Move Folders Between Git Repositories preserving history using filter-branch

filter_branch_instructions

Create clean clone of the source repository:
git clone git://server.com/my-repo1.git

Nuke all the entries except the folder you need to move. Use the following command
git filter-branch --subdirectory-filter your_dir -- -- all

This will nuke all the other entries and their history, creating a clean git repository that contains only data and history from the directory you need. 

Create a branch for changes.
git checkout -b repo1_branch

Commit your changes
git commit -m "Collected the data I need to move"

Now go to your destination repository
cd ../my-repo2/

Connect your source repository as a remote using a local reference.
git remote add repo1 ../my-repo1/

After that simply fetch the remote source and merge with it
git fetch repo1
git merge repo1/repo1_branch 

Clean up a bit and push the changes to the server
git remote rm repo1
git push



From:
http://www.ifup.org/2009/02/07/the-right-tool-for-the-job-git-stitch-repo/