diff --git a/src/appendices/entity-table.md b/src/appendices/entity-table.md
index 549b0685fb..bf69bdc863 100644
--- a/src/appendices/entity-table.md
+++ b/src/appendices/entity-table.md
@@ -61,7 +61,3 @@ while entity definitions are in the [Entities Appendix](entities.md).
 ## Motion
 
 {{ MACROS___make_entity_table(datatypes=["motion"]) }}
-
-## Stimulus Files
-
-{{ MACROS___make_entity_table(datatypes=["stimuli"]) }}
diff --git a/tools/mkdocs_macros_bids/macros.py b/tools/mkdocs_macros_bids/macros.py
index 03d0ddc57b..6395ca9641 100644
--- a/tools/mkdocs_macros_bids/macros.py
+++ b/tools/mkdocs_macros_bids/macros.py
@@ -112,7 +112,18 @@ def make_root_filename_template(
     if src_path is None:
         src_path = _get_source_path()
 
-    schema_obj = schema.load_schema()
+    # Load schema with explicit path to avoid caching issues
+    import os
+
+    schema_path = os.path.join(
+        os.path.dirname(os.path.dirname(os.path.dirname(__file__))),
+        "src",
+        "schema.json",
+    )
+    if os.path.exists(schema_path):
+        schema_obj = schema.load_schema(schema_path)
+    else:
+        schema_obj = schema.load_schema()
 
     # Look for rules that have a specific path (root-level organization)
     target_path = kwargs.get("path", "stimuli")  # Default to stimuli
@@ -147,17 +158,30 @@ def make_root_filename_template(
                     template_lines.append(f"    {rule.stem}{ext}")
 
         elif hasattr(rule, "suffixes"):
-            # Handle entity-based files (like stim-<label>_audio.wav)
+            # Handle entity-based files generically using entity definitions from schema
             entities_part = ""
             if hasattr(rule, "entities"):
                 entity_parts = []
                 for entity_name, requirement in rule.entities.items():
-                    if entity_name == "stimulus":
-                        entity_parts.append("stim-<label>")
-                    elif entity_name == "part":
-                        entity_parts.append("[_part-<label>]")
-                    elif entity_name == "annotation":
-                        entity_parts.append("_annot-<label>")
+                    # Look up the entity in the schema to get its prefix and format
+                    if entity_name in schema_obj.objects.entities:
+                        entity_def = schema_obj.objects.entities[entity_name]
+                        entity_prefix = entity_def.get("name", entity_name)
+                        entity_format = entity_def.get("format", "label")
+
+                        # Format based on requirement (required vs optional)
+                        if requirement == "optional":
+                            entity_parts.append(f"[_{entity_prefix}-<{entity_format}>]")
+                        else:
+                            # First entity doesn't need underscore prefix
+                            if not entity_parts:
+                                entity_parts.append(
+                                    f"{entity_prefix}-<{entity_format}>"
+                                )
+                            else:
+                                entity_parts.append(
+                                    f"_{entity_prefix}-<{entity_format}>"
+                                )
                 entities_part = "".join(entity_parts)
 
             for suffix in rule.suffixes:
@@ -353,7 +377,18 @@ def make_sidecar_table(table_name, src_path=None):
     if src_path is None:
         src_path = _get_source_path()
 
-    schema_obj = schema.load_schema()
+    # Load schema with explicit path to avoid caching issues
+    import os
+
+    schema_path = os.path.join(
+        os.path.dirname(os.path.dirname(os.path.dirname(__file__))),
+        "src",
+        "schema.json",
+    )
+    if os.path.exists(schema_path):
+        schema_obj = schema.load_schema(schema_path)
+    else:
+        schema_obj = schema.load_schema()
     table = render.make_sidecar_table(schema_obj, table_name, src_path=src_path)
     return table
 
@@ -412,7 +447,18 @@ def make_columns_table(table_name, src_path=None):
     if src_path is None:
         src_path = _get_source_path()
 
-    schema_obj = schema.load_schema()
+    # Load schema with explicit path to avoid caching issues
+    import os
+
+    schema_path = os.path.join(
+        os.path.dirname(os.path.dirname(os.path.dirname(__file__))),
+        "src",
+        "schema.json",
+    )
+    if os.path.exists(schema_path):
+        schema_obj = schema.load_schema(schema_path)
+    else:
+        schema_obj = schema.load_schema()
     table = render.make_columns_table(schema_obj, table_name, src_path=src_path)
     return table
 
diff --git a/tools/schemacode/src/bidsschematools/render/tables.py b/tools/schemacode/src/bidsschematools/render/tables.py
index e650136fc1..e7ab4062b4 100644
--- a/tools/schemacode/src/bidsschematools/render/tables.py
+++ b/tools/schemacode/src/bidsschematools/render/tables.py
@@ -309,6 +309,10 @@ def make_entity_table(schema, tablefmt="github", src_path=None, **kwargs):
         if not suffixes:
             continue
 
+        # Skip rules that don't have datatypes (e.g., stimuli rules with path-based organization)
+        if not hasattr(rule, "datatypes"):
+            continue
+
         entities = []
         for ent in schema.rules.entities:
             val = rule.entities.get(ent, "")
diff --git a/tools/schemacode/src/bidsschematools/render/text.py b/tools/schemacode/src/bidsschematools/render/text.py
index 6333869f23..6b889cf560 100644
--- a/tools/schemacode/src/bidsschematools/render/text.py
+++ b/tools/schemacode/src/bidsschematools/render/text.py
@@ -324,6 +324,9 @@ def make_filename_template(
     file_rules = schema.rules.files[dstype]
     file_groups = {}
     for rule in file_rules.values(level=2):
+        # Skip rules that don't have datatypes (e.g., stimuli rules with path-based organization)
+        if not hasattr(rule, "datatypes"):
+            continue
         for datatype in rule.datatypes:
             file_groups.setdefault(datatype, []).append(rule)
 
diff --git a/tools/schemacode/src/bidsschematools/tests/test_render_text.py b/tools/schemacode/src/bidsschematools/tests/test_render_text.py
index e4029e49f6..299f1de7e7 100644
--- a/tools/schemacode/src/bidsschematools/tests/test_render_text.py
+++ b/tools/schemacode/src/bidsschematools/tests/test_render_text.py
@@ -93,6 +93,7 @@ def test_make_filename_template(schema_obj, schema_dir, placeholders):
     datatypes = {
         datatype
         for rule in schema_obj.rules.files.raw.values(level=2)
+        if hasattr(rule, "datatypes")  # Skip rules without datatypes (e.g., stimuli)
         for datatype in rule.datatypes
     }