Rudder

To create a new commit containing datas from an old commit you can execute the following git commands :

git rm targetFiles (to remove everything from what you want, could be anything (with .) or a directory or a file ...)
git checkout MyReference targetFiles (My reference is a tag or commit, it will add the content from the reference corresponding to files)
git commit

We have to mimic those command using Jgit

This will need an upgrade of Jgit as the version we use (1.3) can't do that easily.