[SPARK-5604[MLLIB] remove checkpointDir from LDA

[mengxr]

checkpointDir is a Spark global configuration. Users should set it outside LDA. This PR also hides some methods under private[clustering] object LDA, so they don't show up in the generated Java doc (SPARK-5610).

@jkbradley

[SparkQA]

Test build #26834 has started for PR 4390 at commit a34bb39.

• This patch merges cleanly.

[SparkQA]

Test build #26834 has finished for PR 4390 at commit a34bb39.

• This patch fails to build.
• This patch merges cleanly.
• This patch adds no public classes.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/26834/
Test FAILed.

[mengxr]

test this please

[SparkQA]

Test build #26838 has started for PR 4390 at commit a34bb39.

• This patch merges cleanly.

[SparkQA]

Test build #26838 has finished for PR 4390 at commit a34bb39.

• This patch passes all tests.
• This patch merges cleanly.
• This patch adds no public classes.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/26838/
Test PASSed.

[jkbradley]

The changes LGTM

One question: Does private[clustering] on "object LDA" not hide stuff in Java docs because it's an object (not a class)?

[mengxr]

genjavadoc maps methods to Java public/protect/private. I haven't found a way to hide public methods under a package private companion object yet ...

[mengxr]

Merged into master and branch-1.3.