Wonderful thread. I actually use a combination of MarginNote->iThoughtsX, and now->Tinderbox to create these same note output in Tinderbox.
MarginNote is the table settler: it creates discrete annotations, allows users to title each of them, and affix hashtags and additional comments to individual annotations. It allows user to further organize these discrete annotations (w/ or w/o tiles, comments, and hashtags - and links back to the original text).
I export MarginNote annotations to iThoughtsX, and then to Tinderbox. Once complete, this process creates containers and their children in Tinderbox, with the MarginNote-created titled annotation in Tinderbox's title pane, a link back to the the original text (in MargninNote) in Tinderbox's url section, and the MarginNote-created annotated text appearing in Tinderbox's text pane (which is also where MarginNote-created comments and hashtags go).
I use the MarginNote-created titles to label the subcategories for annotations, and hashtags for task - actions (e.g., questions, research, read, etc.).
Here's my situation... In many cases, I include 2 - 3 titles (i.e., subcategories) for an discrete annotation -- because it might fall into multiple subcategories (as replicants in DEVONthink or aliases in Tinderbox). Ditto that with hashtags that carry over from MarginNote to Tinderbox.
So... What's the best way (perhaps through Actions or Agents) to automatically create these titles as aliases within their respective associated containers? Thanks!