In order to prevent a data race in the code indexer it must be wrapped
with a holder otherwise it is possible to Search/Index on an
incompletely initialised indexer, and search will fail with a nil
pointer until the repository indexer is initialised.

Further a completely initialised repository indexer should not be closed
until Termination otherwise actions in Hammer/Shutdown phases could
block or be lost.

Finally, there is a complex dance of shutdown etiquette should the index
initialisation fail. This PR restores that.