I am quite new to Git, thus maybe I am missing something here.
dan@one:/var/www/$ git status -s
M GoogleChromeExtension.js
M ApiClient.js
So
I just recently had this problem, and found it happened because I changed my .gitattributes file for the repository. Have you changed any of your .gitattributes files recently? Are all the files that are changed of the same type? My recent issues affected *.sql files, for example. When I undid the change to .gitattributes, the source files became unchanged again.