Fix: Ensure all skills are tracked as files, not submodules

skills/loki-mode/benchmarks/results/2026-01-05-00-49-17/humaneval-solutions/53.py

@@ -0,0 +1,8 @@
+def add(x: int, y: int):
+    """Add two numbers x and y
+    >>> add(2, 3)
+    5
+    >>> add(5, 7)
+    12
+    """
+    return x + y