Proper framework version upgrade procedure with original author's commit history intact. Follows the git branching model (http://nvie.com/posts/a-successful-git-branching-model/) that I currently use.

git framework patch

Start with cloning the framework's repository (in this example Wordpress) in your local machine.
$ git clone https://github.com/WordPress/WordPress.git

If you get an error like this - "Did you intend to checkout 'tags/xxxxx' which can not be resolved as commit?", fetch new tags. 
$ git fetch origin --tags

Create separate branches for the current verion you are using and the version you want to upgrade to.
$ git checkout -b 3.6-branch tags/3.6
$ git checkout -b 3.6.1-branch tags/3.6.1

Checkout the upgrade target branch(if not already on that branch) and create a patch file agains the current version
$ git checkout 3.6.1-branch
$ git format-patch 3.6-branch --stdout > wp-3.6-to-3.6.1.patch

Create a feature branch from your project's master branch
$ cd ../getfree
$ git checkout master
$ git checkout -b wp-upgrade-361

Test and apply the patch to the feature branch, first one shows changes, second one shows any conflicts
Make sure to use --signoff option
$ git apply --stat ../WordPress/wp-3.6-to-3.6.1.patch
$ git apply --check ../WordPress/wp-3.6-to-3.6.1.patch
$ git am --signoff < ../WordPress/wp-3.6-to-3.6.1.patch

Now the feature branch will have all the upgrade changes in it.
$ git push origin wp-upgrade-361

Create a pull request to master and dev branches as required in BitBucket

That's it! Well done!