I cloned a repo from git. Then removed the .git and .gitignore. The podFile looks like
platform :ios, \'6.1\' pod \'AFNetworking\', \'~>1.3.3\' pod \'AFO
As Kirualex worte,you'll find the correct solution on http://blog.cocoapods.org/Repairing-Our-Broken-Specs-Repository/
Short, do the following:
$ pod repo remove master $ pod setup
You could of course also remove the master as described by the others.