Can't archive after migrating to CocoaPods

We have recently migrated to CocoaPods to make dependencies simpler. It worked very well until today when we tried to archive it for crashlytics. I am using Xcode 6.

I keep getting ld: library not found for -lsqlite3

This is how I have set my Podfile

platform :ios, "7.0"
platform :ios, :deployment_target => '7.0'
target "F11i" do
pod 'NSData+Base64', '~> 1.0'
pod 'Facebook-iOS-SDK', '~> 3.18'
pod 'CrashlyticsFramework', '~> 2.2'
pod 'Localytics-AMP', '~> 2.60'
end

target "F11iTests" do
pod 'NSData+Base64', '~> 1.0'
pod 'Facebook-iOS-SDK', '~> 3.18'
pod 'CrashlyticsFramework', '~> 2.2'
pod 'Localytics-AMP', '~> 2.60'
end

After running pod install, this is what I see:

Analyzing dependencies
Downloading dependencies
Using Bolts (1.1.2)
Using CrashlyticsFramework (2.2.4)
Using Facebook-iOS-SDK (3.18.0)
Using Localytics-AMP (2.60.0)
Using NSData+Base64 (1.0.0)
Generating Pods project
Integrating client project

I am opening the project via xcworkspace

I tried the solution suggested here, but I dont see any $(TARGET_BUILD_DIR) in first place in the suggested solution.

Any advice please?

UPDATE LIBRARY_SEARCH_PATHS looks like this:

Following our comment chain, you have a bad install of Xcode.

The Platform SDK for devices is missing at least 1 file that is in the Platform SDK for the simulator. Who knows what else is wrong.

My suggestion is delete Xcode and do a fresh install from Apple.