Updating Moodle

Using git merge strategies, you can do that:

git checkout -b merge_helper_branch v2.6.1
git merge --strategy=ours v2.5.4

That gives you a commit that is upstream of both v2.5.4 and v2.6.1, and which contains code that is identical to v2.6.1. You can verify that using git diff v2.6.1 merge_helper_branch. That should produce no output.

Having built that helper branch, you can then proceed to upgrade your version of the code. Our version of Moodle lives on a branch called ouvle which we originally branched off Moodle 2.1.2 in October 2011. Since then, we have made lots of changes, including adding many custom plugins, and merging in many Moodle releases. Continuting from the above we do

git checkout my_real_branch
git merge --strategy-option=patience merge_helper_branch

Then

git checkout --theirs lang/en backup lib/filestorage admin/settings/development.php

Source: http://tjhunt.blogspot.co.uk/2014/01/moving-ou-moodle-code-to-moodle-261.html