To have DITA2Go run Indexer for you:
[OracleHelpOptions]
; FTSCommand = for Oracle Help, indexing command, typically:
FTSCommand = java -mx256m oracle.help.tools.index.Indexer
When you specify a value for FTSCommand, DITA2Go uses the command you supply to run Indexer after generating output files for Oracle Help. If your project is very large, you might want to increase the value of the -mx option. If the Indexer command includes spaces, you must enclose it (but not the parameters) in double quotes. Prefix options with a dash (“-”) rather than a forward slash.
If you specify a value for [Automation]WrapPath, DITA2Go copies all needed files from the project directory to the Oracle Help directory structure before running Indexer; see §20.3.6.2 Letting DITA2Go set up the directory structure and copy files.