Auto-import?

Is there a way I can set (or script) EF to import certain folders (and mailboxes?)

Just the new files, ideally. This would avoid having to remember which folders have had new content, and importing them manually.

Yes, but the way you’ve written the question it sounds like maybe it would be better to adjust your workflow a bit. For example, if you use EagleFiler to create the files or use other applications to create them in your EagleFiler folder you won’t have to worry about what’s been imported and what hasn’t. It will just all be in EagleFiler and up-to-date.