Q:

podfile gives an error on install

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'.

A:

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

A:

Take a look up the quick fix here !
https://github.com/CocoaPods/Specs/issues/1268
rm -rf ~/.cocoapods/

A:

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.

