MODE-1876 Removed expensive ops to allow reindexing large repositories

Recently the reindexing operations were changed so that upon "IF_MISSING"
any already-indexed node would be skipped. However, this was not really
the intention of the "IF_MISSING" option, and the logic to determine which
nodes were already indexed was quite expensive. Therefore, the logic
was changed to reindex the entire repository's content whenever the
indexes were missing (e.g., either empty or not yet created).
Corrected compiler warnings
MODE-1876 Corrected the logic that determines if indexes are empty

Because the JcrRepository is trying to determine if the indexes are empty
after the system nodes have already been created, the query components
have to determine when the indexes are first set up whether there is
already content in the persisted indexes (e.g., the files on the directory).
MODE-1894 - When indexes are being updated, the map of computed properties should be passed down, instead of both the old the new values.
MODE-1887: Merging workspace
MODE-1887: Remove commented out lines
MODE-1887 Removed commented out criteria in if-check
MODE-1841 - Added a test case which uses a configuration similar to the one described in the issue and stores binary values.
MODE-1895- Fixed Solr and Orm modules from the "patched" hibernate search distribution
MODE-1896 Deprecated the "transactionManagerLookup" field

This field in repository configuration files has not been used for some
time, but at the time it was not properly documented in the schema as
being "deprecated". This has been done, and any use of this field in
our test configurations have been removed.

Note that the RepositoryConfiguration constructors now log warning messages
when this or any other deprecated fields are used.