With this patch the Main group of the Pods project is also sorted.

Closes #647
Closes #588

This includes a fix for an issue which caused the use of the incorrect
specification for dependencies from external sources.

Closes #548.

- added support for manifest.lock.
- added support for checking specifications checksums.
- removed lazy repo update as the check for the specifications checksums
  requires an up to date repo.

Closes #604.

Closes #658.

* master:
  corrected some typos
  [Spec] Make green by updating Reachability fixture.
  Fix RubyGems version too old error message to show current version instead of hardcoded value.

Conflicts:
	lib/cocoapods/specification.rb

- handles source logic in a central place.
- the installer does not need to run `pod repo update` anymore.
- similar argument for `pod setup` which now has programmatic access to almost all the needed methods.
- removes a lot of duplicated class-instance methods in the subcommands.

- Moved Project::Library to Pod::Library.
- Removed logic from Pod::Library.
- Restored logic for user build configurations.
- CocoaPods now can infer the platform from the user targets.