It's not only about funding agencies, though. Researchers need to be trained in the use of a GitHub like system - as a former graduate student, I knew NO ONE using Github. Furthermore, after working in scientific publishing where it was MS Office or bust, I doubt you will convince Elsevier and the publishing giants that GitHub for Science is the way to go. How do these huge companies make money if scientists are sharing their work for free online? Meanwhile, you have scientists themselves, many of whom are required to hit certain numbers of articles in certain "prestige tiers" of journals in order to get tenure. If you're an extremely busy junior faculty member who will be FIRED when tenure review comes up if you don't have 1 paper per year, will you risk it on a GitHub scheme? I doubt that.

These problems are not unique to science. Take any large group of humans, be it government, the military, a company, a set of companies: they will coalesce onto the use of a certain number of tools, and it will take a LOT of energy and work to switch tools. Getting an entire industry to switch tools is extremely hard, perhaps downright impossible, and I'm not sure if it can be done in the rather slow-moving world of academic science. It simply won't be possible to enact a huge change on the system with so much institutional momentum built up.

It seems to me the best solution is to make incremental changes toward a github like system, training new scientists in grad programs to have better practices. Maybe we can't get researchers to post their full data set for all the public, but perhaps it can be made available to non-competitors, those who researchers aren't actively competing with for the same grants. Maybe researchers can be required by journals to post the peer-review comments/responses, as well as the drafts of the article, alongside the article itself. Maybe we can have researchers posting extremely detailed code/methodological information alongside the article, without forcing them to give over the entire dataset to other researchers?

Finally, maybe the whole incentive structure of academic science needs to change: maybe articles/publishing metrics should be de-valued in favor of teaching skills, mentorship ability, and collaboration within and across disciplines?