more sga no workie
fixed degnerancy issues.
We have some real results. Many things matter. Right now we estimate
bandwidth every 20 iterations, otherwise this add too much varaiance.
M-estimators also make a fairly big difference. Better a inital values
also matter a lot.

Right now the outstanding issue is how to pick c. Its a bit large often
currenlty. Small values with large ranges means that we push agaist the boundry a bit.

Thinking of maxamizing a \bar{x}/\sigma parameter. Or at least ensuring its no silly.
while keeping c as small as possible.

Next to do. Fix the code to not be a pile hack.
SGA is working quite well now. Still needs a clean up
Mostly working. Need to finish the stoping conditions etc.
Adding the Colt lib. Will slowly move functions over to this. Main reason for using this
is to calculate critical values for a t test with unequal stds.
SGA with bootstraping now at final prototype stage. If this pass the tests this code will be finialized
and released. We need a bit of clean up for finalization. It is most just a monolithic class with much
of it as legacy ideas that didn't pan out. There is room for more cmd line options.

We have added the colt lib directly. Note that we are still using the cut/paste/fixed version of binomal
in the core code. Some glue classes have been added. Overall colt is pretty good but beware the binomal.

We perhaps should add a config file pipeline that plugs into the current command line annotations.
We also have some performance gains (small for real problems) by bypassing the string parsing for
msms. Perhaps some direct type passing again via the command line annotations?
Added Weighted mutations. Currently only BinJAFS is weight awear. Will extend to other stats as it makes sense to do so.
Added a warning in the -help for the weighted mutations (-wc) that is not a general user option.
minor changes and tweaks.
Merge branch 'master' into sga

Conflicts:
	ant/build.num
	html/download.shtml
auto build changes.
Apply -stat to SNP data

New class in External package, convert SNP data into a format
compatible with -stat
Merge remote-tracking branch 'remotes/grillino/staging' into staging

Adds some support for data import from SNP data. Writen by Andrea.
Sync update. Bit messy sorry
No idea where this is right now.
Merge branch 'master' into sga
Added gauss and nonlinear gauss.
need a better way to track build numbers!
Merge branch 'master' into staging