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Shameless plug, searchco.de allows you to search over github's public repositories,

Filename search is available for all repositories - hit "t" and start typing your search query. It's fantastic.

A "search source code" box is available for my paid for private repos, so I guess it's a premium feature.

Thank you!

Code search is available - if somewhat hidden. Add /search to the end of the repository url on github (eg. https://github.com/rails/rails/search ).

On any repo page you can just press t and you can search by filename.

for filename, go to the repository (code) window and press 't' , it will give you a command-t type interface to search for filenames in the project.