reordered files
added @include markers

attempt to make oxygen work
Merge branch 'Binned-Data'

Conflicts:
DSsim/DESCRIPTION
DSsim/R/DDF.Analysis.R
DSsim/R/Simulation.R
DSsim/R/generic.functions.R
DSsim/R/single.simulation.loop.R
Resolving merge conflicts

Still need to deal with some documentation issues for
make.ddf.analysis.list and run.analysis