Add debug logging in ClassfileManager

Add logging of various operations the transactional class file manager is
doing. You can pass logger to be used by the transactional class file
manager by using overloaded definition of `ClassfileManager.transactional`
method. The old overload has been deprecated.

The factory methods for class file manager in IncOptions companion object
has been deprecated in favor of using ClassfileManager companion object
directly. The code in Defaults.scala has been updated to use non-deprecated
methods. The logging is turned off by default.

The canonical way of enabling transactional class file manager in sbt
project is:

```
incOptions := incOptions.value.withNewClassfileManager(
  sbt.inc.ClassfileManager.transactional(
    crossTarget.value / "classes.bak",
    (streams in (compile, Compile)).value.log
  )
)
```

It's a bit verbose which shows that the api for this is not the best.
However, I don't expect sbt users to need this code very often.

This patch should help debug the problem described in #1184