We've been told that when a user adds a tool to a site, no component initialization code will be called. Instead, it was suggested that the Gradebook code (for example) automatically create the gradebook data for the new instance when it starts up and doesn't find anything there.
In the long run, it would be good to give site set-up a hook to to trigger tool initialization directly. There are a number of reasons for preferring that software make changes when a user explicitly requests them instead of waiting to do them later. It makes bugs easier to find. It avoids the problem of what should be readonly methods making persistent updates unexpectedly. And it makes it possible to initialize the tool's instance with more complex metadata.
In the short run, though, we changed the Gradebook code to do implicit creation.
The problem we're facing now is that there are two different paths to an instantiated Gradebook. First, the user can go to the Gradebook tool through the UI. Second, the user can use Samigo to export assessments and scores to the Gradebook tool.