Your repo don't contain any submodule's code, it only store a pointer to some commit in your submodule
So, if you want to take in modifications from 3rd party submodules, you should
$ cd /path/to/submodule/in/your/work/tree # enter your submodule directory
$ git fetch origin # update
$ git checkout origin/master # take in the modifications
$ cd /path/to/your/work/tree
$ git add /path/to/submodule/in/your/work/tree # add your modification for submodule pointer
$ git commit -m "update xxx module to x.x.x.x" # commit
HOPE I CAN HELP YOU!