I am interpreting this to mean that what you showed is not your application data folder. In that case, it doesn’t matter at all what else is there. The only important thing is that you are not backing up on the same machine you are storing your primary data files. (Lose one, lose all.) But if you’ve moved everything to Dropbox, you’re being backed up there, so no worries.
Right. The program currently creates an index file in whatever folder you open a data file from (unless there is already one there). If you were to open a backup stored on your desktop, it would create an index file on your desktop.
That’s a hopeless cause, because it will be recreated every time you open a file directly. But it’s very small, so really not worth worrying about.
It is describing exactly your situation. I included that link only because it was not clear what folder you were showing. Since you were not showing your application data folder, you can ignore it.
I knew this, but it seemed easier to suggest that the primary application data folder be kept clear of other files. Although they would do no harm, they have the potential to be confusing to anyone who doesn’t really understand what is there. And they present a risk that someone who is over-eager could accidentally delete important data while trying to clean up the folder or reorganize their storage.