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 'AFOAuth1Client'
After "pod install" I get the following errors:
$ pod install
Analyzing dependencies
[!] Pod::Executable pull
A ALPValidator/0.0.1/ALPValidator.podspec
A APAsyncDictionary/0.0.3/APAsyncDictionary.podspec
A ASCScreenBrightnessDetector/0.1.0/ASCScreenBrightnessDetector.podspec
A AdBrixSDK/3.0.8/AdBrixSDK.podspec
A AlertShortkut/1.0/AlertShortkut.podspec
A AppStoreOpener/0.0.1/AppStoreOpener.podspec
A Appboy-iOS-SDK/2.3.1/Appboy-iOS-SDK.podspec
A Apptimize/1.5.8/Apptimize.podspec
A AtkDragAndDrop/0.1.0/AtkDragAndDrop.podspec
A AuthorizeNet/0.1.0/AuthorizeNet.podspec
A BloodMagic/0.5.2/BloodMagic.podspec
A CKStringUtils/1.1.1/CKStringUtils.podspec
A CMHTMLView/0.2.0/CMHTMLView.podspec
A CTAssetsPickerController/1.5.0/CTAssetsPickerController.podspec
A CTFeedback/1.0.8/CTFeedback.podspec
U CardIO/3.2.0/CardIO.podspec
U CardIO/3.2.2/CardIO.podspec
U CardIO/3.3.0/CardIO.podspec
U CardIO/3.4.1/CardIO.podspec
U CardIO/3.4.3/CardIO.podspec
U CardIO/3.4.4/CardIO.podspec
A CargoBay/2.0.2/CargoBay.podspec
U CocoaSPDY/1.0.0/CocoaSPDY.podspec
A Colours/4.1/Colours.podspec
M CorePlot/1.0/CorePlot.podspec
M CorePlot/1.1/CorePlot.podspec
M CorePlot/1.2/CorePlot.podspec
M CorePlot/1.3/CorePlot.podspec
M CorePlot/1.4/CorePlot.podspec
M DB5/0.0.1/DB5.podspec
A DCTextEngine/0.1.0/DCTextEngine.podspec
A DUIToolbox/0.1.1/DUIToolbox.podspec
M FMDB/2.0/FMDB.podspec
A FXBlurView/1.5.2/FXBlurView.podspec
A FXBlurView/1.5.3/FXBlurView.podspec
A FXKeychain/1.5/FXKeychain.podspec
M Facebook-iOS-SDK/3.9.0/Facebook-iOS-SDK.podspec
A FlatUI/0.1.0/FlatUI.podspec
A FlatUIKit/1.3/FlatUIKit.podspec
A FreeStreamer/1.5.3/FreeStreamer.podspec
A Functional.m/1.0.0/Functional.m.podspec
A GCDWebServer/1.2.1/GCDWebServer.podspec
A GCDWebServer/1.2.2/GCDWebServer.podspec
A GHUnit/0.5.9/GHUnit.podspec
A GlitchKit/0.0.3/GlitchKit.podspec
A GoldenFleece/1.1/GoldenFleece.podspec
A Google-Mobile-Ads-SDK/6.8.0/Google-Mobile-Ads-SDK.podspec
A Heyzap/6.2.2/Heyzap.podspec
A Heyzap/6.2.4/Heyzap.podspec
U IGIdenticon/0.1/IGIdenticon.podspec
A IOSLinkedInAPI/2.0.0/IOSLinkedInAPI.podspec
A JDStatusBarNotification/1.4.7/JDStatusBarNotification.podspec
A JFOpenWeatherMapManager/1.0.0/JFOpenWeatherMapManager.podspec
A JSONJoy/0.1.0/JSONJoy.podspec
A KTBTaskQueue/1.0.0/KTBTaskQueue.podspec
A LINEActivity/0.2.0/LINEActivity.podspec
U LetsMove/1.9/LetsMove.podspec
A LumberjackPrettyClassInformation/1.0.0/LumberjackPrettyClassInformation.podspec
A M13CSVParser/1.0.0/M13CSVParser.podspec
A M13Checkbox/1.0.0/M13Checkbox.podspec
A M13InfiniteTabBar/2.0.1/M13InfiniteTabBar.podspec
A MSCachedAsyncViewDrawing/1.0.1/MSCachedAsyncViewDrawing.podspec
A MSSlidingPanelController/1.1.1/MSSlidingPanelController.podspec
A MUKAdMobViewController/1.2.1/MUKAdMobViewController.podspec
A MUKAdMobViewController/1.2.2/MUKAdMobViewController.podspec
A MUKAdMobViewController/1.2/MUKAdMobViewController.podspec
A MUKToolkit/1.1.1/MUKToolkit.podspec
U MapBox/1.1.0/MapBox.podspec
A NCICharts/1.0.0/NCICharts.podspec
A NSObjectProperties/0.0.3/NSObjectProperties.podspec
A NSOrderedDictionary/1.0.0/NSOrderedDictionary.podspec
A NSOrderedDictionary/1.0.1/NSOrderedDictionary.podspec
A NXOAuth2Client/1.2.5/NXOAuth2Client.podspec
A OCBorghettiView/0.0.5/OCBorghettiView.podspec
A OpenSSL-Universal/1.0.1.f/OpenSSL-Universal.podspec
A PMAudioRecorderViewController/0.5/PMAudioRecorderViewController.podspec
A PXSourceList/2.0.1/PXSourceList.podspec
A PayPal-iOS-SDK/1.4.6/PayPal-iOS-SDK.podspec
A PopulateKit/0.0.1/PopulateKit.podspec
A PopulateKit/0.0.2/PopulateKit.podspec
A PopulateKit/0.0.3/PopulateKit.podspec
A PopulateKit/0.0.4/PopulateKit.podspec
A PubNub/3.5.5/PubNub.podspec
A RMPickerViewController/1.0.0/RMPickerViewController.podspec
A RZSquaresLoading/1.0/RZSquaresLoading.podspec
A RestReaper/0.1.0/RestReaper.podspec
A RestReaper/0.1.1/RestReaper.podspec
A SVBlurView/0.0.1/SVBlurView.podspec
A SatelliteStore/1.0.0/SatelliteStore.podspec
A TPMapsApp/1.0.0/TPMapsApp.podspec
A Taplytics/1.1.0/Taplytics.podspec
A Typhoon/1.7.3/Typhoon.podspec
A Typhoon/1.7.4/Typhoon.podspec
A UICustomizeKit/0.1.0/UICustomizeKit.podspec
A UIImage+Dummy/0.0.2/UIImage+Dummy.podspec
A WJHXCTest/0.0.2/WJHXCTest.podspec
A WYPopoverController/0.1.8/WYPopoverController.podspec
A YISplashScreen/1.2.1/YISplashScreen.podspec
A YandexMobileMetrica/1.2.0/YandexMobileMetrica.podspec
A ZumeroSync/1.1.0.1729/ZumeroSync.podspec
A wpxmlrpc/0.4/wpxmlrpc.podspec
Pull is not possible because you have unmerged files.
Please, fix them up in the work tree, and then use 'git add/rm <file>'
as appropriate to mark resolution, or use 'git commit -a'.
Answer
A bug was found in libgit2 and they had to execute a force push on the specs repo. This is what broke everyone's CocoaPods setup.
You can find the official post about this issue on the CocoaPods blog : http://blog.cocoapods.org/Repairing-Our-Broken-Specs-Repository/
The recommended way to fix your setup is to execute the following commands :
$ pod repo remove master
$ pod setup
If that doesn't work, you can also delete manually all your cached specs :
$ rm -rf ~/.cocoapods/
$ pod setup