When working with a non-Textmind repo, at some point the complexity of tasks related to the external repo starts to clutter and conflict with Textmind. At that point, it's time to export the whole mess to the external repo.
I suggest creating a mini-Textmind within the external repo to control development. A mini-Textmind is a partial Textmind instance. For example, there is no need for separation of ~Agenda~, ~Linked~ and ~Non~, since it's unlikely to contain bulk text that would cause lag. Suggested directory name: ~1-Textmini~
This permits export of Textmind atoms about an external repo to that repo. Then Textmind can merely store a task, "Do next steps on repo Y," without further detail. Only info specific to the repo belongs in Textmini. For example, the fact that Python function A can't do B belongs in Textmind. The fact that A's inability to B forced the frobnicator repo to use workaround C belongs in frobnicator's Textmini.
Textmini is a necessary innovation to let me comfortably manage the burgeoning complexity of Cyborganize's code and docs. It organizes exported atoms for easy access before they're implemented in the destination repo, and keeps them from cluttering the primary repo.
Executive refactoring loop and semver
A Textmini has no daylog processing loop; it uses Textmind's daylog. It does have an executive refactoring loop. Instead of daylog and journal loops, Textmini supplements the executive refactoring loop with software project management concepts such as semantic versioning, roadmap, issue tracking, etc.
Textmini is not documentation. It can control the process of writing documentation. Textmini is for a single author only. Thus Textmini should be kept on a personal branch, if the project is collaborative. It may be useful to allow others to view one's Textmini to improve coordination, in the same way that a collaborator may find it useful to look at someone else's notes or todo list.
Use git subrepo
To avoid mixing Textmini commits with the repo's commits, Textmini should be a git submodule.
Do not simply clone into a subdirectory; that is git subtree.
Do not use git subrepo. Magit prefers and supports submodule.