The first question I'd have to ask back is, how are you expecting to have splunk see ANY files?
One way would be to have a script copy the directory to a file, then process the file.
For windows/dos shell commands,here's a page with a list of the switches that show hidden files and directories -
for unix/linux, it is LS with the -a flag.
See more at wikipedia here - https://en.wikipedia.org/wiki/Hidden_file_and_hidden_directory
... View more