compiler: do not overwrite top level __init__.py

Resolves: #168 #260

Author: Gobot1234

src/betterproto/plugin/parser.py

@@ -131,6 +131,7 @@ def generate_code(request: CodeGeneratorRequest) -> CodeGeneratorResponse:
         directory.joinpath("__init__.py")
         for path in output_paths
         for directory in path.parents
+        if not directory.joinpath("__init__.py").exists()
     } - output_paths
 
     for init_file in init_files: