What preferences can be set for Transaction, Query and Foundation from the Foundation site?
11.x and above
Here you can select the overall review process for scripts submitted to Foundation, whether users can schedule jobs to be run later, the library where completed data files are stored, which files are subject to being stored in this library, and your auto run preferences:
Here you can control which file types can be scheduled by users, select the Query document library, the account that is used to connect to SharePoint (for SharePoint lists), and the account that is used to connect to SQL:
Here is where you can set approval and user settings, as well as some workflow settings: