I know that the GitHub web interface lets you search all repositories for files with a particular pathname (e.g. searching for path:/app/models/user.rb yields >
path:/app/models/user.rb
In search input, you can use filename parameter to search in multiple repositories, for example:
filename
filename:my_filename.txt
If you're looking for a filename in specific repository, you can just press t and start typing the file name (see: GH keyboard shortcuts).