For what it's worth, we're having the same issue. Github's approach to merging conflicts causes us great difficulty--we are forced to merge all conflicts on the command line because our workflow does not support polluting a feature branch with dev branch content (for us, dev is where separate developers' code meets for the first time, and often contains code not considered ready for production). The Github approach forces dev-branch content to be merged into feature branches, which then means those feature branches cannot be merged to production because they now contain dev-branch content. No option is provided in the Github interface to resolve these merge conflicts, and what's worse is that after the merge conflict is resolved locally, Github does not resolve the merge conflict when those changes are pushed to remote (i.e. Github itself). The desired solution would be to provide options, within Github, specifying how merge conflicts are handled, instead of forcing us to merge the pull-request target ("base") branch into the source ("compare") branch.
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