How do I clean out All the Data in the files and leave the Business Spaces App that I've been working on?
When you delete a business space using Delete from the Configuration Tool Aware IM physically deletes everything related to the business space - both configuration and data. There is absolutely no way that you can log into the deleted business space or see it in any list. So when you are saying that you have deleted the business space - do you mean that you physically deleted it from the Configuration Tool?
There is another aspect of it - that is, visibility of a business space from other business spaces. This is controlled by "Visible to all" flag in the properties of a business space. If a business space is not visible to all you will not see it anywhere, other than when you log into it. So the business spaces you see in a list may be invisible rather than deleted. If they are, you have to log into them and either delete them using Delete or make them visible to all by checking the corresponding flag in the properties.
I just noticed if I'm in the Library Sample App and Logout. It takes me to a login screen that doesn't ask for a Business Space name. If I login using that login screen it takes me to a Business Space with No menu's or anywhere to go (without error) that I deleted sometime ago?
It is unlikely to have been deleted, otherwise Aware IM wouldn't have been able to log into it. See the answer to the previous question.
How can I cleanout the OLD Business Spaces that are no longer on my Conf Tool screen that I deleted days ago??
See the answer to the first question.
And that takes me to my next question. How is the app and data stored. I'm hoping its in two different files for EACH BUSINESS SPACE. Otherwise, I'm assuming there is no way to backup data for one app?
Each business object is stored in its own database table. The name of the database table has the name of a business space as prefix so it is easy to distinguish them, for example MyBusinessSpace_Employee