Initial shallow clone implementation.
Updated logic and cli output for deepened refs.

findOutdatedRefs will now include refs that need to
be deepened if a depth is specified.
Cleaned up repo depth logic.
Implemented shallow clone for http remotes.
Cleaned up shallow clone implementation

Made some variables more private.
Removed unneeded variables.
Added more javadoc comments.
Added some functional tests for shallow clone.
Merge branch 'ShallowClone' into NewNodeTest

Conflicts:
	src/cli/src/test/java/org/geogit/cli/test/functional/InitSteps.java
	src/core/src/main/java/org/geogit/repository/Repository.java