto-status-summary', newSummary);
+  const result = refresh(before + oldSummary + after);
+  assert.ok(result.startsWith(before));
+  assert.ok(result.includes(after));
+  assert.ok(result.includes(newSummary));
+  assert.equal(refresh(result), result);
+});
+
+for (const templatePath of ['../../../.github/PULL_REQUEST_TEMPLATE.md', '../../../templates/consumer-repo/.github/PULL_REQUEST_TEMPLATE.md']) {
+  test(`metadata refresh removes template controls and retains genuine reviewer tasks (${templatePath})`, () => {
+    const template = require('fs').readFileSync(require('path').resolve(__dirname, templatePath), 'utf8');
+    const summary = '<!-- auto-status-summary:start -->\n## Tasks\n- [x] Source task\n<!-- auto-status-summary:end -->';
+    assert.equal(stripPrTemplateContent(template + summary), summary);
+    const reviewer = '## Review tasks\n> - [ ] Check the error path\n>   and its diagnostic.\n';
+    const cleaned = stripPrTemplateContent(template + reviewer + summary);
+    assert.ok(cleaned.includes(reviewer));
+    assert.doesNotMatch(cleaned, /\[[ xX]\] (?:GitHub issue|Direct PR|Verifier should|Keepalive may)/);
+    assert.equal(stripPrTemplateContent(cleaned), cleaned);
+    // A genuine task in Notes within Workflow Source must also survive.
+    const notes = template.replace('Notes:', 'Notes:\n- [ ] Verify the provenance record');
+    assert.match(stripPrTemplateContent(notes + summary), /- \[ \] Verify the provenance record/);
+  });
+}
+
+for (const hidden of ['<!--\n- [ ] Hidden comment\n-->\n', '```markdown\n- [ ] Fenced example\n```\n', '> ```markdown\n> - [ ] Quoted fenced example\n> ```\n']) {
+  test(`metadata refresh ignores hidden checkbox prefix: ${hidden.split('\n')[0]}`, () => {
+    const summary = '<!-- auto-status-summary:start -->\n## Tasks\n- [x] Source task\n<!-- auto-status-summary:end -->';
+    assert.equal(stripPrTemplateContent('## Stale template\n' + hidden + summary), summary);
+  });
+}

.github/scripts/__tests__/issue_scope_parser.test.js

@@ -8,8 +8,64 @@ const {
   parseScopeTasksAcceptanceSections,
   analyzeSectionPresence,
   hasNonPlaceholderScopeTasksAcceptanceContent,
+  visibleChecklistContent,
 } = require('../issue_scope_parser');
 
+for (const parserPath of ['../issue_scope_parser', '../../../templates/consumer-repo/.github/scripts/issue_scope_parser']) {
+  const parser = require(parserPath);
+  for (const fence of ['```', '~~~']) {
+    for (const quote of ['', '> ', '> > ']) {
+      test(`template controls preserve fenced examples (${parserPath}, ${fence}, ${quote})`, () => {
+        const example = [
+          `${fence}markdown`, '## Workflow Source', 'Started from:',
+          '- [ ] GitHub issue: #123', `    ${fence}`,
+          'Automation intent:', '- [ ] Keepalive may manage this PR',
+          `${fence}not-a-closing-fence`, '- [ ] Direct PR / remote GitHub work', fence,
+        ].map((line) => quote + line).join('\n');
+        const actualControls = [
+          '## Workflow Source', 'Started from:', '- [ ] GitHub issue: #456',
+          'Automation intent:', '- [ ] Keepalive may manage this PR',
+          'Notes:', '- [ ] Retain reviewer work',
+        ].join('\n');
+        assert.equal(parser.stripPrTemplateControls(`${example}\n${actualControls}`),
+          `${example}\n## Workflow Source\nNotes:\n- [ ] Retain reviewer work`);
+        assert.doesNotMatch(parser.visibleChecklistContent(example), /\[ \]/);
+      });
+    }
+  }
+}
+
+test('visible checklist scan handles nested quotes without counting their fenced examples', () => {
+  const body = [
+    '> > - [ ] Visible nested task',
+    '> >   with a continuation.',
+    '> > ```markdown',
+    '> > - [ ] Example only',
+    '> > ```',
+    '>> - [x] Completed nested task',
+  ].join('\n');
+  const visible = visibleChecklistContent(body);
+  assert.match(visible, /^- \[ \] Visible nested task\n  with a continuation\./);
+  assert.match(visible, /- \[x\] Completed nested task/);
+  assert.doesNotMatch(visible, /Example only|>/);
+});
+
+for (const fence of ['```', '~~~']) {
+  test(`visible checklist scan keeps fence and comment state separate (${fence})`, () => {
+    const body = [
+      '<!-- hidden comment', fence, '- [ ] Hidden task', '-->',
+      `${fence}markdown`, '<!-- literal comment opener',
+      `    ${fence}`, '- [ ] Indented fence is still an example',
+      `${fence}not-a-closing-fence`, '- [ ] Still an example', fence,
+      '- [ ] Real task <!-- inline comment --> remains visible',
+      '-->',
+    ].join('\n');
+    const visible = visibleChecklistContent(body);
+    assert.match(visible, /- \[ \] Real task  remains visible/);
+    assert.doesNotMatch(visible, /Hidden task|example|literal comment/);
+  });
+}
+
 test('extracts sections inside auto-status markers', () => {
   const issue = [
     'Intro text',