Why can't you synchronize things I put in Topicscape folders with the contents of Topicscape?
We understand the desire to do this and have given a lot of thought to it. We have cases ourselves when we would like it to happen, but there are logical problems in doing so and performance issues as well.
One of the objectives of Topicscape, is to separate the physical storage from how the user feels the information should be organized so that the user can break away from the rigid tree hierarchy that the Windows file system imposes. As a result, Topicscape allows occurrences to appear in multiple topics, and topics to have multiple parents, both without duplicating files or folders, and without using easily-broken shortcuts. This is why a Topicscape's structure is held in a relational database. That is not compatible with allowing the user to update a Topicscape just by moving files around in the Windows file system.
When you import a folder (including those with subfolders) the structure is retained in that Topicscape's folder. But if you add occurrences to a topic that initially corresponded to a folder, or move occurrences out of it, Topicscape no longer preserves the folder structure. There would be no point in trying, because Topicscape allows relationships (like multi-parent topics and cloned occurrences) that Windows cannot reproduce in its folder hierarchy.
If we were to scan the files to synchronize, there is another logical problem: If a file has been moved, Topicscape would have to scan the computer's disks to find it. This would be extremely time consuming, but even when a file with the same name is found, there is no guarantee that it is the wanted file: Consider how many files called "readme.txt" there are in the average PC, for example. Nor could we know if it's the right version of the same file, as old versions may be kept for reference. And Topicscape cannot tell if a file has been deleted or merely moved.
When an occurrence is deleted in Topicscape, if the files are under Topicscape's control (i.e. in that Topicscape's folder), the file is kept until the user deletes it with the Delete Stray Files function. This is to allow total undo in the same run, and to allow for later recovery if required (independent of the Recycle Bin). But it means that we can't rely on mismatches between files in the Topicscape folder and the source folder to synchronize.
We may at some time offer limited synchronization by allowing only additions to be included, but that will require changes to our Undo logic, which is very comprehensive and an important feature of a reliable system that users trust to look after their significant information store.