Refresh model files for 1.11.0-rc3

[matentzn]

Regenerates the generated artifacts under linkml_model/ against the current source schemas in linkml_model/model/schema/ for the upcoming 1.11.0-rc3 release. Two real changes plus some cleanup:

1. Picks up the permissivle → permissible typo fix from Fix mistyping in MatchQuery description #249. That PR fixed the typo in meta.yaml but didn't refresh the downstream generated artifacts. This PR propagates the fix into meta.py, jsonld/meta.jsonld, jsonschema/meta.schema.json, protobuf/meta.proto, owl/meta.owl.ttl, shacl/meta.shacl.ttl, and sqlschema/meta.sql.

2. Populates linkml_model/array.py. The file existed but was empty — array.yaml has been part of the schema source for a while but the Python module was never generated from it (see Fix equals_string on enum-ranged array_linearization_order #251). Now it ships properly (285 lines).

3. Removes stale linkml_model/rdf/ and linkml_model/sqlddl/. These directories haven't been refreshed since 2023, are not part of the current gen_project_config.yaml flow, and were drifting (e.g. still contained the old permissivle typo). See linkml/linkml-model#<NEW_ISSUE> for the rationale and a heads-up to downstream consumers. The current rdf/-equivalent surface is covered by owl/, shacl/, and jsonld/; the SQL output lives in sqlschema/. See [LinkML-model] Remove stale linkml_model/rdf/ and linkml_model/sqlddl/ artifacts linkml#3475.

[amc-corey-cox]

This looks good to me. Claude pointed out to me that we now have a few files named in linkml_files.py that we just deleted so they now don't exist. Might be nice to clean that up but it's just a nit. This is ready to go.

[amc-corey-cox]

Removing rdf/ and sqlddl/ leaves dangling references in linkml_model/linkml_files.py, which is part of the public API:

• Format.NATIVE_RDF, Format.RDF, Format.SQLDDL (enum entries, lines 41/48/52)
• _Path.NATIVE_RDF, _Path.RDF, _Path.SQLDDL (_PathInfo mappings, lines 67/74/78)
• Format.SQLDDL is in the META_ONLY tuple (line 100)
• ModelFile.model_rdf() and ModelFile.rdf() accessors (lines 230/250)

After this merges, calls like LOCAL_PATH_FOR(Source.META, Format.RDF) will silently return paths to files that no longer exist. tests/test_linkml_files.py:52 still references Format.RDF; the test happens to pass only because it asserts on URL-string construction, not file existence.

Could you either drop these enum entries / accessors (with a short deprecation note in CHANGELOG/release notes) or keep the directories? Whichever way, the in-repo API surface should match what's on disk.

[matentzn]

I will wait for @dalito to re-assure me that removal is the right path over "revival" and then I will deal with this! Thank you @amc-corey-cox

[rly]

This and the other generated Python files that I looked at report a metamodel version of 1.7.0. I think this should be updated to 1.11.0.

[rly]

One minor comment above about metamodel_version in the python files, but otherwise the array parts that I am knowledgeable about look good to me.