Fix MSA path resolution skipping the 'empty' sentinel value

The jwohlwend#500 change resolved all MSA paths relative to the input file, but
the special 'empty' string (meaning no MSA) was also being resolved as
a file path, breaking inference tests.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: volgin

src/boltz/data/parse/schema.py

@@ -1122,15 +1122,15 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
             msa = items[0][entity_type].get("msa", 0)
             if (msa is None) or (msa == ""):
                 msa = 0
-            if msa != 0:
+            if msa not in (0, "empty"):
                 msa = str((parent / msa).resolve())
 
             # Check if all MSAs are the same within the same entity
             for item in items:
                 item_msa = item[entity_type].get("msa", 0)
                 if (item_msa is None) or (item_msa == ""):
                     item_msa = 0
-                if item_msa != 0:
+                if item_msa not in (0, "empty"):
                     item_msa = str((parent / item_msa).resolve())
 
                 if item_msa != msa: