Accidentally branched off of the wrong branch, and when I want to merge into the master I have to merge both branches

Question

Try git rebase --onto with the following syntax:

To put branch2's changes on to the master without including branch1's

git rebase --onto master branch1 branch2

Relevant output from git help rebase:

Here is how you would transplant a topic branch based on one branch to another, to pretend that you forked the topic branch from the latter branch, using rebase --onto.

First let’s assume your topic is based on branch next. For example, a feature developed in topic depends on some functionality which is found in next.

              o---o---o---o---o  master
                   \
                    o---o---o---o---o  next
                                     \
                                      o---o---o  topic

We want to make topic forked from branch master; for example, because the functionality on which topic depends was merged into the more stable master branch. We want our tree to look like this:

              o---o---o---o---o  master
                  |            \
                  |             o'--o'--o'  topic
                   \
                    o---o---o---o---o  next

We can get this using the following command:

git rebase --onto master next topic

Keep in mind the risks and pitfalls of rebasing, mentioned here: http://git-scm.com/book/en/Git-Branching-Rebasing

One way to do it is, use cherry-pick. Do a git log branch2 and find the commit id's you want and then switch to master branch using git checkout master then use git cherry-pick <commit_id>

Refer to this post for more details

How to merge a specific commit in Git