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'

Check out the master branch 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'.

then, add and commit the files,

$ git add *

$ git commit -m "new" 
[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

check out the branch name 

$ git branch


Now, Push the files from 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