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.
I've seen a few projects use Phabricator, but I can't seem to understand how to use it.
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.
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.