Once the code changes have been completed and tested in the local environment; a GIT commit must be created. This is easily done using the git commit command through the command line, or using an IDE such as Eclipse or a GIT client such as SourceTree. Make sure only the files and changes which are relevant to the documented issue are submitted. This can be done through the use of git status and git add/remove.
*Note: You won't normally need the --set-upstream argument unless you created the branch from the command line instead of through JIRA or Bitbucket.