Xcode 8 swift pod headers empty after pod install - xcode

Question

I am trying to compile an existing xcode project written in swift. The project uses Alamofire. I installed xcode 8 beta and opened the project. There were many errors with Alamofire which I learned need to be updated to version 3.2.1.
I edited my Podfile and fixed the version number then ran pod update alamofire. Instead of only updating Alomfire, every pod was updated. This is apparently a bug.
The Podfile contains the directive use_frameworks! After updating the pods, the pods/headers directory was completely empty, without either Public or Private directories and the project failed to build with 356 missing file errors.
Changing the build search settings for ALWAYS_SEARCH_USER_PATHS to no (or yes) in accordance with a recommendation here https://github.com/CocoaPods/CocoaPods/issues/4605#issuecomment-208822149 then deleting the pods and running pod install again did nothing.
There are a number of different questions on stackoverflow asking the same question with no answers. Here is a list of the ones I can find.
Pods/Headers empty after pod install
Empty Pod Headers Folder after `pod install`
After pod install Public folder is empty
From Pods-Myproject.debug.xconfig
EMBEDDED_CONTENT_CONTAINS_SWIFT = YES
FRAMEWORK_SEARCH_PATHS = $(inherited) "$PODS_CONFIGURATION_BUILD_DIR/AFNetworking" "$PODS_CONFIGURATION_BUILD_DIR/Alamofire" "$PODS_CONFIGURATION_BUILD_DIR/Bolts-iOS8.0" "$PODS_CONFIGURATION_BUILD_DIR/CocoaLumberjack" "$PODS_CONFIGURATION_BUILD_DIR/DBAlertController-iOS8.0" "$PODS_CONFIGURATION_BUILD_DIR/FBSDKCoreKit-iOS8.0" "$PODS_CONFIGURATION_BUILD_DIR/FBSDKLoginKit-iOS8.0" "$PODS_CONFIGURATION_BUILD_DIR/ISO8601DateFormatterValueTransformer" "$PODS_CONFIGURATION_BUILD_DIR/MBProgressHUD" "$PODS_CONFIGURATION_BUILD_DIR/RESideMenu-iOS8.0" "$PODS_CONFIGURATION_BUILD_DIR/RKValueTransformers" "$PODS_CONFIGURATION_BUILD_DIR/RestKit" "$PODS_CONFIGURATION_BUILD_DIR/SOCKit" "$PODS_CONFIGURATION_BUILD_DIR/TransitionKit" "$PODS_CONFIGURATION_BUILD_DIR/iCarousel-iOS8.0" "${PODS_ROOT}/Crashlytics/iOS" "${PODS_ROOT}/Fabric/iOS"
GCC_PREPROCESSOR_DEFINITIONS = $(inherited) COCOAPODS=1
HEADER_SEARCH_PATHS = $(inherited) "${PODS_ROOT}/Headers/Public" "${PODS_ROOT}/Headers/Public/Crashlytics" "${PODS_ROOT}/Headers/Public/Fabric"
LD_RUNPATH_SEARCH_PATHS = $(inherited) '#executable_path/Frameworks' '#loader_path/Frameworks'
OTHER_CFLAGS = $(inherited) -iquote "$PODS_CONFIGURATION_BUILD_DIR/AFNetworking/AFNetworking.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/Alamofire/Alamofire.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/Bolts-iOS8.0/Bolts.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/CocoaLumberjack/CocoaLumberjack.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/DBAlertController-iOS8.0/DBAlertController.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/FBSDKCoreKit-iOS8.0/FBSDKCoreKit.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/FBSDKLoginKit-iOS8.0/FBSDKLoginKit.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/ISO8601DateFormatterValueTransformer/ISO8601DateFormatterValueTransformer.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/MBProgressHUD/MBProgressHUD.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/RESideMenu-iOS8.0/RESideMenu.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/RKValueTransformers/RKValueTransformers.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/RestKit/RestKit.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/SOCKit/SOCKit.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/TransitionKit/TransitionKit.framework/Headers" -iquote "$PODS_CONFIGURATION_BUILD_DIR/iCarousel-iOS8.0/iCarousel.framework/Headers" -isystem "${PODS_ROOT}/Headers/Public" -isystem "${PODS_ROOT}/Headers/Public/Crashlytics" -isystem "${PODS_ROOT}/Headers/Public/Fabric"
OTHER_LDFLAGS = $(inherited) -ObjC -l"c++" -l"z" -framework "AFNetworking" -framework "Alamofire" -framework "Bolts" -framework "CocoaLumberjack" -framework "Crashlytics" -framework "DBAlertController" -framework "FBSDKCoreKit" -framework "FBSDKLoginKit" -framework "Fabric" -framework "ISO8601DateFormatterValueTransformer" -framework "MBProgressHUD" -framework "RESideMenu" -framework "RKValueTransformers" -framework "RestKit" -framework "SOCKit" -framework "Security" -framework "SystemConfiguration" -framework "TransitionKit" -framework "UIKit" -framework "iCarousel"
OTHER_SWIFT_FLAGS = $(inherited) "-D" "COCOAPODS"
PODS_BUILD_DIR = $BUILD_DIR
PODS_CONFIGURATION_BUILD_DIR = $PODS_BUILD_DIR/$(CONFIGURATION)$(EFFECTIVE_PLATFORM_NAME)
PODS_ROOT = ${SRCROOT}/Pods
I really need to find a solution to this problem so I would be grateful if anybody can answer this question.

Answer 1

git add -A followed by Product -> Clean removed all errors except Alamofire.

Answer 2

When you want to update a particular POD, you run pod update PODNAME as given in the Docs. I suggest you delete all the pods and run pod install with the latest version of Alamofire.