All of the hypotheses that have been developed should remain represented in the debates (even if disproved). But then the hypotheses that are designated as proven should be cross-linked into a "Working Theories" folder (or something similar). These will then be designated with the "approved" icon (
) to show that they are the working hypotheses.
For example, when people start a new research effort from scratch, they generally begin by consulting Wikipedia, to familiarize themselves with the standard model. If they're satisfied with that, that's the end of the effort. If not, they'll follow the links to supporting material, and branch off from there, in search of what they're missing.
We should have something similar, with a presentation of what we believe to be correct, all in one place, without any of the other hypotheses cluttering up the presentation. But the other hypotheses should be accessible, if somebody doesn't find the current consensus to be satisfying.
If the system supports cross-linking, the "Correct Theories" folder will be just a sub-set of the "All Theories" folder, without any duplication of material. If one theory gets promoted, and another demoted, it won't change the structure of the "All Theories" folder, but the link to the bad theory will be replaced by a link to the good theory in the "Correct Theories" folder.
Cross-link just the proven hypotheses into the Scientific Knowledge folder.