Fix remaining URL references to use https://w3id.org/valuesets

- Update merged_hierarchy.yaml id and valuesets prefix
- Update merge_enums_hierarchy.py script with correct URLs
- Update sssom_generator.py with correct mapping_set_id
- Update docs and test files

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: dragon-ai-agent

docs/manuscript/manuscript.md

@@ -98,7 +98,7 @@ CVS schemas are authored in YAML following LinkML syntax. Each schema file defin
 
 ```yaml
 name: schema_name
-id: https://w3id.org/linkml/valuesets/domain/schema_name
+id: https://w3id.org/valuesets/domain/schema_name
 prefixes:
   ontology_prefix: http://purl.obolibrary.org/obo/ONTOLOGY_
 

docs/schema/valuesets.yaml

@@ -68947,5 +68947,5 @@ metamodel_version: 1.7.0
 source_file: valuesets.yaml
 source_file_date: '2026-01-30T18:18:29'
 source_file_size: 3472
-generation_date: '2026-01-30T18:19:30'
+generation_date: '2026-01-30T18:35:49'
 

docs/slides/valuesets-slides.pdf

@@ -87,14 +87,14 @@ def build_hierarchical_schema(schema_dir: Path) -> Dict[str, Any]:
 
     # Initialize the merged schema
     merged_schema = {
-        'id': 'https://w3id.org/linkml/valuesets/merged',
+        'id': 'https://w3id.org/valuesets/merged',
         'name': 'valuesets_merged_hierarchy',
         'title': 'Merged Value Sets with Hierarchical Structure',
         'description': 'All value sets merged into a single hierarchical structure with is_a relationships',
         'license': 'MIT',
         'prefixes': {
             'linkml': 'https://w3id.org/linkml/',
-            'valuesets': 'https://w3id.org/linkml/valuesets/',
+            'valuesets': 'https://w3id.org/valuesets/',
         },
         'default_prefix': 'valuesets',
         'imports': ['linkml:types'],