[Clustersim] Update Version 1.0

[John Schneiderman]

I have tracked down the error that was causing the seg fault today, finally 
got around to it. :) I have also redone how confParser deals with key-value 
requests. There seems to be a problem with the way the neighbourlist 
interacts with the MDLJ simulation as nothing ever moves. I haven't had the 
time to look at it, but I ws hopping that Dr. Moore might be able to take a 
look at it. The API has all be updated on the website. I have merged the 
neighbourlist branch back into the main branch as there was just too much 
done already in the neighbourlist that I didn't want them to be too far 
divergent. The monte carlo seems to be fine, I have done any verification of 
any numbers, just varified that we get numbers. Where do we want to go from 
here?

John

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