The "file has to end with newline" should not be triggered if a file does not contain anything.

if the file size is 0 bytes, that file does not contain lines of text (as for example defined by posix: https://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_206) and thus does not have to end in a newline.

the problem occurs for example in protoc-generated c#-code - for some reason the protobuf compiler creates some empty (0bytes) files and these then trigger the error.

Obviously, if these files would contain a line marking the file as autogenerated the check would be all right, because the file would not be empty anymore.