commit

git add -u

picks up the deleted files, and stages their deletion to be committed.

Also gets modified files. Still needs git add . to pick up the new files.

git diff of files that have been staged ie 'git add'ed
git diff --cached

http://www.commandlinefu.com/commands/view/1242/git-diff-of-files-that-have-been-staged-ie-git-added

$ git commit ...
$ git reset --soft HEAD^ (1)
$ edit (2)

And just commit again.

The video of contributors to Drupal core commits and how it was made:
http://marvil07.net/blog/using-codeswarm-watch-a-video-about-drupal-core-history

Learned something new about git!

If you git add filename and then make some changes to that file before running git commit -m "Helpful commit message." those changes that you saved and tested are not part of that commit. You have to run git add again-- git add adds the exact version of the file at that time, not simply adding the file as a concept to staging.