Pro Git

Another useful thing you may want to do is to keep the file in your working tree but remove it from your staging area. In other words, you may want to keep the file on your hard drive but not have Git track it anymore. This is particularly useful if you forgot to add something to your .gitignore file and accidentally staged it, like a large log file or a bunch of .a compiled files. To do this, use the --cached option:
$ git rm --cached README
You can pass files, directories, and file-glob patterns to the git rm command. That means you can do things such as:
$ git rm log/\*.log
Note the backslash (\) in front of the *. This is necessary because Git does its own filename expansion in addition to your shell’s filename expansion. This command removes all files that have the .log extension in the log/ directory. Or, you can do something like this:
$ git rm \*~
This command removes all files whose names end with a ~.

Notice how you don’t have to run git add on the CONTRIBUTING.md file in this case before you commit. That’s because the -a flag includes all changed files. This is convenient, but be careful; sometimes this flag will cause you to include unwanted changes.

you run git rm, it stages the file’s removal