If a folder is given as an input path to GiraphFileInputFormat, the default hidden file filter is not applied to the files in the folder. That is, hidden files (e.g. files preceded by underscores) that would not normally be handled if targeted directly are unexpectedly being passed as input if the parent folder is targeted instead.
I would expect that when a folder is specified as input, only non-hidden files in that folder will be processed. This is consistent with the base hadoop FileInputFormat.