Refactor lineage JSON serilization with a root element including version, kind and spec properties

[jorgee]

This PR refactors the Lineage data encoder to serialize lineage records using the following structure:

{
  "version": <lineage version>,
  "kind": <lineage record class>,
  "spec": <record description>
}

For instance a FileOutput type is serialized as:

{
  "version": "lineage/v1beta1",
  "kind": "FileOutput",
  "spec": {
    "path": "/home/jorgee/nextflow_tests/provenance-test/results/samples.json",
    "checksum": {
      "value": "30a926dd315d4f4b9d6389803a1324ff",
      "algorithm": "nextflow",
      "mode": "standard"
    },
    "source": "lid://31e092e42c71b9545a9c5fa91689340c",
    "workflowRun": "lid://31e092e42c71b9545a9c5fa91689340c",
    "taskRun": null,
    "size": 201,
    "createdAt": "2025-05-14T10:25:51.563182873+02:00",
    "modifiedAt": "2025-05-14T10:25:51.563182873+02:00",
    "labels": [
      "foo"
    ]
  }
}

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[pditommaso]

This looks nice, likely we needed to update the version to v1beta2 if we go ahead with this. Also in a ideal world, it should be possible to keep backward compatibility with previous spec version, but I can understand that cannot be that simple

[jorgee]

For these PR, as there aren't changes in the model I think there is no need to update the version. I can make able to read both with spec and without with a small change. However, with changes such as in #6069 a mechanism for version compatibility is required.

[bentsherman]

It might be enough to simply ignore records that have an incompatible version and warn about them so that the user is aware. At least while the version is in beta. Maybe in the future we could add backwards compatibility, e.g. v1 / v2 data models, but hopefully we can iron out any changes in the beta period