JSON-LD Parser adds unnecessary namespaces - Serializer fails to resolve namespace

Hi,

I am using rdflib to parse json-lds from a database which at a later point will be serialized again.
As part of this I want to ensure that the resulting serialized graph is as close as possible to the original json-ld.
However, I noticed that the serialized graph contains a lot of extra namespace definitions in its context that are unneeded.
Even when setting `bind_namespaces` to `"none"` for the namespace manager.
Additionally the namespace `https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/` is not mapped back to its prefix `mds`.

I am running Python 3.10.12 and rdflib 7.5.0

Would this be expected behavior? 

Thanks for your support!

MWE:

```{python}
from rdflib import Graph

source = "path_to_original_jsonld"

graph = Graph(
    store="Memory",
    bind_namespaces="none",
)

print(len(tuple(graph.namespaces()))) # 0

graph.parse(
    source=source
)

print(len(tuple(graph.namespaces()))) # 33

graph.serialize(
    destination="serialized.jsonld",
    format="json-ld",
    auto_compact=True,
)
```

Original JSON-LD:
```{json}
{
  "@context": {
    "mds": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/",
    "obo": "http://purl.obolibrary.org/obo/",
    "cco": "https://www.commoncoreontologies.org/",
    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
    "skos": "http://www.w3.org/2004/02/skos/core#",
    "qudt": "http://qudt.org/schema/qudt/",
    "owl": "http://www.w3.org/2002/07/owl#",
    "xsd": "http://www.w3.org/2001/XMLSchema#",
    "dcterms": "http://purl.org/dc/terms/"
  },
  "@graph": [
    {
      "@id": "mds:XrayResult_re00007-is00002-im0081",
      "@type": "mds:XrayResult",
      "cco:ont00001808": {
        "@id": "mds:sa50002"
      },
      "dcterms:created": {
        "@value": "2018-03-26T20:45:39",
        "@type": "xsd:dateTime"
      }
    },
    {
      "@id": "mds:ResultID_re00007-is00002-im0081",
      "@type": "mds:ResultID",
      "cco:ont00001765": "u-sa50002-si0001-to50001-re00007-is00002-im0081-or0000000205935222-ts20180326204539",
      "cco:ont00001916": {
        "@id": "mds:XrayResult_re00007-is00002-im0081"
      }
    },
    {
      "@id": "mds:re00007",
      "@type": "mds:XrayRecipe",
      "cco:ont00001986": {
        "@id": "mds:XrayResult_re00007-is00002-im0081"
      },
      "obo:BFO_0000057": [
        {
          "@id": "mds:sa50002"
        },
        {
          "@id": "mds:to50001"
        },
        {
          "@id": "mds:ge02"
        }
      ]
    },
    {
      "@id": "mds:ImageFile_re00007-is00002-im0081",
      "@type": "mds:ImageFile",
      "rdfs:label": "ff_011276_ge2_0081.tiff"
    },
    {
      "@id": "mds:ImageStack_re00007-is00002-im0081",
      "@type": "mds:ImageStack",
      "obo:BFO_0000176": {
        "@id": "mds:XrayResult_re00007-is00002-im0081"
      },
      "obo:BFO_0000178": {
        "@id": "mds:DiffractionPattern_re00007-is00002-im0081"
      }
    },
    {
      "@id": "mds:DiffractionPattern_re00007-is00002-im0081",
      "@type": "mds:DiffractionPattern",
      "obo:BFO_0000084": {
        "@id": "mds:ImageFile_re00007-is00002-im0081"
      }
    }
  ]
}
```

Serialized Graph:
```{json}
{
  "@context": {
    "brick": "https://brickschema.org/schema/Brick#",
    "cco": "https://www.commoncoreontologies.org/",
    "csvw": "http://www.w3.org/ns/csvw#",
    "dc": "http://purl.org/dc/elements/1.1/",
    "dcam": "http://purl.org/dc/dcam/",
    "dcat": "http://www.w3.org/ns/dcat#",
    "dcmitype": "http://purl.org/dc/dcmitype/",
    "dcterms": "http://purl.org/dc/terms/",
    "doap": "http://usefulinc.com/ns/doap#",
    "foaf": "http://xmlns.com/foaf/0.1/",
    "geo": "http://www.opengis.net/ont/geosparql#",
    "mds": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/",
    "obo": "http://purl.obolibrary.org/obo/",
    "odrl": "http://www.w3.org/ns/odrl/2/",
    "org": "http://www.w3.org/ns/org#",
    "owl": "http://www.w3.org/2002/07/owl#",
    "prof": "http://www.w3.org/ns/dx/prof/",
    "prov": "http://www.w3.org/ns/prov#",
    "qb": "http://purl.org/linked-data/cube#",
    "qudt": "http://qudt.org/schema/qudt/",
    "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
    "schema": "https://schema.org/",
    "sh": "http://www.w3.org/ns/shacl#",
    "skos": "http://www.w3.org/2004/02/skos/core#",
    "sosa": "http://www.w3.org/ns/sosa/",
    "ssn": "http://www.w3.org/ns/ssn/",
    "time": "http://www.w3.org/2006/time#",
    "vann": "http://purl.org/vocab/vann/",
    "void": "http://rdfs.org/ns/void#",
    "wgs": "https://www.w3.org/2003/01/geo/wgs84_pos#",
    "xsd": "http://www.w3.org/2001/XMLSchema#"
  },
  "@graph": [
    {
      "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/re00007",
      "@type": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/XrayRecipe",
      "cco:ont00001986": {
        "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/XrayResult_re00007-is00002-im0081"
      },
      "obo:BFO_0000057": [
        {
          "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/sa50002"
        },
        {
          "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/to50001"
        },
        {
          "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/ge02"
        }
      ]
    },
    {
      "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/DiffractionPattern_re00007-is00002-im0081",
      "@type": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/DiffractionPattern",
      "obo:BFO_0000084": {
        "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/ImageFile_re00007-is00002-im0081"
      }
    },
    {
      "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/ImageFile_re00007-is00002-im0081",
      "@type": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/ImageFile",
      "rdfs:label": "ff_011276_ge2_0081.tiff"
    },
    {
      "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/ImageStack_re00007-is00002-im0081",
      "@type": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/ImageStack",
      "obo:BFO_0000176": {
        "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/XrayResult_re00007-is00002-im0081"
      },
      "obo:BFO_0000178": {
        "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/DiffractionPattern_re00007-is00002-im0081"
      }
    },
    {
      "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/ResultID_re00007-is00002-im0081",
      "@type": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/ResultID",
      "cco:ont00001765": "u-sa50002-si0001-to50001-re00007-is00002-im0081-or0000000205935222-ts20180326204539",
      "cco:ont00001916": {
        "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/XrayResult_re00007-is00002-im0081"
      }
    },
    {
      "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/XrayResult_re00007-is00002-im0081",
      "@type": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/XrayResult",
      "cco:ont00001808": {
        "@id": "https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html#https://cwrusdle.bitbucket.io/mds/sa50002"
      },
      "dcterms:created": {
        "@type": "xsd:dateTime",
        "@value": "2018-03-26T20:45:39"
      }
    }
  ]
}
```

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JSON-LD Parser adds unnecessary namespaces - Serializer fails to resolve namespace #3373

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JSON-LD Parser adds unnecessary namespaces - Serializer fails to resolve namespace #3373

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