Sorry about not having those configuration options documented.
There really are just 3 query-related configuration options for a repository, but only one is related to Lucene. From the JavaDoc on the JcrRepository.Option enumeration:
The system may maintain a set of indexes that improve the performance of searching and querying the content. These size of these indexes depend upon the size of the content being stored, and thus may consume a significant amount of space. This option defines a location on the file system where this repository may (if needed) store indexes so they don't consume large amounts of memory.
If specified, the value must be a valid path to a writable directory on the file system. If the path specifies a non-existant location, the repository may attempt to create the missing directories. The path may be absolute or relative to the location where this VM was started. If the specified location is not a readable and writable directory (or cannot be created as such), then this will generate an exception when the repository is created.
The default value is null, meaning the search indexes may not be stored on the local file system and, if needed, will be stored within memory.
As with the other JcrRepository.Option values, they're set in the configuration file for each repository under the mode:options elements. See Section 8.1 of the Reference Guide for details and examples.