I've come across this problem before (as a third party - I don't do research) and I've considered writing software to help solve it. Maybe something like a Jupyter notebook with an attached mini-filesystem that can be easily shared with colleagues? What do you think would be a required to solve this?

If you're really interested in this, you should contact Ivo Jimenez and Felix Z. Hoffmann. Although there's not much information available, under the heading of " Reproducible Computational Research – a case study " at [0], they tentatively explored such an idea at a hackathon in Cambridge in May.

[0] https://elifesciences.org/labs/bdd4c9aa/elife-innovation-spr...

It depends a lot on the field. In my own work (I'm out of academia now, but it still applies), there's often very complex network setups involved, so a Jupyter notebook won't quite cut it. Many things in this particular domain can be nowadays solved with SDN, but it is still a complicated issue. I'm sure people from other fields have analogous problems, too. And this is in CS, I suspect that anything which implies more "physical" setup is orders of magnitude more complex.