some code sanity:

make methods and constants static when they can be,
replace LinkedLists with ArrayLists in ModuleRegistry
remove redundant null/truth check,
generic iterator instead of casting,
combine multiple calculations into one formula
move calculation of gamma (1 / stage) into HMMData function
get rid of (duplicate?) Pdf arrays.

It appears that nobody ever sets nor gets them.
use an Enum to describe types of HMM data streams (instead of consts)
JAVAify HTSEngine.processTargetList() which now returns the HTSUttModel

Previously, processTargetList() filled in the data into a model given
as a parameter (C-style)
JAVAify HMM optimization

clarify code, move boundary check into HTSPStream,
also, remove debug output from HMM optimization.
JAVAify vocoding, taking away most unused options (sorry).

turn the vocoder into real Java, by acquiring variables only as needed
and then making all functions static for which it is feasible.
Also, this patch removes most of the unused options (lpcVocoding,
debug output, gaussian noise, NGAIN) and some potential debug/standalone
code. I hope this is acceptable, I had to somehow reduce complexity
to be able to analyze what's happening.
some cleanup in CartTreeSet

also, store duration errors from CART selection directly in HTSModel
inline HTSDWin into HTSPStream

an arguable change to get rid of HTSDWin as a a separate object
and icorporating HTSPStream into it. I don't believe that the
current modularization would work with any other windowing
implementation anyway, so very little is lost. At the same time,
I found quite a runtime difference when I profiled the inlined
vs. non-inlined versions (some time ago, though).
finally: changes that are necessary for incremental processing

add a few methods, make a bunch of static methods public (instead
of private) and one more protected.