Interim commit. Continuing to refactor the package. "init.r" code split into the ExploraAnalysis class (in configuration.r) and lines of initialization code (moved into the workbench() function).
Cleaned up @imports for various modules (by exclusion).  Not sure why the "cluster" package is imported.  We'll delete it for now.

Package installs fairly cleanly - just one "note" warning to be fixed. However, the application as a whole doesn't yet really work.