Check for data entity existence in the RO-Crate payload

[simleo]

As pointed out by @elichad in ResearchObject/ro-crate#390 (comment), the RO-Crate Structure section of the spec states that:

Data Entities in the RO-Crate MUST either be payload files/directories present within the RO-Crate root directory or its subdirectories, or be Web-based Data Entities.

We are currently not checking that the RO-Crate payload (i.e. the contents of the crate's directory tree) actually contains files and directories listed in the metadata. We need to add this check, but we should consider having an option to disable it in order to support use cases where one just wants to check the metadata, e.g. for performance reasons. In particular, it should be noted that many of our tests do not include payload files, taking advantage of the current situation to avoid adding a large number of files overall.

important: the check needs to take into account the escaping of special characters in data entity @ids, see Describing entities in JSON-LD where it says that:

Care must be taken to express any relative paths using / separator and escape special characters like space (%20).