ci: standardize workflow permissions and fix configs

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.github/workflows/no-legacy-paths.yml on: push 1

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.github/workflows/swarm-pipeline.yml on: push 1

.github/workflows/trivy-scan.yml on: push 1

.github/workflows/hyper-agents-ci.yml on: push 1

.github/workflows/docs-lint.yml on: push 1

.github/workflows/iac-scan.yml on: push 1

.github/workflows/ci-cd.yml on: push 1

.github/workflows/docs-check.yml on: push 1

.github/workflows/security-comprehensive.yml on: push 1

.github/workflows/ci-security.yml on: push 1

.github/workflows/playwright-dashboard.yml on: push 1

.github/workflows/prune_audit.yml on: push 1

.github/workflows/secret-redaction-guard.yml on: push 1

.github/workflows/health.yml on: push 1

.github/workflows/hyper-agents-gate2-e2e.yml on: push 1

.github/workflows/trivy-weekly.yml on: push 1

.github/workflows/ci-python.yml on: push 1

.github/workflows/promote-dashboards.yml on: push 1

.github/workflows/ci-js.yml on: push 1

.github/workflows/docker.yml on: push 1

.github/workflows/tests.yml on: push 1

.github/workflows/sse-tests.yml on: push 1

.github/workflows/quality-gate.yml on: push 1

.github/workflows/docker-push.yml on: push 1

.github/workflows/lean-review.yml on: push 1

.github/workflows/evo-harness.yml on: push 1

.github/workflows/health-check.yml on: push 1

.github/workflows/performance.yml on: push 1

.github/workflows/docker-build.yml on: push 1

Security — CodeQL on: pull_request 2

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