Forcing first listed FASTA to always be first in the merge order
Made some thread pooling, may or may not work
Changing from a constant thread count to a thread limit.
Adding a check for work that somehow never got done.
Merging in threading chenges and order enforcement for first MHC in cluster runs with random order.
Merge commit 'cb927379ac1d5245bb866b61a1bd15349a7fb21a' into yohei-master

Conflicts:
	createIndex/MappingMergeScheme.cpp
	createIndex/MappingMergeScheme.hpp