I\'m just entering into the wonderful world of git.
I have to submit a bunch of changes that I\'ve made on my program, located in a directory called /var/www/myapp
First in the clone folder you can create a Branch (so the master stay untouched)
git branch [branch_name]
After, just copy the files you want from your old folder to the clone folder.
When you are done, just add / commit your change and Merge your branch into the "master" branch. It will look like to something like this:
git add .
git commit -m "Comments"
git checkout master
git merge [new_branch]
Try this tutorial from GitHub.