feat(scripts): improve types-vocab extraction to derive all vocabulary from schema

- Remove hardcoded type mappings, derive dynamically from LinkML
- Extract keywords from annotations, structured_aliases, and comments
- Add rename_plural_slot.py utility for schema slot renaming

scripts/rename_plural_slot.py

@@ -0,0 +1,201 @@
+#!/usr/bin/env python3
+"""
+Rename a plural slot to singular form following Rule 43.
+
+This script:
+1. Renames the slot file (identifiers.yaml → identifier.yaml)
+2. Updates slot name inside the file
+3. Updates all class files that reference the slot
+4. Preserves natural language descriptions containing the plural word
+
+Usage:
+    python scripts/rename_plural_slot.py identifiers identifier --dry-run
+    python scripts/rename_plural_slot.py identifiers identifier
+"""
+
+import argparse
+import os
+import re
+import sys
+from pathlib import Path
+
+SLOTS_DIR = Path("schemas/20251121/linkml/modules/slots")
+CLASSES_DIR = Path("schemas/20251121/linkml/modules/classes")
+
+
+def rename_slot_file(old_name: str, new_name: str, dry_run: bool = False) -> bool:
+    """Rename the slot YAML file and update its contents."""
+    old_path = SLOTS_DIR / f"{old_name}.yaml"
+    new_path = SLOTS_DIR / f"{new_name}.yaml"
+    
+    if not old_path.exists():
+        print(f"ERROR: Slot file not found: {old_path}")
+        return False
+    
+    if new_path.exists():
+        print(f"ERROR: Target slot file already exists: {new_path}")
+        return False
+    
+    # Read the file
+    content = old_path.read_text()
+    
+    # Update the slot definition inside the file
+    # Pattern 1: id field
+    content = re.sub(
+        rf"^id: (.*/slot/){old_name}$",
+        rf"id: \g<1>{new_name}",
+        content,
+        flags=re.MULTILINE
+    )
+    
+    # Pattern 2: name field (e.g., name: identifiers_slot → name: identifier_slot)
+    content = re.sub(
+        rf"^name: {old_name}_slot$",
+        f"name: {new_name}_slot",
+        content,
+        flags=re.MULTILINE
+    )
+    content = re.sub(
+        rf"^name: {old_name}$",
+        f"name: {new_name}",
+        content,
+        flags=re.MULTILINE
+    )
+    
+    # Pattern 3: slots section - the slot key itself
+    # Be careful: only match when it's a YAML key (followed by :)
+    content = re.sub(
+        rf"^(slots:\s*\n  ){old_name}:",
+        rf"\g<1>{new_name}:",
+        content,
+        flags=re.MULTILINE
+    )
+    # Also handle when the slot key is not right after slots:
+    content = re.sub(
+        rf"^  {old_name}:$",
+        f"  {new_name}:",
+        content,
+        flags=re.MULTILINE
+    )
+    
+    if dry_run:
+        print(f"[DRY-RUN] Would rename: {old_path} → {new_path}")
+        print(f"[DRY-RUN] Updated content preview:")
+        # Show first 30 lines
+        for i, line in enumerate(content.split('\n')[:30], 1):
+            print(f"  {i:3d}| {line}")
+    else:
+        # Write the updated content
+        new_path.write_text(content)
+        # Remove the old file
+        old_path.unlink()
+        print(f"✓ Renamed slot file: {old_path.name} → {new_path.name}")
+    
+    return True
+
+
+def update_class_files(old_name: str, new_name: str, dry_run: bool = False) -> int:
+    """Update all class files that reference the slot."""
+    updated_count = 0
+    
+    for class_file in sorted(CLASSES_DIR.glob("*.yaml")):
+        content = class_file.read_text()
+        original_content = content
+        
+        # Pattern 1: Import statement
+        # - ../slots/identifiers → - ../slots/identifier
+        content = re.sub(
+            rf"^(- \.\./slots/){old_name}$",
+            rf"\g<1>{new_name}",
+            content,
+            flags=re.MULTILINE
+        )
+        
+        # Pattern 2: Slot reference in slots list (under class definition)
+        # slots:
+        #   - identifiers
+        content = re.sub(
+            rf"^(\s+- ){old_name}$",
+            rf"\g<1>{new_name}",
+            content,
+            flags=re.MULTILINE
+        )
+        
+        # Pattern 3: Slot usage as YAML key (indented)
+        # Be careful: only match YAML keys (word at start of logical line, followed by :)
+        # This handles cases like:
+        #       identifiers:
+        #         range: CustodianIdentifier
+        # But NOT: "External identifiers assigned"
+        content = re.sub(
+            rf"^(\s+){old_name}:$",
+            rf"\g<1>{new_name}:",
+            content,
+            flags=re.MULTILINE
+        )
+        
+        # Also handle key with value on same line
+        content = re.sub(
+            rf"^(\s+){old_name}: ",
+            rf"\g<1>{new_name}: ",
+            content,
+            flags=re.MULTILINE
+        )
+        
+        if content != original_content:
+            updated_count += 1
+            if dry_run:
+                print(f"[DRY-RUN] Would update: {class_file.name}")
+                # Show diff-like output
+                old_lines = original_content.split('\n')
+                new_lines = content.split('\n')
+                for i, (old, new) in enumerate(zip(old_lines, new_lines), 1):
+                    if old != new:
+                        print(f"  Line {i}:")
+                        print(f"    - {old}")
+                        print(f"    + {new}")
+            else:
+                class_file.write_text(content)
+                print(f"✓ Updated class: {class_file.name}")
+    
+    return updated_count
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Rename a plural slot to singular form (Rule 43)"
+    )
+    parser.add_argument("old_name", help="Current slot name (e.g., 'identifiers')")
+    parser.add_argument("new_name", help="New slot name (e.g., 'identifier')")
+    parser.add_argument("--dry-run", action="store_true", 
+                       help="Show what would be changed without making changes")
+    
+    args = parser.parse_args()
+    
+    # Change to repo root
+    repo_root = Path(__file__).parent.parent
+    os.chdir(repo_root)
+    
+    print(f"{'='*60}")
+    print(f"Renaming slot: {args.old_name} → {args.new_name}")
+    print(f"Mode: {'DRY-RUN' if args.dry_run else 'LIVE'}")
+    print(f"{'='*60}")
+    
+    # Step 1: Rename slot file
+    print("\n[Step 1] Renaming slot file...")
+    if not rename_slot_file(args.old_name, args.new_name, args.dry_run):
+        sys.exit(1)
+    
+    # Step 2: Update class files
+    print("\n[Step 2] Updating class files...")
+    count = update_class_files(args.old_name, args.new_name, args.dry_run)
+    print(f"\n{'Would update' if args.dry_run else 'Updated'} {count} class files")
+    
+    if args.dry_run:
+        print("\n[DRY-RUN] No changes made. Run without --dry-run to apply changes.")
+    else:
+        print(f"\n✓ Successfully renamed slot: {args.old_name} → {args.new_name}")
+
+
+if __name__ == "__main__":
+    main()