Set stalker extension defaults for java projects.

Update README.md to reflect latest changes for stalker extension defaults.
Iterate over all sourceSets instead of hardcoding them.

* Fix bug where classpath directory was incomplete, buildDir.name was used
instead of the buildDir.path
* Improve logging by moving log messages to closure for inputs.
Merge pull request #35 from Lien/set-defaults-java

Set stalker extension defaults for java projects.