DRILL-384: Move some Fragment initialization work to run() method
Enable sv2 support for project operator.

Currently, this will do copies for all vectors if their is incoming sv2.
Fix minor bugs in ParquetWriter.
clear sv2 in FilterBatch when new schema
increase timeout for External sort test.
Fix bug in MergeJoin when there are repeating values across left batches.  Ensure join type is specified. Add join type to some physical plan in unit test case.

Re-enable a testcase for MergeJoin. +
DRILL-754: Scan of HBase table timed out

+ RAT: Ignore "*.patch" file in the project root directory.