How to squash commits which have merge-commit in between?

You can rebase -i starting with commit 2's parent (that is, the commit on master that you branched from. You'll likely have to re-resolve conflicts when you get to the merge commit.

So if your history looks like

  * D commit 3 (HEAD)  * M merge /|| * C commit 2* | B commit on master|/* A (master)

Start with git rebase -i A. You'll see a list of commits including both master and your_branch, but not the merge commit. pick the first one (B or C, depending on timing) and squash the rest.

You can use the tool I've created specifically for this task:

https://github.com/sheerun/git-squash

It's only necessary to merge master branch, and then run squashing command:

git merge mastergit squash master

In my case, I started working with a branch that had several commits, then a merge with the main/source branch, then more commits and I wanted to squash all commits, but kept running into an error because of the merge commit:

error: commit is a merge but no -m option was given.

->C1->C2->M(merge with source branch)->C3->C4

There's probably a better way (and I look forward to learning), but what I ended up doing after much reading and trial and error was creating a copy branch for reference, then reverting the current branch to C1,

reset --hard (C1 hash)

then cherry-picking C2, C3, C4, then squashing, then rebasing ... resulting in:

M->C

(just one commit that has been rebased with source!)

I hope this helps someone else with the same problem.