You can try the command to clear your untracked files from your local
Git 2.11 and newer versions as below:
git clean -d -f .
Older versions of Git as below :
git clean -d -f ""
-d can be replaced with the below options:
-x ignored files are also removed as well as the files unknown to Git are also removed.
-d removed the untracked directories in addition to untracked the files.
-f is necessary to force it to run.
The problem with you is that you are not tracking your files locally but identical files are getting tracked remotely so in order to "pull" the system must be forced to overwrite your local files which are not the version controlled.
Try running below commands :
git add *
This will solve your issue.