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I have a repository that is forked from GitHub that has a few modifications made to it. However, in a certain commit, a few files were changed that I want to submit a pull-request for, leaving the other modified files out of the request.
Do pull requests merge all commits, or do I need to do something special to isolate this commit?
A pull request being made of whole commits, you need to split this commit into two separate commits one containing the change to put in the pull request, and the other holding the other changes. To do this you need
git rebase -i, see for example How can I split up a Git commit buried in history? for a good explanation on how to do it.Once you have split the commit, move the ones you want to include into a topic branch, see for example How to move certain commits to another branch in git?, but it depends if the commits that make your pull request are sequential.
Then finally you can push to Github and create the pull request from your topic branch.