I am writing a web application-scoped feature which will provision a site collection and a small number of sites.
The problem is that I have my own style files (.js, .css, images) and even some custom pages. If this were a site collection or web-scoped feature, I would use a module to deploy these files. However, modules are not available in web application-scoped features. I could deploy the style files to the _layouts folder, but I would prefer if these files were not available outside my own site collection. That also doesn't solve the problem of my custom site pages.
I was thinking of putting all those files in the _layouts folder, then copying them in the feature event. But I don't really know how to access hive files programmatically.