[SPARK-4672][Core]Checkpoint() should clear f to shorten the serialization chain

The related JIRA is https://issues.apache.org/jira/browse/SPARK-4672

The f closure of `PartitionsRDD(ZippedPartitionsRDD2)` contains a `$outer` that references EdgeRDD/VertexRDD, which causes task's serialization chain become very long in iterative GraphX applications. As a result, StackOverflow error will occur. If we set "f = null" in `clearDependencies()`, checkpoint() can cut off the long serialization chain. More details and explanation can be found in the JIRA.

Author: JerryLead <JerryLead@163.com>
Author: Lijie Xu <csxulijie@gmail.com>

Closes #3545 from JerryLead/my_core and squashes the following commits:

f7faea5 [JerryLead] checkpoint() should clear the f to avoid StackOverflow error
c0169da [JerryLead] Merge branch 'master' of https://github.com/apache/spark
52799e3 [Lijie Xu] Merge pull request #1 from apache/master

(cherry picked from commit 77be8b986fd21b7bbe28aa8db1042cb22bc74fe7)
Signed-off-by: Ankur Dave <ankurdave@gmail.com>