Folders are created for each plugin
run the analysis after simulation

We now run the analysis directly after running the simulation. There is
some stuff to clean up here though.
Remove activation (will screw multiproc)
.DS_Store files suck
Analysis appears to work
Prompt before deleting run experiment
change name to make_experiment_folder
Allow for redoing of analyses
Reconfig of the experiment ordering
Remove ANALYSED mark when re-running analyses
Record current treatment in experiment
Copy script to output folder again
Allow selection of replicates and treatments
Support for specifiying a particular plugin
New plugin loading is running
Tuning, and now with history base class
Proper replicate class now.
Fixes for new replicate class
Merge branch 'feature/progressive-plugin' into develop
mark_time function