Fix e2e automation

[bentsherman]

This PR attempts to restore the structure of build/plugins that was present in Nextflow 25.04 and likely was removed by #6379

build/plugins/
├── nf-amazon-3.3.0
│   ├── classes
│   │   ├── META-INF
│   │   │   ├── extensions.idx
│   │   │   └── services
│   │   │       └── java.nio.file.spi.FileSystemProvider
│   │   └── nextflow
│   │       └── cloud
│   │           └── aws
│   │               ├── AmazonPlugin.class
│   │               ├── ...
│   ├── lib
│   │   ├── annotations-2.33.2.jar
│   │   ├── apache-client-2.33.2.jar
│   │   ├── arns-2.33.2.jar
│   │   ├── ...
│   └── META-INF
│       └── MANIFEST.MF

This structure is required by the e2e automation to bake the local plugin builds in the launcher image

I just added a Gradle task to re-create this structure with direct file copies, but I assume there is a more idiomatic way to do it

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[bentsherman]

Runs: https://cloud.seqera.io/orgs/seqeralabs/workspaces/showcase/watch?search=20251017_91cfb17acea5431

They are still failing with the class-not-found error

[bentsherman]

Closing in favor of #6495