Clean up method names and variables

- Rename GetChangedFiles to Changes
- Rename GetChangedFilesTests to ChangesTests
- Rename getModifiedFiles to getChangedFiles
- Rename usages() to findUsages()
Deprecate afterStalk and add a message
Fix build.gradle

- Add mavenCentral() to repositories for buildscript to allow
  Stalker to use its own dependencies.

- Add source roots for Groovy source files.
Move final logging out to StalkerPlugin

Clean up info logging in Usages
Log when a file is skipped

Files are skipped when they are not found in any source roots.
This logs tells the user when this happens.