Revert "Revert "Copy indexes on copy store in HA.""

This reverts commit 9bc18e1a2ca06d55ad07bf0fddc55a37da3a3ca3.
Fixes unclosed file issue on windows, and another issue that was uncovered related to closing lucene snapshots without commits in them.
Merge pull request #1370 from jakewins/more-copy-indexes

Fix for the copy indexes reverted commit