The now defunct Google Code had a very good solution for this. You could create additional "sub" repositories alongside the "main" one. Github already does that for the wiki, but doesn't generalise it to allowing additional ones. I'm somewhat convinced this is because github has the whole "charge by the repository" model, which is at odds for being useful for projects that require multiple git level repos.
My view is: unless you have an inescapable security, physical or performance reason not to have a single repo, have a single repo.
Directories are for managing directories.
Version branches are for managing versions.
They are not the same thing.
This sounds like a security nightmare, that also significantly impacts local update times and makes for a huge repo.
Issues and projects are global and not bound to a single repository. In my experience, this is the only approach that works in a company. JIRA does the same thing.
It's the closest to a fully open source Atlassian suite that you get. Phabricator has code review, repository hosting, project management and even a CI tool.
Github's issues, despite it's flaws, is easy enough that non-programmers can use it. Phabricator is complicated enough that it's actually caused me to not report a bug at one point.
Works pretty well, if a little awkward at first.
[0] - http://purpleapp.com
I personally use it on my team at the moment - it's been pretty useful and we've passed along frequent feedback to the platform team responsible for it.
It sort of boggles the mind, really - and makes me feel like they did not really take the community's desires seriously.
I suspect it's still a lot better than the alternative but not having org-wide Projects is a little sad.
https://github.com/issues?q=repo%3Areactjs%2Fredux+repo%3Are...
We also add a host of project management functionality on top of GitHub issues like advanced filtering/sorting, dependency tracking, and the ability to setup your own dev/release workflow.
I know there are some tools to manage Issues across repos, but for the most part, the tools seem to assume you work on only one repo, or that milestones only affect a single repo.
I would love to see projects/milestones become more capable when dealing with cross-repo issues.