Update generated timestamp in manifest.json

frontend/public/schemas/20251121/linkml/manifest.json

@@ -1,5 +1,5 @@
 {
-  "generated": "2026-01-29T16:10:26.031Z",
+  "generated": "2026-01-29T16:40:47.585Z",
   "schemaRoot": "/schemas/20251121/linkml",
   "totalFiles": 3003,
   "categoryCounts": {

scripts/trace_dead_links.py

@@ -0,0 +1,82 @@
+import os
+import re
+import glob
+
+ARCHIVE_DIR = "/Users/kempersc/apps/glam/schemas/20251121/linkml/modules/slots/archive/"
+CLASSES_DIR = "/Users/kempersc/apps/glam/schemas/20251121/linkml/modules/classes/"
+
+def get_archived_slot_names():
+    slots = set()
+    files = os.listdir(ARCHIVE_DIR)
+    for f in files:
+        if not f.endswith(".yaml"):
+            continue
+        # Filename pattern: name.yaml or name_archived_YYYYMMDD.yaml
+        name = f[:-5] # remove .yaml
+        if "_archived_" in name:
+            name = name.split("_archived_")[0]
+        slots.add(name)
+    return slots
+
+def find_references(archived_slots):
+    references = {} # {slot_name: [file_paths]}
+    
+    class_files = glob.glob(os.path.join(CLASSES_DIR, "*.yaml"))
+    
+    for cls_file in class_files:
+        with open(cls_file, 'r') as f:
+            lines = f.readlines()
+            
+        for i, line in enumerate(lines):
+            stripped = line.strip()
+            
+            # Check for imports: "- ../slots/slotname"
+            # Check for slot usage: "- slotname" (in slots list)
+            # Check for slot_usage keys: "slotname:"
+            
+            for slot in archived_slots:
+                # Import check
+                if f"../slots/{slot}" in stripped and not stripped.strip().startswith("#"):
+                    if slot not in references: references[slot] = []
+                    references[slot].append(f"{cls_file} (line {i+1}): Import")
+                    continue
+                
+                # Loose usage check (can be false positive if slot name is common word like 'description')
+                # But we restrict to archived slots.
+                
+                # Check for "- slotname"
+                if stripped == f"- {slot}":
+                    if slot not in references: references[slot] = []
+                    references[slot].append(f"{cls_file} (line {i+1}): Usage in slots list")
+                    continue
+                    
+                # Check for "slotname:"
+                if stripped.startswith(f"{slot}:"):
+                    if slot not in references: references[slot] = []
+                    references[slot].append(f"{cls_file} (line {i+1}): Usage as key")
+                    continue
+
+    return references
+
+def main():
+    print("Identifying archived slots...")
+    slots = get_archived_slot_names()
+    print(f"Found {len(slots)} archived slots.")
+    
+    # Filter out common false positives if necessary, but better to check everything
+    # 'description' is a common metadata field, but if it's archived as a slot, we should use has_or_had_description
+    
+    print("Scanning class files for references...")
+    refs = find_references(slots)
+    
+    if refs:
+        print(f"Found {len(refs)} archived slots still referenced in classes:")
+        for slot, locations in refs.items():
+            print(f"\nSLOT: {slot}")
+            for loc in locations:
+                print(f"  {loc}")
+    else:
+        print("No dead links found.")
+
+if __name__ == "__main__":
+    main()