revise many variables in examples that start with "." (they're hidden!)

[wStockhausen]

Many of the variables in the global environment in the examples (e.g., "A basic workflow...") start with ".", with the result that they are invisible in the RStudio and R GUIs (and aren't shown by ls() by default). Makes debugging problems with the values for these variables very difficult. Would suggest appending "_" to variable names, rather than prepending "." to those names, assuming there is a need to distinguish them from inputs to functions.