Unreferenced data entites are invalid about ro-crate-java

[Pfeil]

For clarification:

• The builder's builder.addDataEntity(DataEntity) does add it correctly.
• The crate's crate.addDataEntity does add it correctly with crate.addDataEntity(DataEntity, true). It does not add it correctly, if the second parameter is false or without it (crate.addDataEntity(DataEntity)).

At first glance, it seems to be used with the boolean being false only once in the whole code, at the RoCrateReader, for each DataEntity. Currently, I do not understand why, but I assume that it is because in this case, it is already inside. I think we should:

• change the default from "not being added" to "being added" at least.
• But ideally, we should figure out if we can remove this "feature" completely in the end. For example, if this is about not adding something twice, we may use a set in the background (this is already the case!) and simply add it anyway. It should not change anything, then.