Rename `protofiles` config to `inputfiles`

[paulheinr]

Since the code is smart enough to use the corresponding reader based on the file name ending, the config accepts xml as well. The config struct should be renamed to InputFiles and integration tests should read xml files instead of binpb for better readability. One unit test should be created that checks if all 3 file endings (xml, xml.gz, binpb) are accepted and read in.