Git supports a git rebase todo file that handles merges that occur during rebase. For example:
$ git rebase @~3 -i -r
label onto
# Branch MitMaro/tim/use-try-from
reset onto
pick 08d9e70 Use TryFrom trait now that it is stable
label MitMaro/tim/use-try-from
# Branch MitMaro/tim/basic-break-support
reset onto
merge -C 88cdea0 MitMaro/tim/use-try-from # Merge pull request #104 from MitMaro/tim/use-try-from
label branch-point
pick ac02006 Add basic support for the break instruction
label MitMaro/tim/basic-break-support
reset branch-point # Merge pull request #104 from MitMaro/tim/use-try-from
merge -C c9a6c7f MitMaro/tim/basic-break-support # Merge pull request #105 from MitMaro/tim/basic-break-support
pick 3a46420 Add full support for the break action
# Rebase 371df63..3a46420 onto 371df63 (12 commands)
#
# Commands:
# p, pick <commit> = use commit
# r, reword <commit> = use commit, but edit the commit message
# e, edit <commit> = use commit, but stop for amending
# s, squash <commit> = use commit, but meld into previous commit
# f, fixup <commit> = like "squash", but discard this commit's log message
# x, exec <command> = run command (the rest of the line) using shell
# b, break = stop here (continue rebase later with 'git rebase --continue')
# d, drop <commit> = remove commit
# l, label <label> = label current HEAD with a name
# t, reset <label> = reset HEAD to a label
# m, merge [-C <commit> | -c <commit>] <label> [# <oneline>]
# . create a merge commit using the original merge commit's
# . message (or the oneline, if no original merge commit was
# . specified). Use -c <commit> to reword the commit message.
#
# These lines can be re-ordered; they are executed from top to bottom.
#
# If you remove a line here THAT COMMIT WILL BE LOST.
#
# However, if you remove everything, the rebase will be aborted.
#
# Note that empty commits are commented out