Copy indexes on copy store in HA.

o Indexes are now included in the file listing for files to copy in HA and backup.
o Refactored out the logic for listing store files into its own class, and added tests for that.
o Don't copy populating indices in HA
o Integration tests for multiple use cases related to this.
Merge pull request #1345 from jakewins/new-copy-indexes

Copy indexes on copy store in HA.