How to merge two branches without a common ancestor?

Disclaimer: I've only used "graft points" myself once in a toy repository. But it is an obscure feature which you may not have heard of, and which _may_ be helpful in your situation.

You could use "graft points" to fake the ancestry information. See, e.g., What are .git/info/grafts for? or proceed immediately to the git wiki entry on graft points.

In essence, you would create a file .git/info/grafts that tricks git into thinking that commit M1 is an ancestor of commit M2:

$ cat .git/info/grafts
<your M2 commit hash> <your M1 commit hash>

Subsequently, it would look like M2 was an empty commit that just merged I2 and M1 into a common tree.

The major downside: the graft point is not committed; therefore, it is not checked out, but needs to be added to each local working copy of the repository manually.

Update: use git replace --graft instead.

Graft points, as described above, have been superseded. Run

git replace --graft <your M2 commit hash> <your M1 commit hash>

to create the graft. This is stored in .git/refs/replace/. Although git does not fetch, or push, these refs by default, they can be synchronized between repositories using:

git push origin 'refs/replace/*'
git fetch origin 'refs/replace/*:refs/replace/*'

(StackOverflow: How to push 'refs/replace' without pushing any other refs in git?)

The most elegant solution would be to rebase the changes introduced by N .. Z commits on top of svn branch, but I didn't found yet the required syntax for two branches without a common ancestor.

Try to first cherry-pick I1 and I2 onto M1, and after that use the command git rebase --onto M1' M2 Z (where M1' is the M1-I1-I2 branch). I'm not sure whether rebase --onto works when there are no common ancestors, but if it doesn't, there is the possibility of using patches. Use the git format-patch to generate the patches of M2..Z and then git am to apply them on top of M1. Here are some experience reports on using it in converting old SVN and CVS repositories.

I'd do the following:

git checkout M1
git cherry-pick I1
git cherry-pick I2

That adds .gitignore and .gitattributes to your branch containing the nicer history.

And then just set the new commits on top of that one:

git filter-branch --parent-filter 'if $GIT_COMMIT = $hash_of_N; then printf -- '-p
$hash_of_cherrypicked_I2\n'; else cat; fi'

The downside of this is you rewrite history.

So an alternative approach is to create a script similar to the one for the Linux kernel and put that in your repository.