If you are asking what the scrum guide has to say about this, it says nothing. The scrum guide doesn't differentiate between the types of work that is managed by scrum. All work are simply product backlog items.
While user stories are a useful manifestation of product backlog items, there's nothing particularly special about them. Scrum is about visibility and adapting to change, and you can (and should) do that for all work, not just user stories.
All of the things you mentioned -- Create project skeleton, Create continuous integration system, etc -- are product backlog items that need to be done by the team to accomplish the sprint and release goals.
If you are concerned about how to bill them, the simplest solution is to add a "billable" flag to all of your billable backlog items. For example, use different colored story cards, or configure your software to add a tag or other identifying mark. Or, simply prefix non-billable items with "NB" in the item title or name if you have no other options.
TL;DR: The three pillars of the scrum process are "transparency, inspection, and adaptation", not "transparency, inspection, and adaptation for billable hours only".