Copy (e.g.) the Scala .gitignore template into my project in such a way that the upstream version and my version can be kept in sync or diverge, and make it so that it's very explicit what's happening.
A subrepo is kept in a long running branch. (in this case gitignore) I add
adapter commits on top of it to change the directory structure of the original
repo into what I want (e.g. 1e2c9417f25c0242eb723c0b39d6d46b1d3e5c0d) and I
merge that into the master branch. Then, to keep in sync, I go in the long
running branch, do a subrepo pull, and merge again. Conflicts are often
brought up, but it's normally clear why they happened and trivial how to
respond to them.