[WIP][SPARK-1594] Cleaning up MLlib APIs and guide

Final pass before the v1.0 release.

* Remove `VectorRDDs`
* Move `BinaryClassificationMetrics` from `evaluation.binary` to `evaluation`
* Mark main methods experimental
* Change default value of `addIntercept` to false and allow to add intercept in Ridge and Lasso.
* Clean `DecisionTree` package doc and test suite.
* ...