Merged 12_check_phase.tll files.

[EttoreM]

This PR addresses #79.

The work done for this PR consists only of flattening the ttl files pertaining to the 12_check_phase ruleset with no change in the code, apart from moving sh:severity from the SPARQL constraints to the parent sh:NodeShape , when needed.

Currently there are 4 tests failing

FAILED tests/integration/profiles/five-safes-crate/test_5src_1_root_data_entity_metadata.py::test_5src_root_data_entity_source_organization_not_organization - AssertionError: RO-Crate should be invalid
FAILED tests/integration/profiles/five-safes-crate/test_5src_2_requesting_agent.py::test_createaction_does_not_have_agent - AssertionError: RO-Crate should be invalid
FAILED tests/integration/profiles/five-safes-crate/test_5src_2_requesting_agent.py::test_createaction_agent_is_not_person - AssertionError: RO-Crate should be invalid
FAILED tests/integration/profiles/five-safes-crate/test_5src_2_requesting_agent.py::test_agent_affiliation_not_organization - AssertionError: RO-Crate should be invalid

None of these is directly related to the ruleset in question.