Data management improvements

[akokai]

• Keep data, results, logs, etc. separate from repo, code.
• The run script should set up, all at once, proper directories to keep these data. Location should be based on user environment.
  • Rather than creating fixed directories on import of various modules.
• Add option in run script to configure special/alternative locations for particular sets of files – like 'projects' that have names, and so on.