Why haven't we hosted research publications as repositories yet? This just makes so much sense for several reasons: 


Let's say I find errors in a very long research publication - A code repository like issue system would allow me to highlight this and notify the owner 
Let's say I want to add to a research work incrementally in an effort to make it complete - A code repository like PR mechanism would enable me to publish my work and notify the author without "citing" the said work and having to mention all the details again.
Let's say I want to make updates on continued research and not just stop at one publications - A code repository like version control would allow making several releases based on work that could be published, moreover it allows maintaining a timeline of all releases for better clarity.


Every shortcoming I can think of can possibly addressed by treating research publications as repositories instead of standalone PDF documents. 


What are your thoughts on this and has anyone thought of implementing this already?


Shouldn't one of the primary attributes of research be to enable collaboration after publication for the study of a subject?


Why haven't there been the tools to do that yet?
There are journals that do that. Here is one: https://joss.readthedocs.io/en/latest/submitting.html

In some sense, arXiv.org is also doing that, allowing to version preprints. It doesn't use a "repository" in the sense of git or subversion, but it allows you to keep track of different versions of a manuscript, and that's really what is key: Any system that allows you what's in a paper at a later time must allow identifying and accessing a particular version of the paper.