A JSON-LD document with a top-level @id and a top-level @graph is a named
graph. Its members become quads named by that @id, and the default graph is
left empty. rdflib.Graph.parse() keeps the default graph and discards the
rest without reporting anything, so every consumer that loads an export the
ordinary way saw the document header and none of the data.
_convert_to_jsonld wrote the payload into @graph and then stamped a document
@id beside it, which named every list export and every generic-dict export.
export_knowledge_graph made it worse: it converted the graph to JSON-LD and
handed the finished document back to export(), which converted it a second
time. The converted document no longer carries entities/relationships keys,
so the second pass treated it as opaque and buried the whole knowledge graph
inside @graph, under a name that is a wall-clock timestamp.
A two-entity, one-relationship graph exported to JSON-LD parsed as 2 triples
with Graph() and 21 quads with Dataset(). The 19 missing triples were the
entire knowledge graph.
The document node now goes inside @graph when the payload lives there, and is
the document itself otherwise, so no export names its own graph by accident.
An already-converted document is merged rather than nested, which also stops
the export carrying two document nodes and two @context blocks.
Semantica's reader has the mirror of this bug (#1129), so these exports could
not be read back by Semantica either.