Rename LogEngineCollection to LogEngineRegistry

In preparation for converting the logging collection into the newer
style registry rename the internal property and collection class.
Deprecate several Log methods.

Having both loaded/enabled modes makes Log more complex than it needs to
be. There are very few cases where you need to disable/enable loggers.
These can generally be solved by droping loggers.
Remove deprecated method use.

Stop calling deprecated features of Log.
Convert Log to use new Registry object.

Update the registry and Log to use the new Registry base class.
Remove dependency on Configure for logging.

Not using Configure to setup logging has a couple benefits.

* Using Configure creates magic at a distance. Setting things in one
  class creates effects in another.
* Loggers at bootstrap and loggers created at runtime are handled
  consistently.
* Dropped loggers don't magically re-create themselves once Log has been
  reset.
* It is still simple to create loggers using configuration files, or
  inject instances directly.

With this change we are still able to lazily load loggers once Log is
used.
Remove dependency on Configure from Cache.

Not using Configure to setup caching has a couple benefits.

* Using Configure creates magic at a distance. Setting things in one
  class creates effects in another.
* Cache engines are always configured the same way.
* Dropped cache engines don't magically re-create themselves.
* It is still simple to create cache adapters using configuration files, or
  inject instances directly.

With this change we still lazily load cache adapters once they are
used. Add a CacheRegistry to make Cache similar to log and other registy
based classes in CakePHP.
Remove now useless methods from UpgradeShell.
Add missing import.
Fix coding standards error.
Add some newlines around conditionals that return.
Fix failing tests caused by Cache/Log changes.

Use mocks where possible to make tests simpler and hit the filesystem
less frequently.
Merge branch '3.0' into 3.0-logcollection
Convert trigger_error to an exception.
Merge pull request #1517 from markstory/3.0-logcollection

3.0 - Use registry objects in Cache & Log and remove Configure based configuration.