ci: add top-level permissions to GHA workflows (#3255)

Adds `permissions: contents: read` to the 10 workflows that had no
top-level permissions block. Workflows that already declared
permissions, or individual jobs that need elevated permissions (`issues:
write`, `pull-requests: write`, `contents: write`), are left unchanged.

Affected workflows: `dev.yml`, `java-publish.yml`, `java.yml`,
`license-header-check.yml`, `nodejs.yml`, `pypi-publish.yml`,
`python.yml`, `rust.yml`, `update_package_lock_run.yml`,
`update_package_lock_run_nodejs.yml`

.github/workflows/nodejs.yml

@@ -15,6 +15,9 @@ on:
       - .github/workflows/nodejs.yml
       - docker-compose.yml
 
+permissions:
+  contents: read
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true