diff --git a/.github/scripts/__tests__/agents-verifier-context.test.js b/.github/scripts/__tests__/agents-verifier-context.test.js
index b12e66c85..765a28797 100644
--- a/.github/scripts/__tests__/agents-verifier-context.test.js
+++ b/.github/scripts/__tests__/agents-verifier-context.test.js
@@ -111,6 +111,13 @@ const buildGithubStub = ({
   },
 });
 
+const withEmptyJobs = (result) => ({
+  ...result,
+  jobs_summary: { total: 0, conclusions: {}, samples: [], truncated: false },
+  jobs_error_category: '',
+  jobs_error_message: '',
+});
+
 test('buildVerifierContext skips when pull request is not merged', async () => {
   const core = buildCore();
   const context = {
@@ -768,27 +775,27 @@ test('buildVerifierContext selects CI results for the merge commit SHA', async (
   assert.ok(headShas.length > 0);
   assert.ok(headShas.every((sha) => sha === 'merge-sha-333'));
   assert.deepEqual(result.ciResults, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'success',
       run_url: 'https://ci/gate-merge',
       error_category: '',
       error_message: '',
-    },
-    {
+    }),
+    withEmptyJobs({
       workflow_name: 'Selftest CI',
       conclusion: 'success',
       run_url: 'https://ci/selftest-merge',
       error_category: '',
       error_message: '',
-    },
-    {
+    }),
+    withEmptyJobs({
       workflow_name: 'PR 11 - Minimal invariant CI',
       conclusion: 'success',
       run_url: 'https://ci/pr11-merge',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
 
   const contextPath = result.contextPath || path.join(process.cwd(), 'verifier-context.md');
@@ -896,27 +903,27 @@ test('buildVerifierContext falls back to head SHA when merge runs are missing',
 
   assert.equal(result.shouldRun, true);
   assert.deepEqual(result.ciResults, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'success',
       run_url: 'https://ci/pr-00-gate.yml',
       error_category: '',
       error_message: '',
-    },
-    {
+    }),
+    withEmptyJobs({
       workflow_name: 'Selftest CI',
       conclusion: 'success',
       run_url: 'https://ci/selftest-ci.yml',
       error_category: '',
       error_message: '',
-    },
-    {
+    }),
+    withEmptyJobs({
       workflow_name: 'PR 11 - Minimal invariant CI',
       conclusion: 'success',
       run_url: 'https://ci/pr-11-ci-smoke.yml',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
   for (const workflowId of workflowIds) {
     assert.ok(calls.includes(`${workflowId}:merge-sha-555`));
@@ -983,27 +990,27 @@ test('buildVerifierContext uses merge commit SHA for push events', async () => {
   assert.ok(headShas.length > 0);
   assert.ok(headShas.every((sha) => sha === 'merge-sha-444'));
   assert.deepEqual(result.ciResults, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'success',
       run_url: 'https://ci/gate-push',
       error_category: '',
       error_message: '',
-    },
-    {
+    }),
+    withEmptyJobs({
       workflow_name: 'Selftest CI',
       conclusion: 'success',
       run_url: 'https://ci/selftest-push',
       error_category: '',
       error_message: '',
-    },
-    {
+    }),
+    withEmptyJobs({
       workflow_name: 'PR 11 - Minimal invariant CI',
       conclusion: 'success',
       run_url: 'https://ci/pr11-push',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
 
   const contextPath = result.contextPath || path.join(process.cwd(), 'verifier-context.md');
diff --git a/.github/scripts/__tests__/verifier-ci-query.test.js b/.github/scripts/__tests__/verifier-ci-query.test.js
index 1de96c270..0bf8a9e93 100644
--- a/.github/scripts/__tests__/verifier-ci-query.test.js
+++ b/.github/scripts/__tests__/verifier-ci-query.test.js
@@ -5,6 +5,13 @@ const assert = require('node:assert/strict');
 
 const { queryVerifierCiResults } = require('../verifier_ci_query.js');
 
+const withEmptyJobs = (result) => ({
+  ...result,
+  jobs_summary: { total: 0, conclusions: {}, samples: [], truncated: false },
+  jobs_error_category: '',
+  jobs_error_message: '',
+});
+
 const buildGithubStub = ({
   runsByWorkflow = {},
   errorWorkflow = null,
@@ -57,27 +64,27 @@ test('queryVerifierCiResults selects runs and reports conclusions', async () =>
   });
 
   assert.equal(results.length, 3);
-  assert.deepEqual(results[0], {
+  assert.deepEqual(results[0], withEmptyJobs({
     workflow_name: 'Gate',
     conclusion: 'success',
     run_url: 'gate-url',
     error_category: '',
     error_message: '',
-  });
-  assert.deepEqual(results[1], {
+  }));
+  assert.deepEqual(results[1], withEmptyJobs({
     workflow_name: 'Selftest CI',
     conclusion: 'in_progress',
     run_url: 'selftest-url',
     error_category: '',
     error_message: '',
-  });
-  assert.deepEqual(results[2], {
+  }));
+  assert.deepEqual(results[2], withEmptyJobs({
     workflow_name: 'PR 11',
     conclusion: 'not_found',
     run_url: '',
     error_category: '',
     error_message: '',
-  });
+  }));
 });
 
 test('queryVerifierCiResults supports workflowId/workflowName aliases', async () => {
@@ -101,13 +108,13 @@ test('queryVerifierCiResults supports workflowId/workflowName aliases', async ()
   });
 
   assert.deepEqual(results, [
-    {
+    withEmptyJobs({
       workflow_name: 'Selftest CI',
       conclusion: 'success',
       run_url: 'selftest-alias-url',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
 });
 
@@ -124,13 +131,13 @@ test('queryVerifierCiResults treats query errors as api_error', async () => {
   });
 
   assert.deepEqual(results, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'api_error',
       run_url: '',
       error_category: 'resource',
       error_message: 'listWorkflowRuns:pr-00-gate.yml failed after 1 attempt(s): boom',
-    },
+    }),
   ]);
 });
 
@@ -153,13 +160,13 @@ test('queryVerifierCiResults uses latest run when no target SHA is provided', as
   });
 
   assert.deepEqual(results, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'success',
       run_url: 'gate-latest-url',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
 });
 
@@ -194,13 +201,13 @@ test('queryVerifierCiResults falls back to secondary SHA when primary has no run
   });
 
   assert.deepEqual(results, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'success',
       run_url: 'head-url',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
   assert.deepEqual(headShas, ['merge-sha', 'head-sha']);
 });
@@ -228,27 +235,27 @@ test('queryVerifierCiResults falls back to default workflows', async () => {
   });
 
   assert.deepEqual(results, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'success',
       run_url: 'gate-default-url',
       error_category: '',
       error_message: '',
-    },
-    {
+    }),
+    withEmptyJobs({
       workflow_name: 'Selftest CI',
       conclusion: 'failure',
       run_url: 'selftest-default-url',
       error_category: '',
       error_message: '',
-    },
-    {
+    }),
+    withEmptyJobs({
       workflow_name: 'PR 11 - Minimal invariant CI',
       conclusion: 'success',
       run_url: 'pr11-default-url',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
 });
 
@@ -269,13 +276,13 @@ test('queryVerifierCiResults uses API url when html_url is missing', async () =>
   });
 
   assert.deepEqual(results, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'success',
       run_url: 'api-url',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
 });
 
@@ -296,13 +303,13 @@ test('queryVerifierCiResults treats completed runs without conclusion as unknown
   });
 
   assert.deepEqual(results, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'unknown',
       run_url: 'gate-url',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
 });
 
@@ -341,13 +348,13 @@ test('queryVerifierCiResults retries transient errors and returns success', asyn
   assert.equal(attempts, 3);
   assert.equal(warnings.length, 2);
   assert.deepEqual(results, [
-    {
+    withEmptyJobs({
       workflow_name: 'Gate',
       conclusion: 'success',
       run_url: 'retry-url',
       error_category: '',
       error_message: '',
-    },
+    }),
   ]);
 });
 
@@ -381,13 +388,13 @@ test('queryVerifierCiResults returns api_error after max retries', async (t) =>
       assert.equal(attempts, 4);
       assert.equal(warnings.length, 4);
       assert.deepEqual(results, [
-        {
+        withEmptyJobs({
           workflow_name: 'Gate',
           conclusion: 'api_error',
           run_url: '',
           error_category: 'transient',
           error_message: `listWorkflowRuns:pr-00-gate.yml failed after 4 attempt(s): status-${status}`,
-        },
+        }),
       ]);
     });
   }
diff --git a/.github/workflows/agents-auto-pilot.yml b/.github/workflows/agents-auto-pilot.yml
index 981bd066d..4339eaa01 100644
--- a/.github/workflows/agents-auto-pilot.yml
+++ b/.github/workflows/agents-auto-pilot.yml
@@ -115,6 +115,16 @@ jobs:
         if: steps.check_enabled.outputs.enabled == 'true'
         uses: actions/checkout@v6
 
+      - name: Set up Node
+        if: steps.check_enabled.outputs.enabled == 'true'
+        uses: actions/setup-node@v6
+        with:
+          node-version: '20'
+
+      - name: Install GitHub API dependencies
+        if: steps.check_enabled.outputs.enabled == 'true'
+        run: npm install --no-save --no-package-lock @octokit/rest @octokit/auth-app
+
       - name: Export load balancer tokens
         if: steps.check_enabled.outputs.enabled == 'true'
         uses: ./.github/actions/export-load-balancer-tokens
@@ -128,10 +138,17 @@ jobs:
         uses: actions/github-script@v8
         with:
           script: |
-            const { data } = await github.rest.repos.get({
+            const { createTokenAwareRetry } = require('./.github/scripts/github-api-with-retry.js');
+            const { withRetry } = await createTokenAwareRetry({
+              github,
+              core,
+              task: 'auto-pilot-resolve-workflows-ref',
+            });
+
+            const { data } = await withRetry((client) => client.rest.repos.get({
               owner: 'stranske',
               repo: 'Workflows'
-            });
+            }));
             if (!data?.default_branch) {
               core.setFailed('Could not determine Workflows default branch');
               return;
diff --git a/.github/workflows/agents-bot-comment-handler.yml b/.github/workflows/agents-bot-comment-handler.yml
index 2d4fb815a..8322e345f 100644
--- a/.github/workflows/agents-bot-comment-handler.yml
+++ b/.github/workflows/agents-bot-comment-handler.yml
@@ -67,6 +67,7 @@ jobs:
           sparse-checkout: |
             .github/actions/export-load-balancer-tokens
             .github/scripts/github-api-with-retry.js
+            .github/scripts/token_load_balancer.js
           sparse-checkout-cone-mode: false
       - name: Export load balancer tokens
         uses: ./.github/actions/export-load-balancer-tokens
@@ -74,6 +75,12 @@ jobs:
           github_token: ${{ github.token }}
           token_rotation_json: ${{ secrets.TOKEN_ROTATION_JSON }}
           token_rotation_env_keys: ${{ vars.TOKEN_ROTATION_ENV_KEYS }}
+      - name: Set up Node
+        uses: actions/setup-node@v6
+        with:
+          node-version: '20'
+      - name: Install GitHub API dependencies
+        run: npm install --no-save --no-package-lock @octokit/rest @octokit/auth-app
       - name: Resolve PR number and check conditions
         id: resolve
         uses: actions/github-script@v8
@@ -81,14 +88,17 @@ jobs:
           script: |
             const fs = require('fs');
             const retryHelperPath = './.github/scripts/github-api-with-retry.js';
-            const retryHelpers = fs.existsSync(retryHelperPath)
-              ? require(retryHelperPath)
-              : {
-                  withRetry: (fn) => fn(),
-                  paginateWithRetry: (githubInstance, method, params) =>
-                    githubInstance.paginate(method, params),
-                };
-            const { withRetry } = retryHelpers;
+            const retryHelpers = fs.existsSync(retryHelperPath) ? require(retryHelperPath) : null;
+            let withRetry = (fn) => fn();
+            if (retryHelpers?.createTokenAwareRetry) {
+              ({ withRetry } = await retryHelpers.createTokenAwareRetry({
+                github,
+                core,
+                task: 'bot-comment-handler',
+              }));
+            } else if (retryHelpers?.withRetry) {
+              ({ withRetry } = retryHelpers);
+            }
 
             const eventName = context.eventName;
             let prNumber = null;
@@ -116,10 +126,10 @@ jobs:
 
               let defaultBranch = context.payload.repository?.default_branch;
               if (!defaultBranch) {
-                const repoResponse = await github.rest.repos.get({
+                const repoResponse = await withRetry((client) => client.rest.repos.get({
                   owner: context.repo.owner,
                   repo: context.repo.repo
-                });
+                }));
                 defaultBranch = repoResponse.data?.default_branch;
               }
               if (!defaultBranch) {
@@ -154,7 +164,7 @@ jobs:
               // Check if PR has agent label
               let pr;
               try {
-                const response = await withRetry(() => github.rest.pulls.get({
+                const response = await withRetry((client) => client.rest.pulls.get({
                   owner: context.repo.owner,
                   repo: context.repo.repo,
                   pull_number: prNumber
diff --git a/.github/workflows/autofix.yml b/.github/workflows/autofix.yml
index 9c8676e37..633aa0048 100644
--- a/.github/workflows/autofix.yml
+++ b/.github/workflows/autofix.yml
@@ -38,19 +38,41 @@ jobs:
       - name: Checkout for API helpers
         uses: actions/checkout@v6
         with:
-          sparse-checkout: .github/scripts
+          sparse-checkout: |
+            .github/actions/export-load-balancer-tokens
+            .github/scripts/github-api-with-retry.js
+            .github/scripts/token_load_balancer.js
           sparse-checkout-cone-mode: false
 
+      - name: Export load balancer tokens
+        uses: ./.github/actions/export-load-balancer-tokens
+        with:
+          github_token: ${{ github.token }}
+          token_rotation_json: ${{ secrets.TOKEN_ROTATION_JSON }}
+          token_rotation_env_keys: ${{ vars.TOKEN_ROTATION_ENV_KEYS }}
+
+      - name: Set up Node
+        uses: actions/setup-node@v6
+        with:
+          node-version: '20'
+
+      - name: Install GitHub API dependencies
+        run: npm install --no-save --no-package-lock @octokit/rest @octokit/auth-app
+
       - name: Resolve PR context
         id: context
         uses: actions/github-script@v8
         with:
           github-token: ${{ secrets.AGENTS_AUTOMATION_PAT || secrets.ACTIONS_BOT_PAT || github.token }}
           script: |
-            const path = require('path');
-            const { paginateWithBackoff } = require(
-              path.join(process.env.GITHUB_WORKSPACE, '.github/scripts/api-helpers.js')
+            const { createTokenAwareRetry } = require(
+              './.github/scripts/github-api-with-retry.js'
             );
+            const { paginateWithRetry } = await createTokenAwareRetry({
+              github,
+              core,
+              task: 'autofix-loop-resolve-context',
+            });
 
             const pr = context.payload.pull_request;
             if (!pr) {
@@ -103,11 +125,10 @@ jobs:
             const { owner, repo } = context.repo;
             let files = [];
             try {
-              files = await paginateWithBackoff(
-                github,
+              files = await paginateWithRetry(
                 github.rest.pulls.listFiles,
                 { owner, repo, pull_number: pr.number, per_page: 100 },
-                { maxRetries: 3, core }
+                { maxRetries: 3 }
               );
             } catch (error) {
               const message = String(error?.message || error || '');
diff --git a/.github/workflows/pr-00-gate.yml b/.github/workflows/pr-00-gate.yml
index 8ed983536..a5313cd42 100644
--- a/.github/workflows/pr-00-gate.yml
+++ b/.github/workflows/pr-00-gate.yml
@@ -246,10 +246,23 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
           ref: ${{ github.event.pull_request.head.sha || github.sha }}
           sparse-checkout: |
+            .github/actions/export-load-balancer-tokens
             .github/scripts
             .github/config
             tools
           sparse-checkout-cone-mode: false
+      - name: Export load balancer tokens
+        uses: ./.github/actions/export-load-balancer-tokens
+        with:
+          github_token: ${{ github.token }}
+          token_rotation_json: ${{ secrets.TOKEN_ROTATION_JSON }}
+          token_rotation_env_keys: ${{ vars.TOKEN_ROTATION_ENV_KEYS }}
+      - name: Set up Node
+        uses: actions/setup-node@v6
+        with:
+          node-version: '20'
+      - name: Install GitHub API dependencies
+        run: npm install --no-save --no-package-lock @octokit/rest @octokit/auth-app
       - name: Handle docs-only change
         if: needs.detect.outputs.doc_only == 'true'
         id: docs_only
@@ -416,6 +429,12 @@ jobs:
           FAILURE_CHECKS: ${{ steps.summarize.outputs.failure_checks || '' }}
         with:
           script: |
+            const { createTokenAwareRetry } = require('./.github/scripts/github-api-with-retry.js');
+            const { withRetry, paginateWithRetry } = await createTokenAwareRetry({
+              github,
+              core,
+              task: 'gate-autofix-label',
+            });
             const { owner, repo } = context.repo;
             const pr = context.payload.pull_request;
             core.setOutput('applied', 'false');
@@ -450,12 +469,15 @@ jobs:
               return;
             }
 
-            const iterator = github.paginate.iterator(github.rest.pulls.listFiles, {
-              owner,
-              repo,
-              pull_number: pr.number,
-              per_page: 100,
-            });
+            const files = await paginateWithRetry(
+              github.rest.pulls.listFiles,
+              {
+                owner,
+                repo,
+                pull_number: pr.number,
+                per_page: 100,
+              },
+            );
 
             const allowedExtensions = String(process.env.ALLOWED_EXTENSIONS || '')
               .split(',')
@@ -464,20 +486,15 @@ jobs:
               .map(ext => (ext.startsWith('.') ? ext : `.${ext}`));
 
             const disallowed = [];
-            for await (const page of iterator) {
-              if (!Array.isArray(page.data)) {
+            for (const file of files || []) {
+              const filename = file?.filename;
+              if (typeof filename !== 'string' || filename.length === 0) {
                 continue;
               }
-              for (const file of page.data) {
-                const filename = file?.filename;
-                if (typeof filename !== 'string' || filename.length === 0) {
-                  continue;
-                }
-                const lower = filename.toLowerCase();
-                const allowed = allowedExtensions.some(ext => lower.endsWith(ext));
-                if (!allowed) {
-                  disallowed.push(filename);
-                }
+              const lower = filename.toLowerCase();
+              const allowed = allowedExtensions.some(ext => lower.endsWith(ext));
+              if (!allowed) {
+                disallowed.push(filename);
               }
             }
 
@@ -487,12 +504,12 @@ jobs:
               return;
             }
 
-            await github.rest.issues.addLabels({
+            await withRetry((client) => client.rest.issues.addLabels({
               owner,
               repo,
               issue_number: pr.number,
               labels: ['autofix:clean'],
-            });
+            }));
             core.info('Applied autofix:clean label for cosmetic failure.');
             core.setOutput('applied', 'true');
 
@@ -554,6 +571,12 @@ jobs:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
             const fs = require('fs');
+            const { createTokenAwareRetry } = require('./.github/scripts/github-api-with-retry.js');
+            const { withRetry } = await createTokenAwareRetry({
+              github,
+              core,
+              task: 'gate-keepalive-checklist',
+            });
             const prNumber = Number(process.env.PR_NUMBER || '0');
             const payloadBody = context.payload.pull_request?.body || '';
 
@@ -566,7 +589,11 @@ jobs:
             if (!prBody && prNumber) {
               const { owner, repo } = context.repo;
               try {
-                const pr = await github.rest.pulls.get({ owner, repo, pull_number: prNumber });
+                const pr = await withRetry((client) => client.rest.pulls.get({
+                  owner,
+                  repo,
+                  pull_number: prNumber
+                }));
                 prBody = pr.data.body || '';
               } catch (error) {
                 const hitRateLimit = error?.status === 403 && /rate limit/i.test(error?.message || '');
@@ -716,6 +743,12 @@ jobs:
           TARGET_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
         with:
           script: |
+            const { createTokenAwareRetry } = require('./.github/scripts/github-api-with-retry.js');
+            const { withRetry } = await createTokenAwareRetry({
+              github,
+              core,
+              task: 'gate-commit-status',
+            });
             const owner = context.repo.owner;
             const repo = context.repo.repo;
             const sha = context.payload.pull_request?.head?.sha ?? context.sha;
@@ -727,7 +760,7 @@ jobs:
             const targetUrl = process.env.TARGET_URL;
 
             try {
-              await github.rest.repos.createCommitStatus({
+              await withRetry((client) => client.rest.repos.createCommitStatus({
                 owner,
                 repo,
                 sha,
@@ -735,7 +768,7 @@ jobs:
                 context: 'Gate / gate',
                 description,
                 target_url: targetUrl,
-              });
+              }));
             } catch (error) {
               const hitRateLimit = error?.status === 403 && /rate limit/i.test(error?.message || '');
               if (hitRateLimit) {
diff --git a/scripts/check_issue_consistency.py b/scripts/check_issue_consistency.py
index 9b4e37702..6080257e0 100755
--- a/scripts/check_issue_consistency.py
+++ b/scripts/check_issue_consistency.py
@@ -64,6 +64,15 @@ def extract_title_issue_number(title: str) -> int | None:
     return None
 
 
+def extract_head_ref_issue_numbers(head_ref: str) -> set[int]:
+    return extract_issue_numbers(head_ref or "", include_hash=False)
+
+
+def is_autofix_context(pr_title: str, head_ref: str) -> bool:
+    combined = f"{pr_title or ''}\n{head_ref or ''}".lower()
+    return "autofix" in combined or (head_ref or "").lower().startswith("autofix/")
+
+
 def _run_git(args: list[str]) -> str:
     result = subprocess.run(
         ["git", *args],
@@ -104,12 +113,40 @@ def collect_changed_files(
 
 def collect_header_issue_numbers(file_path: Path, max_lines: int) -> set[int]:
     numbers: set[int] = set()
+    in_docstring = False
+    docstring_delim = ""
+
+    def is_comment_line(line: str) -> bool:
+        stripped = line.lstrip()
+        return stripped.startswith(("#", "//", "/*", "*", "--", ";", "<!--"))
+
     try:
         with file_path.open("r", encoding="utf-8", errors="ignore") as handle:
             for _ in range(max_lines):
                 line = handle.readline()
                 if not line:
                     break
+                if in_docstring:
+                    if "issue" in line.lower():
+                        numbers.update(extract_issue_numbers(line, include_hash=True))
+                    if docstring_delim and docstring_delim in line:
+                        in_docstring = False
+                        docstring_delim = ""
+                    continue
+
+                stripped = line.lstrip()
+                if stripped.startswith(('"""', "'''")):
+                    docstring_delim = stripped[:3]
+                    in_docstring = True
+                    if "issue" in line.lower():
+                        numbers.update(extract_issue_numbers(line, include_hash=True))
+                    if stripped.count(docstring_delim) >= 2:
+                        in_docstring = False
+                        docstring_delim = ""
+                    continue
+
+                if not is_comment_line(line):
+                    continue
                 if "issue" not in line.lower():
                     continue
                 numbers.update(extract_issue_numbers(line, include_hash=True))
@@ -142,6 +179,11 @@ def main() -> int:
         default=os.environ.get("PR_TITLE", ""),
         help="Pull request title (defaults to PR_TITLE env).",
     )
+    parser.add_argument(
+        "--head-ref",
+        default=os.environ.get("HEAD_REF") or os.environ.get("GITHUB_HEAD_REF", ""),
+        help="Pull request head ref (defaults to HEAD_REF or GITHUB_HEAD_REF env).",
+    )
     parser.add_argument(
         "--header-lines",
         type=int,
@@ -152,8 +194,22 @@ def main() -> int:
 
     pr_issue = extract_title_issue_number(args.pr_title)
     if not pr_issue:
-        print("Error: Unable to determine issue number from PR title.", file=sys.stderr)
-        return 1
+        head_numbers = extract_head_ref_issue_numbers(args.head_ref)
+        if len(head_numbers) == 1:
+            pr_issue = next(iter(head_numbers))
+        elif len(head_numbers) > 1:
+            print(
+                "Error: Multiple issue numbers detected in head ref:",
+                sorted(head_numbers),
+                file=sys.stderr,
+            )
+            return 1
+        elif is_autofix_context(args.pr_title, args.head_ref):
+            print("Skipping issue consistency check: autofix context with no issue number.")
+            return 0
+        else:
+            print("Error: Unable to determine issue number from PR title.", file=sys.stderr)
+            return 1
 
     base_sha = (args.base_sha or "").strip() or None
     base_remote = (args.base_remote or "origin").strip() or "origin"
diff --git a/tests/scripts/test_issue_consistency_check.py b/tests/scripts/test_issue_consistency_check.py
index e1a215aa4..06ecb595c 100644
--- a/tests/scripts/test_issue_consistency_check.py
+++ b/tests/scripts/test_issue_consistency_check.py
@@ -18,7 +18,7 @@ def test_extract_title_issue_number_prefers_hash() -> None:
 
 def test_collect_header_issue_numbers_reads_issue_lines(tmp_path: Path) -> None:
     path = tmp_path / "sample.txt"
-    path.write_text("Issue: 1075\n# not an issue reference\n", encoding="utf-8")
+    path.write_text("# Issue: 1075\n# not an issue reference\n", encoding="utf-8")
     numbers = check_issue_consistency.collect_header_issue_numbers(path, max_lines=5)
     assert numbers == {1075}
 
@@ -27,3 +27,9 @@ def test_extract_issue_numbers_ignores_pr_hashes() -> None:
     text = "PR #1076 relates to Issue #1075"
     numbers = check_issue_consistency.extract_issue_numbers(text)
     assert numbers == {1075}
+
+
+def test_extract_head_ref_issue_numbers_from_branch() -> None:
+    head_ref = "codex/issue-144-keepalive"
+    numbers = check_issue_consistency.extract_head_ref_issue_numbers(head_ref)
+    assert numbers == {144}
diff --git a/verifier-pr-diff.patch b/verifier-pr-diff.patch
new file mode 100644
index 000000000..16e5331e7
--- /dev/null
+++ b/verifier-pr-diff.patch
@@ -0,0 +1,11 @@
+diff --git a/src/app.py b/src/app.py
+index 111..222 100644
+--- a/src/app.py
++++ b/src/app.py
++print("hello")
+-print("bye")
+diff --git a/docs/readme.md b/docs/readme.md
+deleted file mode 100644
+--- a/docs/readme.md
++++ /dev/null
+-Old content