Are you trying to create an entirely new tree structure apart from the file system tree structure? If so, I don’t think AF will do that. You can create flat lists, which contain pointers to files anywhere on your system, but that is not the same as a freeform tree with hierarchical navigation.
You can create an alternative tree structure within Finder itself, by making folders and placing symbolic links to other locations within them. But that can become confusing as the same file or folder appears to be in two “places” at once.
Ultimately, I think you are facing a moment of truth regarding how to view your library - canonical hierarchy versus tagging and lists. Audiofinder is allows you to view your file system hierarchy, and even place folders in lists (not sure how well this is supported), but it is primarily a search tool focused on tags and other clip properties.
I am personally fond of the tree structure, and I manage my file system organization carefully when bringing new libraries in. But I don’t do this for navigation, I do it in order to:
- utilize well-chosen folder names during search
- understand what I own from a vendor/library/collection/licensing standpoint
- keep my sanity while protecting my library investment
For these reasons, I have gone to lengths to organize and reorganize, at the file system level, my library over time. However, I have not hit the issue that prevents you from doing the same, because my projects never reference clips at their library location. I always re-spot any clip as a copy to a project, so that all its resources are local to the project. That way I can copy a project folder and be sure that all necessary resources go with it. That involves duplication, but it is worth it in my view.
After copying a new library and scanning it in to AF, I essentially forget about the file tree structure and go back to searching via tags and collecting ideas via lists. Since I spot copies to projects, the original file location within my library does not matter. When I want to reorganize my file system, I only have to rescan in Audiofinder, and repair any broken lists.
I guess this is a long way of saying, if you want to use Audiofinder, Soundminer, Basehead etc, these are fundamentally tag/property search tools. Until you convert your thinking to that paradigm, I don’t think you’ll get much value from the tools, and you’ll certainly be working against their intent.
Speaking to your reuse scenario, if you have a large set of projects that share clips, I would consider creating a shared resource folder for that set of projects - but copy new clips from your library into that folder. That way, you can avoid duplication, but still maintain independence between your library storage structure and your project space. Doing that will prevent the situation you’re having now, where your hands are tied because of old projects.