Avoid caching patched node modules

What does this MR do and why?

This is based on !128768 (merged)

Avoid caching patched node modules

If we cache patched node modules, whenever we change the patch, it'll not apply to the patched modules. Patching is very fast so this should not be an issue.

Using after_script is fine because we run it before uploading cache: https://docs.gitlab.com/ee/ci/caching/#how-archiving-and-extracting-works

We also don't need to touch apt sources because it's left out from d2cc841c which was long ago. It's needed when we're running install_api_client_dependencies_with_apt and we're not doing that anymore.

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