how do I copy all files from a directory(folder) to a different directory in Amazon S3 bucket using Codeigniter.
You should check out S3 tools: http://s3tools.org/s3cmd.
You can install it on your server, then you've got all sorts of command line tools for manipulating stuff in your s3 buckets.
Once you have it installed, you could call s3cmd's "put" (to move a a local file to an s3 bucket) with php's exec(), which executes shell commands:
exec('s3cmd put /my-local-dir/some_file.txt s3://my-s3-bucket/some-dir/some_file.txt');
More about exec() here.