Updates for pydantic 2 compatibility

[caufieldjh]

This updates the Makefile to ensure that linkml's gen-pydantic produces pydantic 2 classes.
Pydantic imports elsewhere in the project have been updated accordingly.

This also involves skipping export tests and removing full exports from make all, as templates prepared with a Pydantic version differing from that expected by linkml (which is not specifically pinned to pydantic 2) will cause errors when exporting to OWL, RDF, etc. This isn't essential to core functionality of OntoGPT, though it's otherwise useful, so it will soon return.

[caufieldjh]

Unit tests are failing because they rely on pickled fixtures (ooh, that's a good tongue twister):

======================================================================
ERROR: test_export (tests.unit.test_exporters.test_html_exporter.TestExportHTML)
Test export.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/unit/test_exporters/test_html_exporter.py", line 17, in setUp
    self.extraction_result = pickle.load(f)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/pydantic/main.py", line 816, in __setstate__
    _object_setattr(self, '__pydantic_fields_set__', state['__pydantic_fields_set__'])
KeyError: '__pydantic_fields_set__'

======================================================================
ERROR: test_export (tests.unit.test_exporters.test_markdown_exporter.TestExport)
Test export.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/unit/test_exporters/test_markdown_exporter.py", line 17, in setUp
    self.extraction_result = pickle.load(f)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/pydantic/main.py", line 816, in __setstate__
    _object_setattr(self, '__pydantic_fields_set__', state['__pydantic_fields_set__'])
KeyError: '__pydantic_fields_set__'

======================================================================
ERROR: test_export (tests.unit.test_exporters.test_owl_exporter.TestExportOWL)
Test export.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/unit/test_exporters/test_owl_exporter.py", line 21, in setUp
    self.extraction_result = pickle.load(f)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/pydantic/main.py", line 816, in __setstate__
    _object_setattr(self, '__pydantic_fields_set__', state['__pydantic_fields_set__'])
KeyError: '__pydantic_fields_set__'

======================================================================
ERROR: test_export2 (tests.unit.test_exporters.test_owl_exporter.TestExportOWL)
Test export.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/unit/test_exporters/test_owl_exporter.py", line 21, in setUp
    self.extraction_result = pickle.load(f)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/pydantic/main.py", line 816, in __setstate__
    _object_setattr(self, '__pydantic_fields_set__', state['__pydantic_fields_set__'])
KeyError: '__pydantic_fields_set__'

======================================================================
ERROR: test_export (tests.unit.test_exporters.test_rdf_exporter.TestExportRDF)
Test export.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/harry/ontogpt/tests/unit/test_exporters/test_rdf_exporter.py", line 21, in setUp
    self.extraction_result = pickle.load(f)
  File "/home/harry/ontogpt/.venv/lib/python3.9/site-packages/pydantic/main.py", line 816, in __setstate__
    _object_setattr(self, '__pydantic_fields_set__', state['__pydantic_fields_set__'])
KeyError: '__pydantic_fields_set__'

----------------------------------------------------------------------
Ran 19 tests in 23.257s

FAILED (errors=5, skipped=3)