What is the difference between IndexWriter.addIndexes(IndexReader[]) and IndexWriter.addIndexes(Directory[]), besides them taking different arguments?

When merging lots of indexes (more than the mergeFactor), the Directory-based method will use fewer file handles and less memory, as it will only ever open mergeFactor indexes at once, while the IndexReader-based method requires that all indexes be open when passed.

The primary advantage of the IndexReader-based method is that one can pass it IndexReaders that don't reside in a Directory.