I've changed my settings to do a rebase instead of a merge when pulling, however it seems a lot safer to me to also use the "-p" flag. Can this be added so that it's the default for a merge? If not, how might I add this myself? Thanks!
According to the git manual, the -p option (--preserve-merges) to rebase is only usable in interactive mode: http://linux.die.net/man/1/git-rebase. Therefore it's not really usable from SourceTree. It might be safer for you to not use the rebase option by default if you have merges you want to preserve.
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