Add JGit as a compile-time dependency
Implement diff-tree using JGit

- Add tests
Throw UnknownRepositoryException for invalid repo

Throw the exception when either the commit id could not be resolved or
the repository is invalid.

- Rename test method names

- Use single quotes for literals and double-quotes for GStrings
Refactor getChanges

- Rename to getModifiedFiles

- Add helper methods: getCommit and getFromCommit

Throw exceptions for the error cases:

- Local repo not found
- Invalid revision string
Use files as input instead of outputStream

- Remove unused outputStream field
Add info logging to GetChangedFiles task
Add logging explaining why the stalk task might be skipped
Set stalker extension defaults for java projects.

Update README.md to reflect latest changes for stalker extension defaults.
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.
Make afterStalk inclusive with printing output
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.
Rename Tasks

By convention, Tasks should be named as verbs.

- Changes => DetectChanges
- Usages => Inspect
Rename methods and fields

- Remove unused Inspect.files property

- Rename Inspect.classNames to Inspect.affectedClasses and leave
  a comment

- Rename TaskAction methods
Reverse order of from and to commits in log

The log should read: "from..to"
Merge pull request #35 from Lien/set-defaults-java

Set stalker extension defaults for java projects.
Remove afterStalk Closure field

This field should no longer be used.