First pass at JGitTree
Fix for adding new paths.
Switch Repository#commit_content to use JGitTree
Move commit into JGitTree class
Use JGitTree in Repository#rename_file
Use JGitTree in Publication#flatten_commits
Use JGit to resolve branch in Repository#copy_branch_from_repo, verbose/cleaned up create_branch
JGit Publication#head, JGitTree Publication#copy_back_to_user