[scripts] Update generate_manifest.py to handle the new JSON:API export format

[guzmud]

Use case

Support the upload of payloads in the new export format (JSON:API) in the repository.

Current Workaround

Manually edit the exported payloads to imitate the impact of the generate_manifest.py on payload JSON export.

Proposed Solution

Update the generate_manifest.py to handle both the legacy format (flat JSON) and the new format (JSON:API).

Additional Information

Sister issue: OpenAEV-Platform/collectors#317