[SourcesManager] Ensure the master repo is shallow cloned

Closes https://github.com/CocoaPods/CocoaPods/issues/2586.
[Resolver] Take into account versions from all sources (CocoaPods/CocoaPods#2556)
[Resolver] Added tests, notice if the required version exists in multiple sources (CocoaPods/CocoaPods#2556)
[Gemfile] Fetching Core gem version from depending PR https://github.com/CocoaPods/Core/pull/181
[Style] Processed feedback from @segiddins on https://github.com/CocoaPods/CocoaPods/pull/2595