diff --git a/README.md b/README.md
index a68f876..77f14da 100644
--- a/README.md
+++ b/README.md
@@ -83,7 +83,8 @@ LoD2 CityGML tiles can be converted to GLB per tile while preserving roof/wall s
    ```bash
    for f in work/cityjson/*.city.json; do
      base="$(basename "$f" .city.json)"
-     uv run cjio "$f" upgrade triangulate vertices_clean \
+     input_json="$f/$base.json"  # citygml-tools writes a .json inside the .city.json folder
+     uv run cjio "$input_json" upgrade triangulate vertices_clean \
        save "work/cityjson_tri/${base}.tri.city.json"
    done
    ```
diff --git a/scripts/split_semantics.py b/scripts/split_semantics.py
index 2bc1948..c25245f 100644
--- a/scripts/split_semantics.py
+++ b/scripts/split_semantics.py
@@ -41,8 +41,8 @@ def parse_args(argv: Iterable[str] | None = None) -> argparse.Namespace:
     )
     parser.add_argument(
         "--pattern",
-        default="*.city.json",
-        help="Glob pattern for input files (defaults to all .city.json files).",
+        default="**/*.json",
+        help="Glob pattern for input files (defaults to any .json under the input dir).",
     )
     return parser.parse_args(argv)
 
@@ -65,9 +65,26 @@ def base_name(path: Path) -> str:
         return name[: -len(".tri.city.json")]
     if name.endswith(".city.json"):
         return name[: -len(".city.json")]
+    if name.endswith(".json"):
+        return name[: -len(".json")]
     return path.stem
 
 
+def resolve_input_file(path: Path) -> Path | None:
+    """Handle both flat files and citygml-tools style output directories."""
+    if path.is_file():
+        return path
+    if path.is_dir():
+        # citygml-tools writes <name>.city.json/<name>.json
+        candidate = path / f"{path.stem}.json"
+        if candidate.is_file():
+            return candidate
+        matches = list(path.glob("*.json"))
+        if len(matches) == 1:
+            return matches[0]
+    return None
+
+
 def allowed_semantic_indices(semantics: dict[str, Any], allowed_types: set[str]) -> set[int]:
     surfaces = semantics.get("surfaces") or []
     return {idx for idx, surface in enumerate(surfaces) if surface.get("type") in allowed_types}
@@ -156,7 +173,12 @@ def filter_cityjson(cityjson: dict[str, Any], allowed_types: set[str]) -> dict[s
 
 
 def process_file(path: Path, targets: list[str], output_dir: Path) -> int:
-    cityjson = read_json(path)
+    resolved = resolve_input_file(path)
+    if not resolved:
+        print(f"[skip] cannot resolve CityJSON file for {path}", file=sys.stderr)
+        return 0
+
+    cityjson = read_json(resolved)
     written = 0
     base = base_name(path)
 
diff --git a/scripts/verify_pipeline.py b/scripts/verify_pipeline.py
index 4351273..5831c61 100644
--- a/scripts/verify_pipeline.py
+++ b/scripts/verify_pipeline.py
@@ -86,9 +86,22 @@ def discover_tiles(raw_dir: Path, provided: Sequence[str] | None) -> list[str]:
     return sorted(path.stem for path in raw_dir.glob("LoD2_*.gml"))
 
 
+def path_exists(path: Path) -> bool:
+    if path.exists():
+        return True
+    if path.is_dir():
+        return True
+    # citygml-tools may output a directory named *.city.json containing a *.json
+    if path.suffixes == [".city", ".json"]:
+        candidate = path / f"{path.stem}.json"
+        if candidate.exists():
+            return True
+    return False
+
+
 def collect_missing(tile_ids: Sequence[str], directory: Path, pattern: str) -> list[Path]:
     expected = [directory / pattern.format(tile_id=tile_id) for tile_id in tile_ids]
-    return [path for path in expected if not path.exists()]
+    return [path for path in expected if not path_exists(path)]
 
 
 def summarize_missing(label: str, missing: list[Path]) -> str: