Fix behavior wrt "missing" data entities

[simleo]

After the merge of #75, we allow data entities whose @id does not map to an existing file or directory, even if local. While this adds flexibility for use cases like #73, such crates are not supported by other libraries. Specifically, I got reports of crates generated with ro-crate-py that lead to errors when submission to WorkflowHub is attempted. The main issue is that it's too easy to add a "missing" data entity:

crate.add_file("/this/does/not/exist")  # Adds a File entity with @id = "exist"

This means it can be done involuntarily, by simply mistyping the path. It should be harder to do so (advanced usage), and we should issue a warning when it's done.