i deleted a folder from my local Git repository then i committed and pushed the changes to the remote repository, the files are deleted but the folder and the sub folder are sti
You can force git to quit tracking a local file by calling:
git rm file.txt #warning, this also deletes the file from your filesystem
You can delete an entire directory (and it's contents) by calling:
git rm -rf directory
Git doesn't actually store directories. It just makes directories wherever it needs them to hold the files that are in the repository. If a new clone still creates those directories, make sure you don't have files you can't see (like .gitignore) present.