Require a NestedWorkflow() to asign nested workflows.

Explicit is better than implicit. Makes files more readable, and removes
special case code to detect non-Activity assignment.
Added support for reading nested workflows from files.
Add examples for nested workflows from file.
Renamed example directory to 'nested'
Tidy up example files
Rename Boolean to Logical, to better match Taverna Workbench.

These Booleans are only used for RShell, where they are mapped to R types.
Anywhere else, they are simply strings containing TRUE or FALSE.