The problem: 
In case of deleted files we are not able do "add" deletion to the index.
The simple use of
git add 
command does not work and git again shows us the "Changes not stagged for commit" message.
Example of output:
Changes not staged for commit:
 (use "git add/rm <file>..." to update what will be committed)
 (use "git checkout -- <file>..." to discard changes in working directory)
 deleted:    myFyle
The solution:
gitt add -u 
This updates all your change.
With -u option,  it will removes files
        from the index if the corresponding files in the working tree
        have been removed.

 
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