Waived zizmor template-injection issues (#46994)

<!-- Add the related story/sub-task/bug number, like Resolves #123, or
remove if NA -->
**Related issue:** Resolves #41198

Also fixed the currently failing check on main.

Final zizmor PR


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

* **Security & Infrastructure**
* Enhanced credential handling in automated workflows by disabling
unnecessary credential persistence
* Strengthened security scanning configuration to enforce additional
checks on GitHub Actions workflows while maintaining a curated allowlist
for compatibility

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

.github/workflows/close-stale-eng-initiated-issues.yml

@@ -50,6 +50,8 @@ jobs:
 
       - name: Checkout repo
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Stale and close eng-initiated issues
         uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0

.github/zizmor-gate.yml

@@ -1,12 +1,6 @@
 # zizmor "blocking gate" configuration.
 #
-# This config is used by the zizmor job in .github/workflows/zizmor.yml. It disables the
-# audit rules for which we currently carry a backlog of findings, so the job fails the
-# build only for rules the repository ALREADY passes (catching regressions).
-#
-# As the backlog is burned down in follow-up work, delete the corresponding `disable: true`
-# entry below to start enforcing that rule too. The current finding counts (in our
-# .github/workflows + .github/actions scope) are noted for reference.
+# This config is used by the zizmor job in .github/workflows/zizmor.yml.
 #
 # This file is passed explicitly via the action's `config:` input rather than being named
 # .github/zizmor.yml, so a plain `zizmor .` run still reports the full backlog locally.
@@ -25,5 +19,55 @@ rules:
       - fleet-and-orbit.yml
       - generate-osqueryd-targets.yml
       - goreleaser-fleet.yaml
-  template-injection: # 234 findings
-    disable: true
+  # The template-injection rule stays ENABLED so new workflows are checked, and we waive only the
+  # workflows that carry the existing backlog (listed below). We audited every current finding by
+  # trigger and source: none are reachable by untrusted input. There are no pull_request_target /
+  # workflow_run / issue_comment workflows; the one issues-triggered workflow
+  # (auto-tag-unreleased-bugs.yml) reads the issue body via actions/github-script's context object,
+  # never interpolated into a shell. The remaining findings draw only from maintainer-/runner-
+  # controlled sources (static matrix values, workflow_dispatch inputs gated behind write access,
+  # push/tag refs, github.sha, and internal step outputs), so they are not externally exploitable.
+  # This waiver freezes the backlog: any template-injection in a NEW workflow, or any NEW finding
+  # in a workflow not listed here, fails the gate.
+  #
+  # Matching is by filename only (zizmor does not match on path), so keep these names unique.
+  # NOTE: `action.yml` matches every composite-action manifest. Today only .github/actions/r2-upload
+  # carries findings; a future finding in another composite action (e.g. eng-metrics) would also be
+  # suppressed. Revisit if more composite actions are added.
+  template-injection:
+    ignore:
+      - action.yml # .github/actions/r2-upload/action.yml (bash; env/inputs from trusted callers)
+      - build-fleetctl-msi.yml
+      - build-fleetctl-pkg.yml
+      - build-fleetd-base-msi.yml
+      - build-fleetd-base-pkg.yml
+      - build-fleetdm-fleetctl-check-vulnerabilities.yml
+      - check-bomutils-vulnerabilities.yml
+      - check-vulnerabilities-in-released-docker-images.yml
+      - check-wix-vulnerabilities.yml
+      - code-sign-windows.yml
+      - db-upgrade-test.yml
+      - dogfood-automated-policy-updates.yml
+      - dogfood-update-testing-qa-apps.yml
+      - e2e-agent.yml
+      - fleet-and-orbit.yml
+      - generate-desktop-targets.yml
+      - golangci-lint.yml
+      - goreleaser-fleet.yaml
+      - goreleaser-orbit.yaml
+      - goreleaser-snapshot-fleet.yaml
+      - ingest-maintained-apps.yml
+      - loadtest-infra.yml
+      - loadtest-osquery-perf.yml
+      - product-eng-handbook-summary.yml
+      - publish-go-module.yml
+      - randokiller-go.yml
+      - release-fleetd-base.yml
+      - release-fleetd-chrome-beta.yml
+      - release-fleetd-chrome.yml
+      - tag-aging-bugs.yml
+      - test-db-changes.yml
+      - test-fma-darwin-pr-only.yml
+      - test-fma-windows-pr-only.yml
+      - test-go-suite.yaml
+      - verify-fleetd-base.yml