chore(workflows): disable all GitHub Actions workflows

- Add `workflow: disable: true` to 23 workflow files to temporarily disable CI/CD automation
- Affects agent-contributions, build-macos-packages, ci, cli-tests, comprehensive-tests, configuration-security, contracts-ci, dotenv-check, file-organization, markdown-link-check, phase8-integration, production-deploy, publish-github-packages, publish-native-packages-simple, publish-native-packages, publish-npm-packages, publish-packages-to-registry

.github/workflows/security-scanning.yml

@@ -344,3 +344,5 @@ jobs:
           } catch (error) {
             console.log('Could not read security summary:', error.message);
           }
+workflow:
+  disable: true