Text Links / Bookmarks
Regarding linking to specific bits of text, here is my how-to on that. Much of the technique is already described above by Vincent_Vincent, though. I use this technique rather heavily, and in fact in a way that transcends Scrivener, as a technique that can be employed through multiple pieces of software, or even just within loose files on the disk. It’s one of the reasons I feel this approach is in fact superior to anything provided by features in software.
Replicants
A good way of describing replicas or clones is closer to how Scrivener’s Collection feature works. The item is listed in more than one place at a time, but all of these different references point back to the same exact underlying asset. Some tools embed such clones directly into the outline structure itself, as nodes in the outline, rather than Scrivener’s approach of using separate lists.
The closest Scrivener has to that is purely content based, not outline node based. The <$include> placeholder can inject content from one area of the binder into another. It’s a bit more flexible than node-based cloning, because such injections can be done into larger textual contexts—for example a sentence in a snippet item in your Research folder can be injected into several different footnotes in the main Draft.
The downsides to the approach are:
- Only text content is cloned. This isn’t a solution for having a full binder item in two or more places at once, with all of the support you get for it (representation on the corkboard, etc.)
- The cloning is a single-direction operation, you can’t see and edit the text in place, but need to click through to the included content to edit it. It’s also a bit “blind” from the perspective where the placeholder is used, to the point that I sometimes use inline annotations to describe what will be injected there. That avoids having to click through links to see what’s going on.
- A secondary implication of the above is that such text cloning isn’t “all are one” in the sense that replicants are, where in that system you can delete any of the clones. They are all equal, and nothing is lost until the last instance is deleted. In Scrivener’s case, the core binder item all Collections point to, or all <$include> text points to, is the one single master copy. Delete that, and all of the clones are lost or broken. This can mean record-keeping is necessary so you know what not to delete. I use a Keyword, “Master Copy” for items that other items make use of with <$include>—but do note that if you make a habit of checking back-references in the Bookmarks pane, you do get a free back-ref when creating the link to the master copy, from the item that linked to it.
So it’s a pretty good approach, particularly in that it lets you insert text around other text, even into other paragraphs, which is quite rare to find in other software—but there definitely are areas of this we could improve! Other editors and outliners have outpaced Scrivener in this regard; offering similar capabilities but with a more transparent interface.
Auto-Filing
As you note, there isn’t anything automatic for that as a feature, however I would contend that such a system already for the most part exists.
For one thing, there is a point that could be made for using search collections for this instead of folders. More generally file stuff into larger archive folders, and handle the organisation with collections, that update automatically based on the state of the items you file.
Collections can also be used as filing helpers though. While not automatic, consider that selecting the entirety of a collection result list and using Documents ▸ Move To essentially accomplishes what you want, if you do find having folders is still important to keeping a handle on data, and collections aren’t enough by themselves.
For [[ … ]] style links, I tend to make use of one single “Inbox” style folder somewhere in the binder, so that I can get back to writing as quickly as possible. Creating a link is usually just a matter of hitting the Return key as soon as that dialogue pops up. I defer filing for later, using automation where it helps. Outliner sorting, outliner filtering, collections—all tools that can be used to make item selection and bulk filing simpler.
Arguably, any dedicated feature that did this somehow for you would have to be just as complex as these tools anyway, to be worth creating it.