Use memset to zero out arrays instead of for loops like a noob.  Decent speed up.
Plugged a few memory leaks.  Now that the inference.exe process persists for the analaysis of all trees in a group, rather than handling only one tree, I need to pay more attention to this.
Enable compiler optimisations for inference.exe.
Trivial change for better clarity.
Introduced GSL Workspace object to cut down on repetitive memroy allocation and freeing.  Also using gsl memcpy routines everywhere instead of manually copying with loops.
Got generate.exe working again by bringing it into line with all the new interfaces.  Kind of a hack job, but seems to work.
Added option to control inter-sample lag.
Implemented leaf word order shuffling option.