I am pretty late to joining this thread, but I would like to add a few details and explanations about NotebooksApp.
We started implementing and experimenting with iCloud sync a couple of years ago, but the user experience is not at all what we want. When syncing huge hierarchies of documents, you have no idea about the progress, the process may even stall and maybe continue, or not. Sometimes iCloud thinks that a book/folder has disappeared, so that book disappears from Notebooks as well, just to reappear a few moments or minutes later (the same can happen in Apple’s Calendar, by the way, and even when syncing folders between two Macs via iCloud). This is not the type of sync we want in Notebooks.
Checklists embedded in documents (formatted documents or Markdown) will be available in the next major update; to get an idea you can try the public beta of “Notebooks for Mac 2”.
WebClipper: we do have that on our list of ideas, but currently you can “share” the contents of websites (on iOS), or you can drag & drop the contents of a webpage into Notebooks on a Mac.
Context tags have been available in Notebooks/iOS for a long time, and they are now available in “Notebooks for Mac 2” as well. True, we hardly mentioned them anywhere, because originally they seemed to be for advanced users (who don’t need documentation), but we will detail their use and benefit in more detail.
Tags can be assigned form an item’s info, but Notebooks can extract them for documents’ contents as well. As mentioned, tags can be denoted as @tag or #anotherTag.
OCR is currently not available in Notebooks, but there are a few interesting frameworks that we could implement. We will check that out.
Notebooks for Mac: as mentioned, we just started a public beta program, so everyone interested can give Notebooks for Mac 2 a try. It is a whole new app, and its feature set actually exceeds that of Notebooks on iOS. More details at https://notebooksapp.com/NBMac2-public-beta.