wish helps you I solved this particular problem by creating a new java application in net beans 7.1 and adding both the jar files as library. and inside my new application's main method i have called IndexMergeTool.main
Searching in lucene indexes is bit slow when using azure library for lucene.net
I hope this helps you . creating an AzureDirectory with a RAMDirectory pointed to the blob storage for faster searching. I can load all indexes in RAMDir as my indexes size is small enough to be loaded in RAMDir.Also I using singleton so that same instance of index searcher is user and reloading the RAMDir at specific intervals so that it has latest updated indexes.
Merge arrays into new array based on indexes and repeated indexes