[Installer] Copy Podfile.lock to Manifest.lock rather than using #wri…

[Cache] Fix the cache to handle re-downloads properly

Just remove write permissions from files, so executables are unaffected

[Installer] Check for regular file on lock

[UI] Disambiguate gem and pod updates

This patch check if a file is a regular file instead of checking if the file is a
directory.

It fixes a crash when the file being analysed is a broken symbolic link.

[Sandbox::FileAccessor] Add missing `.cc` extension for C++ to `SOURCE_FILE_EXTENSIONS`.

[TargetIntegrator] Only embed application and unit test bundle targets

[pod] Write the UTF-8 warning to stderr, rather than stdout.

[Executable] Get rid of redundant run calls

This means operations like:

   POD_VERSION="`pod --version`"

Work correctly even if LANG isn't set (e.g. within Jenkins).

Closes https://github.com/CocoaPods/CocoaPods/issues/3477

[Cache] Keep files needed by subspecs that have a higher minimum deploym...

After creating the private config file, apply it as a base_configuration_reference for all resource_bundle_targets of the pod.