Thanks so much for your comment and I am happy you enjoy the book.
I use Jude http://jude.change-vision.com/jude-web/index.html
(now called Astah) community (free) version to make the diagrams.
Sometimes (only when needed) a sequence diagram can help dig deeper to see how a flow is going to develop and to discover where the logic will be housed; a state diagram can be very helpful for workflow questions, as can an activity diagram with swimming lanes. Certainly a deployment diagram (also used in the book)...
Regarding SVN, please note that the Drupal community will be switching (eventually, no hurry! won't start for a year) to Git, which is a big jump from CVS. I will be publishing on my blog Git workflows, and other updates.
Also note that Drush (command line shell for drupal) has changed enormously (for the better) over the past few months.
I will be writing about these things on my blog at http://awebfactory.com.ar