fix broken links, update code example

Also notable is that the Documentation example is out of date.

It links to the [Project](https://github.com/CocoaPods/CocoaPods/blob/master/lib/cocoapods/project.rb#L42) class, but the documentation is quite different from what is actually there.

Just a quick search for `@example` turned up 0 results, so I was unsure as to how to update it.