When you are using the git repository and if you are deleted the files from the git in the local system, it can not remove from reports. So you can use the command

$  git ls-files --deleted -z | xargs -0 git rm 

rm 'thelinuxfaq.c'
rm 'thelinux.h'
rm 'config.c'
rm 'config.h'

Checkout the master branch those files were deleted status
$ git checkout master

D    thelinuxfaq.c
D    thelinux.h
D    config.c
D    config.h
Your branch is up-to-date with 'origin/master'.

If you want to upload into repository again,  add, commit and push  the files,

$  git commit -m " your comments" 

[master 9782acb] new
 34 files changed, 6016 deletions(-)
 delete mode 100644 thelinuxfaq.c
 delete mode 100644 thelinux.h
 delete mode 100644 config.c
 delete mode 100644 config.h

Checkout the branch name,
$ git branch

Now, Push the files to the master branch
$  git push origin master

Counting objects: 4, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (2/2), done.
Writing objects: 100% (2/2), 212 bytes | 0 bytes/s, done.
Total 2 (delta 1), reused 0 (delta 0)
To ssh://repository-url.com/myprojects
   9af8cab..9782acb  master -> master