[andrewray]

If your branch conflicts, rebase off master (the branch you're making a pull request to). Then it will merge cleanly. There's no practical downsides to having merge commits in master, but you should never (or rarely) see merge conflict resolution commits. You should be able to rebase to a mergeable state before merge.

[cmwelsh]

If you use a pull request workflow then at the very least, you're forced to merge master into your branch (if there are conflicts) before merging your branch into master.

You should never (not even rarely) resolve merge conflicts on master...

[gkop]

You probably know this but just to be clear, to resolve conflicts on your pull request branch, you may merge master into your branch or rebase that branch on master; GitHub makes sense of either kind of resolution.