Improve documentation around arrays as values of properties

This issue is opened as a response to https://github.com/kit-data-manager/ro-crate-java/issues/215.

- [ ] document the purpose of add* and set* methods in builders and their difference
- [ ] include array tests like encodingFormat if not already available and test/demonstrate if we can do this with the current API:
```json
{
"@id": "1st-tool.cwl",
"@type": "File",
"name": "First executable tool",
"description": "An example Common Workflow Language File",
"contentSize": "120",
"encodingFormat": ["text/plain", {"@id": "https://www.commonwl.org/v1.0/Workflow.html"}]
}
```
- [ ] There was no code given which generates this, but make sure this error message is only given in appropriate contexts:
```The property:
[ {
"@id" : "xsd:string"
} ]
does not comply with the flattened structure of the RO-Crate json document.
```

Start by inspecting the builder add* and set* methods and the existing tests for array-valued properties. Use the encodingFormat example to check whether the current API supports mixed arrays, document the method differences, and verify when the flattened-structure error is appropriate.

Written by the indexing model from the issue text.