[TargetIntegrator] Ensure to reset the contents of the Manifest.lock Script Phase

Always codesign if target is codesigned, not just if required.

Fixes an issue which prevented using a custom `CONFIGURATION_BUILD_DIR` when integrating CocoaPods via dynamic frameworks.

Support for the new `watchos` platform

Skipped by `examples:build` for now, because it breaks with Xcode < 7.0

This reverts commit 782576c4bf19421534de0b34bba1895ee6df711b.

Fixes #3646.

Closes https://github.com/CocoaPods/CocoaPods/issues/3689.

[Command] Ensure warnings are printed even when theres an exception

Deduplicate pod targets