To remove a file from git, simply delete it.
If you removed a file, FooBar.java, but then thought better of it before committing, do what's below. Nota bene: you can add multiple filenames to each of these git reset -- or git checkout -- commands to save time.
$ git status On branch master Your branch is up to date with 'origin/master'. Changes to be committed: (use "git restore --staged..." to unstage) deleted: project/src/main/java/com/windofkeltia/FooBar.java $ git reset -- project/src/main/java/com/windofkeltia/FooBar.java Unstaged changes after reset: D project/src/main/java/com/windofkeltia/FooBar.java $ git status On branch master Your branch is up to date with 'origin/master'. Changes not staged for commit: (use "git add/rm ..." to update what will be committed) (use "git restore ..." to discard changes in working directory) deleted: project/src/main/java/com/windofkeltia/FooBar.java $ git checkout -- project/src/main/java/com/windofkeltia/FooBar.java $ git status On branch master Your branch is up to date with 'origin/master'. Changes to be committed: (use "git restore --staged ..." to unstage)