remove deprecations from trunk [LUCENE-4095]

We should remove the deprecated code from trunk.

This also has benefits to 4x branch, particularly:
- we should backport fixes to tests to avoid deprecated methods, e.g. IndexReader.open -> DirectoryReader.open. Of course I will add specific deprecated tests testing the back compat. This is all very important to
ensure easier merging from trunk->4x for the future.
- by removing deprecated methods, I found some minor doc bugs, such as javadocs linking to deprecated stuff. I would like to backport these docs fixes as well.

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Migrated from [LUCENE-4095](https://issues.apache.org/jira/browse/LUCENE-4095) by Robert Muir (@rmuir), updated Oct 11 2016
Attachments: [LUCENE-4095.patch](https://apache.github.io/lucene-jira-archive/attachments/LUCENE-4095/LUCENE-4095.patch)