I would recommend rebasing instead of merging here: you replay your commits on top of upstream/master, preserving the history of master
as being the mirror image of upstream/master
(plus all your own commits).
That will also make a future pull request trivial for upstream to apply, since your commits will simply be on top of the most recent version of upstream/master
.
That will involve a for push, but since it is your fork, you are likely to be the only contributor on that repo anyway.
cd ~/Projects/app
cd Libraries/One
git fetch upstream
git rebase upstream/master
(conflicts expected)
(resolve conflicts)
push -f origin master